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Lint a bunch of test tools

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This commit is contained in:
Nicola Soranzo
2021-01-05 12:39:53 +00:00
parent ae49b6b27c
commit 2c9e89a398
110 changed files with 1918 additions and 1748 deletions
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test/functional/tools/bibtex.xml
+66 -64
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@@ -10,10 +10,10 @@
name="Galaxy IUC" />
</creator>
<xrefs>
<xref type="bio.tools">Citation.js</xref>
<xref type="bio.tools">Citation.js</xref>
</xrefs>
<command><![CDATA[
echo "$input1" > "$out_file1"
echo '$input1' > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="integer" help="integer" value="8" />
@@ -21,17 +21,18 @@
<outputs>
<data name="out_file1" format="txt" />
</outputs>
<help>
<tests>
</tests>
<help><![CDATA[
.. class:: warningmark
**WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format.
</help>
]]></help>
<citations>
<citation type="doi">10.1101/gr.4086505</citation>
<citation type="doi">10.6084/m9.figshare.979190</citation>
<citation type="bibtex">
<citation type="doi">10.1101/gr.4086505</citation>
<citation type="doi">10.6084/m9.figshare.979190</citation>
<citation type="bibtex">
@misc{Garrison2015,
author = {Garrison, Erik},
year = {2015},
@@ -40,8 +41,8 @@
journal = {GitHub repository},
url = {https://github.com/ekg/vcflib},
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@online{lh32017,
author = {Heng Li},
year = {2017},
@@ -50,19 +51,19 @@
journal = {GitHub repository},
url = {https://github.com/lh3/bwa},
}
</citation>
<!-- BibTeX examples taken from:
http://www2.galcit.caltech.edu/~jeshep/GraphicsBib/NatBib/node3.html
-->
<citation type="bibtex">
</citation>
<!-- BibTeX examples taken from:
http://www2.galcit.caltech.edu/~jeshep/GraphicsBib/NatBib/node3.html
-->
<citation type="bibtex">
@ARTICLE{article-minimal,
author = {L[eslie] A. Aamport},
title = {The Gnats and Gnus Document Preparation System},
journal = {\mbox{G-Animal's} Journal},
year = 1986,
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@ARTICLE{article-full,
author = {L[eslie] A. Aamport},
title = {The Gnats and Gnus Document Preparation System},
@@ -74,8 +75,8 @@
month = jul,
note = "This is a full ARTICLE entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@INBOOK{inbook-minimal,
author = "Donald E. Knuth",
title = "Fundamental Algorithms",
@@ -83,8 +84,9 @@
year = "{\noopsort{1973b}}1973",
chapter = "1.2",
} </citation>
<citation type="bibtex">
}
</citation>
<citation type="bibtex">
@INBOOK{inbook-full,
author = "Donald E. Knuth",
title = "Fundamental Algorithms",
@@ -100,16 +102,16 @@
pages = "10--119",
note = "This is a full INBOOK entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@BOOK{book-minimal,
author = "Donald E. Knuth",
title = "Seminumerical Algorithms",
publisher = "Addison-Wesley",
year = "{\noopsort{1973c}}1981",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@BOOK{book-full,
author = "Donald E. Knuth",
title = "Seminumerical Algorithms",
@@ -122,8 +124,8 @@
year = "{\noopsort{1973c}}1981",
note = "This is a full BOOK entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@BOOK{whole-set,
author = "Donald E. Knuth",
publisher = "Addison-Wesley",
@@ -132,8 +134,8 @@
year = "{\noopsort{1973a}}{\switchargs{--90}{1968}}",
note = "Seven volumes planned (this is a cross-referenced set of BOOKs)",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@BOOKLET{booklet-full,
author = "Jill C. Knvth",
title = "The Programming of Computer Art",
@@ -143,8 +145,8 @@
year = 1988,
note = "This is a full BOOKLET entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@INCOLLECTION{incollection-minimal,
author = "Daniel D. Lincoll",
title = "Semigroups of Recurrences",
@@ -152,8 +154,8 @@
publisher = "Academic Press",
year = 1977,
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@INCOLLECTION{incollection-full,
author = "Daniel D. Lincoll",
title = "Semigroups of Recurrences",
@@ -171,8 +173,8 @@
year = 1977,
note = "This is a full INCOLLECTION entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@BOOK{whole-collection,
editor = "David J. Lipcoll and D. H. Lawrie and A. H. Sameh",
title = "High Speed Computer and Algorithm Organization",
@@ -185,8 +187,8 @@
month = sep,
year = 1977,
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@MANUAL{manual-full,
author = "Larry Manmaker",
title = "The Definitive Computer Manual",
@@ -197,16 +199,16 @@
year = 1986,
note = "This is a full MANUAL entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@MASTERSTHESIS{mastersthesis-minimal,
author = "{\'{E}}douard Masterly",
title = "Mastering Thesis Writing",
school = "Stanford University",
year = 1988,
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@MASTERSTHESIS{mastersthesis-full,
author = "{\'{E}}douard Masterly",
title = "Mastering Thesis Writing",
@@ -217,8 +219,8 @@
year = 1988,
note = "This is a full MASTERSTHESIS entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@MISC{misc-full,
author = "Joe-Bob Missilany",
title = "Handing out random pamphlets in airports",
@@ -227,16 +229,16 @@
year = 1984,
note = "This is a full MISC entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@INPROCEEDINGS{inproceedings-minimal,
author = "Alfred V. Oaho and Jeffrey D. Ullman and Mihalis Yannakakis",
title = "On Notions of Information Transfer in {VLSI} Circuits",
booktitle = "Proc. Fifteenth Annual ACM" # STOC,
year = 1983,
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@INPROCEEDINGS{inproceedings-full,
author = "Alfred V. Oaho and Jeffrey D. Ullman and Mihalis Yannakakis",
title = "On Notions of Information Transfer in {VLSI} Circuits",
@@ -252,8 +254,8 @@
publisher = "Academic Press",
note = "This is a full INPROCEDINGS entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@INPROCEEDINGS{inproceedings-crossref,
crossref = "whole-proceedings",
author = "Alfred V. Oaho and Jeffrey D. Ullman and Mihalis Yannakakis",
@@ -262,8 +264,8 @@
pages = "133--139",
note = "This is a cross-referencing INPROCEEDINGS entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@PROCEEDINGS{proceedings-full,
editor = "Wizard V. Oz and Mihalis Yannakakis",
title = "Proc. Fifteenth Annual" # STOC,
@@ -276,16 +278,16 @@
publisher = "Academic Press",
note = "This is a full PROCEEDINGS entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@PHDTHESIS{phdthesis-minimal,
author = "F. Phidias Phony-Baloney",
title = "Fighting Fire with Fire: Festooning {F}rench Phrases",
school = "Fanstord University",
year = 1988,
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@PHDTHESIS{phdthesis-full,
author = "F. Phidias Phony-Baloney",
title = "Fighting Fire with Fire: Festooning {F}rench Phrases",
@@ -296,16 +298,16 @@
year = 1988,
note = "This is a full PHDTHESIS entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@TECHREPORT{techreport-minimal,
author = "Tom Terrific",
title = "An {$O(n \log n / \! \log\log n)$} Sorting Algorithm",
institution = "Fanstord University",
year = 1988,
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@TECHREPORT{techreport-full,
author = "Tom T{\'{e}}rrific",
title = "An {$O(n \log n / \! \log\log n)$} Sorting Algorithm",
@@ -317,15 +319,15 @@
year = 1988,
note = "This is a full TECHREPORT entry",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@UNPUBLISHED{unpublished-minimal,
author = "Ulrich {\"{U}}nderwood and Ned {\~N}et and Paul {\={P}}ot",
title = "Lower Bounds for Wishful Research Results",
note = "Talk at Fanstord University (this is a minimal UNPUBLISHED entry)",
}
</citation>
<citation type="bibtex">
</citation>
<citation type="bibtex">
@UNPUBLISHED{unpublished-full,
author = "Ulrich {\"{U}}nderwood and Ned {\~N}et and Paul {\={P}}ot",
title = "Lower Bounds for Wishful Research Results",
@@ -333,6 +335,6 @@
year = 1988,
note = "Talk at Fanstord University (this is a full UNPUBLISHED entry)",
}
</citation>
</citation>
</citations>
</tool>
test/functional/tools/catDocker.xml
+13 -12
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@@ -1,18 +1,17 @@
<tool id="catdc" name="Concatenate datasets (in docker)">
<tool id="catdc" name="Concatenate datasets (in docker)" version="1.0.0">
<description>tail-to-head</description>
<requirements>
<container type="docker">busybox:ubuntu-14.04</container>
<container type="docker">busybox:ubuntu-14.04</container>
</requirements>
<command>
echo "Galaxy slots passed through contain as \$GALAXY_SLOTS";
cat $input1
#for $q in $queries
${q.input2}
#end for
&gt; $out_file1;
echo "Work dir output" &gt; working_file
</command>
<command><![CDATA[
echo "Galaxy slots passed through contain as \$GALAXY_SLOTS" &&
cat '$input1'
#for $q in $queries
'${q.input2}'
#end for
> '$out_file1' &&
echo 'Work dir output' > working_file
]]></command>
<inputs>
<param name="input1" type="data" label="Concatenate Dataset"/>
<repeat name="queries" title="Dataset">
@@ -23,6 +22,8 @@
<data name="out_file1" format="input" metadata_source="input1"/>
<data name="out_file2" format="txt" from_work_dir="working_file" />
</outputs>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/collection_cat_group_tag.xml
+8 -8
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@@ -1,12 +1,12 @@
<tool id="collection_cat_group_tag" name="Concatenate multiple datasets (based on group tag)">
<tool id="collection_cat_group_tag" name="Concatenate multiple datasets (based on group tag)" version="1.0.0">
<description>tail-to-head</description>
<command>
cat
#for $file in $input1.get_datasets_for_group($group):
'$file'
#end for
> '$out_file1'
</command>
<command><![CDATA[
cat
#for $file in $input1.get_datasets_for_group($group):
'$file'
#end for
> '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data_collection" collection_type="list" label="Concatenate Dataset" multiple="true" />
<param name="group" type="group_tag" data_ref="input1" />
test/functional/tools/collection_cat_group_tag_multiple.xml
+8 -8
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@@ -1,13 +1,13 @@
<tool id="collection_cat_group_tag_multiple" name="Concatenate multiple datasets (based on group tags)">
<tool id="collection_cat_group_tag_multiple" name="Concatenate multiple datasets (based on group tags)" version="1.0.0">
<description>tail-to-head</description>
<command>
cat
#for $group in $groups:
#for $file in $input1.get_datasets_for_group($group):
'$file'
#end for
#end for
> '$out_file1'
cat
#for $group in $groups:
#for $file in $input1.get_datasets_for_group($group):
'$file'
#end for
#end for
> '$out_file1'
</command>
<inputs>
<param name="input1" type="data_collection" collection_type="list" label="Concatenate Dataset" multiple="true" />
test/functional/tools/column_multi_param.xml
+24 -24
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@@ -1,25 +1,25 @@
<tool id="column_multi_param" name="Column Param Multi">
<command>
#for $input in $input1#
cut -f '$col' '$input' >> 'col_output';
#end for#
</command>
<inputs>
<param name="input1" type="data" format="tabular" label="Input 1" multiple="true" />
<param name="col" type="data_column" data_ref="input1" label="Column to Use" />
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="col_output" />
</outputs>
<tests>
<test>
<param name="input1" value="2.tabular,2.tabular" />
<param name="col" value="2" />
<output name="outpu1">
<assert_contents>
<has_line line="68" />
</assert_contents>
</output>
</test>
</tests>
<tool id="column_multi_param" name="Column Param Multi" version="1.0.0">
<command><![CDATA[
#for $input in $input1#
cut -f '$col' '$input' >> 'col_output';
#end for#
]]></command>
<inputs>
<param name="input1" type="data" format="tabular" multiple="true" label="Input 1" />
<param name="col" type="data_column" data_ref="input1" label="Column to Use" />
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="col_output" />
</outputs>
<tests>
<test>
<param name="input1" value="2.tabular,2.tabular" />
<param name="col" value="2" />
<output name="outpu1">
<assert_contents>
<has_line line="68" />
</assert_contents>
</output>
</test>
</tests>
</tool>
test/functional/tools/column_param.xml
+46 -46
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@@ -1,50 +1,50 @@
<tool id="column_param" name="Column Param">
<command><![CDATA[
<tool id="column_param" name="Column Param" version="1.0.0">
<command><![CDATA[
cut -f '$col' '$input1' > '$output1' &&
echo "col $col" > '$output2' &&
echo "col_names $col_names" >> '$output2'
]]></command>
<inputs>
<param type="data" format="tabular" name="input1" label="Input 1" />
<param name="col" type="data_column" data_ref="input1" label="Column to Use" />
<param name="col_names" type="data_column" data_ref="input1" use_header_names="true" label="Column to Use" />
</inputs>
<outputs>
<data name="output1" format="tabular" />
<data name="output2" format="txt" />
</outputs>
<tests>
<test>
<param name="input1" value="2.tabular" />
<param name="col" value="2" />
<param name="col_names" value="2" />
<output name="output1">
<assert_contents>
<has_line line="68" />
</assert_contents>
</output>
<output name="output2">
<assert_contents>
<has_line line="col 2" />
<has_line line="col_names 2" />
</assert_contents>
</output>
</test>
<!-- test if non tabular data also creates entries by using the default
value (which is the 1st column, but empty if filling the options fails) -->
<test>
<param name="input1" value="1.bed" />
<output name="output1">
<assert_contents>
<has_line line="chr1" />
</assert_contents>
</output>
<output name="output2">
<assert_contents>
<has_line line="col 1" />
<has_line line="col_names 1" />
</assert_contents>
</output>
</test>
</tests>
]]></command>
<inputs>
<param name="input1" type="data" format="tabular" label="Input 1" />
<param name="col" type="data_column" data_ref="input1" label="Column to Use" />
<param name="col_names" type="data_column" data_ref="input1" use_header_names="true" label="Column to Use" />
</inputs>
<outputs>
<data name="output1" format="tabular" />
<data name="output2" format="txt" />
</outputs>
<tests>
<test>
<param name="input1" value="2.tabular" />
<param name="col" value="2" />
<param name="col_names" value="2" />
<output name="output1">
<assert_contents>
<has_line line="68" />
</assert_contents>
</output>
<output name="output2">
<assert_contents>
<has_line line="col 2" />
<has_line line="col_names 2" />
</assert_contents>
</output>
</test>
<!-- test if non tabular data also creates entries by using the default
value (which is the 1st column, but empty if filling the options fails) -->
<test>
<param name="input1" value="1.bed" />
<output name="output1">
<assert_contents>
<has_line line="chr1" />
</assert_contents>
</output>
<output name="output2">
<assert_contents>
<has_line line="col 1" />
<has_line line="col_names 1" />
</assert_contents>
</output>
</test>
</tests>
</tool>
test/functional/tools/column_param_configfile.xml
+28 -28
View File
@@ -1,10 +1,10 @@
<tool id="column_param_configfile" name="Column Param into configfile" >
<command detect_errors="exit_code"><![CDATA[
python $check_inputs inputs.json
]]></command>
<configfiles>
<inputs name="inputs" filename="inputs.json" />
<configfile name="check_inputs"><![CDATA[
<tool id="column_param_configfile" name="Column Param into configfile" version="1.0.0">
<command detect_errors="exit_code"><![CDATA[
python '$check_inputs' inputs.json
]]></command>
<configfiles>
<inputs name="inputs" filename="inputs.json" />
<configfile name="check_inputs"><![CDATA[
import json
import sys
@@ -19,25 +19,25 @@ assert_equals(as_dict["col_mult"], [1,2,3])
with open("$output1", "w") as f:
f.write("okay\n")
]]></configfile>
</configfiles>
<inputs>
<param type="data" format="tabular" name="input1" label="Input 1" />
<param name="col" type="data_column" data_ref="input1" label="Column to Use"/>
<param name="col_mult" type="data_column" data_ref="input1" label="Columns to Use" multiple="true"/>
</inputs>
<outputs>
<data name="output1" format="data" />
</outputs>
<tests>
<test>
<param name="input1" value="11.tabular" />
<param name="col" value="11" />
<param name="col_mult" value="1,2,3" />
<output name="output1">
<assert_contents>
<has_line line="okay" />
</assert_contents>
</output>
</test>
</tests>
</configfiles>
<inputs>
<param name="input1" type="data" format="tabular" label="Input 1" />
<param name="col" type="data_column" data_ref="input1" label="Column to Use"/>
<param name="col_mult" type="data_column" data_ref="input1" label="Columns to Use" multiple="true"/>
</inputs>
<outputs>
<data name="output1" format="data" />
</outputs>
<tests>
<test>
<param name="input1" value="11.tabular" />
<param name="col" value="11" />
<param name="col_mult" value="1,2,3" />
<output name="output1">
<assert_contents>
<has_line line="okay" />
</assert_contents>
</output>
</test>
</tests>
</tool>
test/functional/tools/composite.xml
+19 -18
View File
@@ -1,20 +1,21 @@
<tool id="composite" name="composite" version="1.0.0">
<command>cat '$input.extra_files_path/Sequences' > $output</command>
<inputs>
<param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
</inputs>
<outputs>
<data format="txt" name="output" label="${tool.name} on ${on_string}: LastGraph">
</data>
</outputs>
<tests>
<test>
<param name="input" value="velveth_test1/output.html" ftype="velvet" >
<composite_data value="velveth_test1/Sequences"/>
<composite_data value="velveth_test1/Roadmaps"/>
<composite_data value="velveth_test1/Log"/>
</param>
<output name="unused_reads_fasta" file="velveth_test1/Sequences" compare="diff"/>
</test>
</tests>
<command><![CDATA[
cat '$input.extra_files_path/Sequences' > '$output'
]]></command>
<inputs>
<param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
</inputs>
<outputs>
<data name="output" format="txt" label="${tool.name} on ${on_string}: LastGraph" />
</outputs>
<tests>
<test>
<param name="input" value="velveth_test1/output.html" ftype="velvet" >
<composite_data value="velveth_test1/Sequences"/>
<composite_data value="velveth_test1/Roadmaps"/>
<composite_data value="velveth_test1/Log"/>
</param>
<output name="unused_reads_fasta" file="velveth_test1/Sequences" compare="diff"/>
</test>
</tests>
</tool>
test/functional/tools/composite_output.xml
+29 -24
View File
@@ -1,26 +1,31 @@
<tool id="composite_output" name="composite_output" version="1.0.0">
<command>mkdir $output.extra_files_path; cp $input.extra_files_path/* $output.extra_files_path; cp $input.extra_files_path/Log $output.extra_files_path/second_log; mkdir $output.extra_files_path/nested; cp $input.extra_files_path/Log $output.extra_files_path/nested/nested_log</command>
<inputs>
<param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
</inputs>
<outputs>
<data format="velvet" name="output" label="">
</data>
</outputs>
<tests>
<test>
<param name="input" value="velveth_test1/output.html" ftype="velvet" >
<composite_data value="velveth_test1/Sequences" />
<composite_data value="velveth_test1/Roadmaps" />
<composite_data value="velveth_test1/Log" />
</param>
<output name="output" file="velveth_test1/output.html">
<extra_files type="file" name="Sequences" value="velveth_test1/Sequences" />
<extra_files type="file" name="Roadmaps" value="velveth_test1/Roadmaps" />
<extra_files type="file" name="Log" value="composite_output_expected_log" />
<extra_files type="file" name="second_log" value="composite_output_expected_log" />
<extra_files type="file" name="nested/nested_log" value="composite_output_expected_log" />
</output>
</test>
</tests>
<command><![CDATA[
mkdir '$output.extra_files_path' &&
cp '$input.extra_files_path'/* '$output.extra_files_path' &&
cp '$input.extra_files_path'/Log '$output.extra_files_path'/second_log &&
mkdir '$output.extra_files_path'/nested &&
cp '$input.extra_files_path'/Log '$output.extra_files_path'/nested/nested_log
]]></command>
<inputs>
<param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
</inputs>
<outputs>
<data name="output" format="velvet" label="" />
</outputs>
<tests>
<test>
<param name="input" value="velveth_test1/output.html" ftype="velvet" >
<composite_data value="velveth_test1/Sequences" />
<composite_data value="velveth_test1/Roadmaps" />
<composite_data value="velveth_test1/Log" />
</param>
<output name="output" file="velveth_test1/output.html">
<extra_files type="file" name="Sequences" value="velveth_test1/Sequences" />
<extra_files type="file" name="Roadmaps" value="velveth_test1/Roadmaps" />
<extra_files type="file" name="Log" value="composite_output_expected_log" />
<extra_files type="file" name="second_log" value="composite_output_expected_log" />
<extra_files type="file" name="nested/nested_log" value="composite_output_expected_log" />
</output>
</test>
</tests>
</tool>
test/functional/tools/create_10.xml
+11 -11
View File
@@ -1,16 +1,16 @@
<tool id="create_10" name="create_10">
<tool id="create_10" name="create_10" version="1.0.0">
<description>create 10 datasets for testing tools with many outputs</description>
<command><![CDATA[
echo "1" > 1;
echo "2" > 2;
echo "3" > 3;
echo "4" > 4;
echo "5" > 5;
echo "6" > 6;
echo "7" > 7;
echo "8" > 8;
echo "9" > 9;
echo "10" > 10;
echo '1' > 1 &&
echo '2' > 2 &&
echo '3' > 3 &&
echo '4' > 4 &&
echo '5' > 5 &&
echo '6' > 6 &&
echo '7' > 7 &&
echo '8' > 8 &&
echo '9' > 9 &&
echo '10' > 10
]]></command>
<inputs>
<param name="input1" type="data" label="Concatenate Dataset"/>
test/functional/tools/create_2.xml
+5 -5
View File
@@ -1,11 +1,11 @@
<tool id="create_2" name="create_2">
<tool id="create_2" name="create_2" version="1.0.0">
<command detect_errors="exit_code"><![CDATA[
echo "1" > '$out_file1';
echo "2" > '$out_file2';
sleep '$sleep_time';
echo '1' > '$out_file1' &&
echo '2' > '$out_file2' &&
sleep $sleep_time
]]></command>
<inputs>
<param name="sleep_time" type="integer" label="Sleep" help="Optionally simulates computation before creating collection" value="0" />
<param name="sleep_time" type="integer" value="0" label="Sleep" help="Optionally simulates computation before creating collection" />
</inputs>
<outputs>
<data name="out_file1" format="txt" />
test/functional/tools/dbkey_filter_input.xml
+9 -10
View File
@@ -1,20 +1,20 @@
<tool id="dbkey_filter_input" name="dbkey_filter_input" version="0.1.0">
<description>Filter (single) input on a dbkey</description>
<command>
cat $inputs > $output
</command>
<command><![CDATA[
cat '$inputs' > '$output'
]]></command>
<inputs>
<param format="txt" name="inputs" type="data" label="Inputs" help="" />
<param name="inputs" type="data" format="txt" label="Inputs" help="" />
<param name="index" type="select" label="Using reference genome">
<options from_data_table="test_fasta_indexes">
<filter type="data_meta" ref="inputs" key="dbkey" column="1" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
<options from_data_table="test_fasta_indexes">
<filter type="data_meta" ref="inputs" key="dbkey" column="1" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
</param>
</inputs>
<outputs>
<data format="txt" name="output" />
<data name="output" format="txt" />
</outputs>
<tests>
@@ -37,7 +37,6 @@
<output name="output" file="simple_line.txt" />
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/dbkey_filter_multi_input.xml
+10 -12
View File
@@ -1,23 +1,22 @@
<tool id="dbkey_filter_multi_input" name="dbkey_filter_multi_input" version="0.1.0">
<description>Filter select on dbkey of multiple inputs and use of named column</description>
<command><![CDATA[
#for $input in $inputs#
cat $input >> $output;
#end for#
]]>
</command>
#for $input in $inputs#
cat '$input' >> '$output';
#end for#
]]></command>
<inputs>
<param format="txt" name="inputs" type="data" label="Inputs" multiple="true" help="" />
<param name="inputs" type="data" format="txt" multiple="true" label="Inputs" help="" />
<param name="index" type="select" label="Using reference genome">
<options from_data_table="test_fasta_indexes">
<filter type="data_meta" ref="inputs" key="dbkey" column="dbkey" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
<options from_data_table="test_fasta_indexes">
<filter type="data_meta" ref="inputs" key="dbkey" column="dbkey" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
</param>
</inputs>
<outputs>
<data format="txt" name="output" />
<data name="output" format="txt" />
</outputs>
<tests>
@@ -40,7 +39,6 @@
<output name="output" file="simple_line_x2.txt"/>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/dbkey_output_action.xml
+9 -7
View File
@@ -1,16 +1,18 @@
<tool id="dbkey_output_action" name="dbkey_output_action" version="0.1.0">
<command>echo foo > $mapped_reads</command>
<command><![CDATA[
echo foo > '$mapped_reads'
]]></command>
<inputs>
<param name="input" type="data" />
<param name="index" type="select" label="Using reference genome">
<options from_data_table="test_fasta_indexes">
<filter type="data_meta" ref="input" key="dbkey" column="1" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
<options from_data_table="test_fasta_indexes">
<filter type="data_meta" ref="input" key="dbkey" column="1" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
</param>
</inputs>
<outputs>
<data format="txt" name="mapped_reads">
<data name="mapped_reads" format="txt">
<actions>
<action type="metadata" name="dbkey">
<option type="from_data_table" name="test_fasta_indexes" column="1" offset="0">
@@ -33,4 +35,4 @@
</output>
</test>
</tests>
</tool>
</tool>
test/functional/tools/detect_errors.xml
+7 -7
View File
@@ -11,13 +11,13 @@
<regex match="^Branch A" level="warning" description="Branch A was taken in execution" />
</stdio>
<command><![CDATA[
#if str($stdoutmsg)!=""
echo "$stdoutmsg";
#end if
#if str($stderrmsg)!=""
>2& echo "$stderrmsg";
#end if
sh -c "exit $exit_code"
#if str($stdoutmsg) != ""
echo '$stdoutmsg' &&
#end if
#if str($stderrmsg) != ""
>2& echo '$stderrmsg' &&
#end if
sh -c 'exit $exit_code'
]]>
</command>
<inputs>
test/functional/tools/disambiguate_cond.xml
+20 -20
View File
@@ -1,47 +1,47 @@
<tool id="disambiguate_cond" name="disambiguate_cond">
<command>
echo "$p1.p1v $p2.p2v $p3.p3v" > $out_file1;
#if $files.attach_files
cat "$files.p4.file" >> $out_file1;
#else
echo "no file specified" >> $out_file1;
#end if
</command>
<tool id="disambiguate_cond" name="disambiguate_cond" version="1.0.0">
<command><![CDATA[
echo "$p1.p1v $p2.p2v $p3.p3v" > '$out_file1' &&
#if $files.attach_files
cat '$files.p4.file' >> '$out_file1'
#else
echo 'no file specified' >> '$out_file1'
#end if
]]></command>
<inputs>
<conditional name="p1">
<param type="boolean" name="use" />
<param name="use" type="boolean" />
<when value="true">
<param name="p1v" value="4" type="integer" />
<param name="p1v" type="integer" value="4" />
</when>
<when value="false">
<param name="p1v" value="7" type="integer" />
<param name="p1v" type="integer" value="7" />
</when>
</conditional>
<conditional name="p2">
<param type="boolean" name="use" />
<param name="use" type="boolean" />
<when value="true">
<param name="p2v" value="4" type="integer" />
<param name="p2v" type="integer" value="4" />
</when>
<when value="false">
<param name="p2v" value="7" type="integer" />
<param name="p2v" type="integer" value="7" />
</when>
</conditional>
<conditional name="p3">
<param type="boolean" name="use" />
<param name="use" type="boolean" />
<when value="true">
<param name="p3v" value="4" type="integer" />
<param name="p3v" type="integer" value="4" />
</when>
<when value="false">
<param name="p3v" value="7" type="integer" />
<param name="p3v" type="integer" value="7" />
</when>
</conditional>
<conditional name="files">
<param name="attach_files" type="boolean" checked="true" />
<when value="true">
<conditional name="p4">
<param type="boolean" name="use" />
<param name="use" type="boolean" />
<when value="true">
<param type="data" name="file" />
<param name="file" type="data" />
</when>
<when value="false" />
</conditional>
test/functional/tools/disambiguate_repeats.xml
+2 -3
View File
@@ -1,6 +1,6 @@
<tool id="disambiguate_repeats" name="disambiguate_repeats">
<tool id="disambiguate_repeats" name="disambiguate_repeats" version="1.0.0">
<command>
cat #for $q in $queries# ${q.input} #end for# #for $q in $more_queries# ${q.input} #end for# > $out_file1
cat #for $q in $queries# '${q.input}' #end for# #for $q in $more_queries# '${q.input}' #end for# > '$out_file1'
</command>
<inputs>
<repeat name="queries" title="Dataset">
@@ -58,6 +58,5 @@
<output name="out_file1" file="simple_lines_interleaved.txt"/>
</test>
</tests>
</tool>
test/functional/tools/exit_code_from_env.xml
+6 -6
View File
@@ -1,9 +1,9 @@
<tool id="exit_code_from_env" name="exit_code_from_env">
<tool id="exit_code_from_env" name="exit_code_from_env" version="1.0.0">
<!-- tool errors out with identified OOM error if less than 10MB are allocated. -->
<command detect_errors="exit_code" oom_exit_code="42"><![CDATA[
echo 'Hello' > '$out_file1';
: \${GX_TARGET_EXIT_CODE:-0};
exit \${GX_TARGET_EXIT_CODE};
echo 'Hello' > '$out_file1' &&
: \${GX_TARGET_EXIT_CODE:-0} &&
exit \${GX_TARGET_EXIT_CODE}
]]></command>
<inputs>
<param name="input" type="integer" label="Dummy" value="6" />
@@ -11,8 +11,6 @@
<outputs>
<data name="out_file1" />
</outputs>
<help>
</help>
<tests>
<test>
<param name="input" value="5" />
@@ -23,4 +21,6 @@
</output>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/exit_code_from_file.xml
+4 -2
View File
@@ -1,6 +1,6 @@
<tool id="exit_code_from_file" name="exit_code_from_file">
<tool id="exit_code_from_file" name="exit_code_from_file" version="1.0.0">
<command detect_errors="exit_code">
sh -c "exit `cat $input`"
sh -c "exit \$(cat '$input')"
</command>
<inputs>
<param name="input" type="data" label="Exit code file" />
@@ -8,6 +8,8 @@
<outputs>
<data name="out_file1" />
</outputs>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/exit_code_oom.xml
+11 -12
View File
@@ -1,16 +1,15 @@
<tool id="exit_code_oom" name="exit_code_oom" version="0.1.1" profile="16.04">
<!-- tool errors out with identified OOM error if less than 10MB are allocated. -->
<command detect_errors="exit_code" oom_exit_code="42"><![CDATA[
mv hi.txt '$out_file1';
echo "\$GALAXY_MEMORY_MB";
: \${GALAXY_MEMORY_MB:=20};
echo "\$GALAXY_MEMORY_MB";
if [ "\$GALAXY_MEMORY_MB" -lt 10 ];
then
exit 42;
else
exit 0;
fi
mv hi.txt '$out_file1' &&
echo "\$GALAXY_MEMORY_MB" &&
: \${GALAXY_MEMORY_MB:=20} &&
echo "\$GALAXY_MEMORY_MB" &&
if [ "\$GALAXY_MEMORY_MB" -lt 10 ]; then
exit 42;
else
exit 0;
fi
]]></command>
<configfiles>
<!-- also tests that configfiles are placed in working dir and that this works on resubmission as well -->
@@ -22,8 +21,6 @@
<outputs>
<data name="out_file1" />
</outputs>
<help>
</help>
<tests>
<test>
<param name="input" value="5" />
@@ -34,4 +31,6 @@
</output>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/expression_forty_two.xml
+5 -1
View File
@@ -11,5 +11,9 @@
<outputs>
<output type="integer" name="out1" from="output" />
</outputs>
<help>Produces the integer 42.</help>
<tests>
</tests>
<help><![CDATA[
Produces the integer 42.
]]></help>
</tool>
test/functional/tools/expression_log_line_count.xml
+4 -1
View File
@@ -10,5 +10,8 @@
<outputs>
<output type="integer" name="out1" from="output" />
</outputs>
<help></help>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/expression_parse_int.xml
+5 -1
View File
@@ -10,5 +10,9 @@
<outputs>
<output type="integer" name="out1" from="output" />
</outputs>
<help>Parse an integer from text.</help>
<tests>
</tests>
<help><![CDATA[
Parse an integer from text.
]]></help>
</tool>
test/functional/tools/expression_pick_larger_file.xml
+5 -5
View File
@@ -16,14 +16,12 @@
}
]]></expression>
<inputs>
<param type="data" label="First file." optional="true" name="input1" />
<param type="data" label="Second file." optional="true" name="input2" />
<param name="input1" type="data" optional="true" label="First file" />
<param name="input2" type="data" optional="true" label="Second file" />
</inputs>
<outputs>
<output type="data" name="larger_file" from="output" />
<output name="larger_file" type="data" from="output" />
</outputs>
<help>
</help>
<tests>
<test>
<param name="input1" value="simple_line.txt" />
@@ -41,4 +39,6 @@
<output name="larger_file" file="simple_line.txt"/>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/fail_identifier.xml
+11 -9
View File
@@ -1,10 +1,13 @@
<tool id="fail_identifier" name="Fail input with identifier that contains fail">
<tool id="fail_identifier" name="Fail input with identifier that contains fail" version="1.0.0">
<stdio>
<exit_code range="127" level="fatal" description="Failing exit code." />
</stdio>
<command><![CDATA[
#if $failbool and 'fail' in $input1.element_identifier
sh -c "exit 127"
#else
cp '$input1' '$out_file1'
#end if
#if $failbool and 'fail' in $input1.element_identifier
sh -c 'exit 127'
#else
cp '$input1' '$out_file1'
#end if
]]></command>
<inputs>
<param name="input1" type="data" label="An input file" />
@@ -13,9 +16,8 @@
<outputs>
<data name="out_file1" format="data"/>
</outputs>
<stdio>
<exit_code range="127" level="fatal" description="Failing exit code." />
</stdio>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/fail_writing_work_dir_file.xml
+6 -4
View File
@@ -1,9 +1,9 @@
<tool id="fail_writing_work_dir_file" name="fail_writing_work_dir_file" version="0.1.0">
<command><![CDATA[
echo 'Some output' ;
#if not $failbool
echo 'Hello World' > 'foo.txt'
#end if
echo 'Some output' &&
#if not $failbool
echo 'Hello World' > 'foo.txt'
#end if
]]></command>
<inputs>
<param name="failbool" type="boolean" label="The failure property" checked="false" />
@@ -11,6 +11,8 @@
<outputs>
<data name="out_file1" format="txt" from_work_dir="foo.txt" />
</outputs>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/filter_static_regexp.xml
+23 -24
View File
@@ -1,45 +1,45 @@
<tool id="filter_static_regexp" name="filter_static_regexp" version="0.1.0">
<description>Filter by static value and regexp</description>
<command>
echo $index_static > '$output'
echo $index_static_keep >> '$output'
echo $index_regexp >> '$output'
echo $index_regexp_keep >> '$output'
</command>
<command><![CDATA[
echo $index_static > '$output' &&
echo $index_static_keep >> '$output' &&
echo $index_regexp >> '$output' &&
echo $index_regexp_keep >> '$output' &&
]]></command>
<inputs>
<!-- tests for static_value filter: remove hp18 from the options by
a) removing it explicitly (due to keep="false")
b) keeping only the other option, i.e. hg19 -->
<param name="index" type="select" label="Using reference genome">
<options from_data_table="test_fasta_indexes">
<filter type="static_value" column="dbkey" value="hg18" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
<options from_data_table="test_fasta_indexes">
<filter type="static_value" column="dbkey" value="hg18" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
</param>
<param name="index2" type="select" label="Using reference genome">
<options from_data_table="test_fasta_indexes">
<filter type="static_value" column="dbkey" value="hg19" keep="true" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
<options from_data_table="test_fasta_indexes">
<filter type="static_value" column="dbkey" value="hg19" keep="true" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
</param>
<!-- tests for regexp filter: remove hp18 from the options
essentially the same as for the static value filter, just using a simple regexp -->
<param name="index_regexp" type="select" label="Using reference genome">
<options from_data_table="test_fasta_indexes">
<filter type="regexp" column="dbkey" value="hg.8" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
<options from_data_table="test_fasta_indexes">
<filter type="regexp" column="dbkey" value="hg.8" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
</param>
<param name="index_regexp_keep" type="select" label="Using reference genome">
<options from_data_table="test_fasta_indexes">
<filter type="regexp" column="dbkey" value="hg.9" keep="true" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
<options from_data_table="test_fasta_indexes">
<filter type="regexp" column="dbkey" value="hg.9" keep="true" />
<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
</options>
</param>
</inputs>
<outputs>
<data format="txt" name="output" />
<data name="output" format="txt" />
</outputs>
<tests>
@@ -88,7 +88,6 @@
<output name="output"/>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/for_workflows/cat.xml
+4 -4
View File
@@ -1,8 +1,8 @@
<tool id="cat" name="Concatenate datasets (for test workflows)">
<tool id="cat" name="Concatenate datasets (for test workflows)" version="1.0.0">
<description>tail-to-head</description>
<command>
cat $input1 #for $q in $queries# ${q.input2} #end for# > $out_file1
</command>
<command><![CDATA[
cat '$input1' #for $q in $queries# '${q.input2}' #end for# > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" label="Concatenate Dataset"/>
<repeat name="queries" title="Dataset">
test/functional/tools/for_workflows/cat_collection.xml
+2 -2
View File
@@ -1,10 +1,10 @@
<tool id="cat_collection" name="Concatenate dataset collection (for test workflows)">
<tool id="cat_collection" name="Concatenate dataset collection (for test workflows)" version="1.0.0">
<description>tail-to-head</description>
<command>
cat #for $q in $input1# '$q' #end for# >'$out_file1'
</command>
<inputs>
<param name="input1" type="data_collection" label="Concatenate Dataset" collection_type="list,paired" />
<param name="input1" type="data_collection" collection_type="list,paired" label="Concatenate Dataset" />
</inputs>
<outputs>
<data name="out_file1" format="input" />
test/functional/tools/for_workflows/cat_interleave.xml
+5 -5
View File
@@ -1,8 +1,8 @@
<tool id="cat_interleave" name="Interleave two inputs (for test workflows)">
<command>
cat $input1 $input2 > $out_file1;
cat $input2 $input1 > $out_file2;
</command>
<tool id="cat_interleave" name="Interleave two inputs (for test workflows)" version="1.0.0">
<command><![CDATA[
cat '$input1' '$input2' > '$out_file1' &&
cat '$input2' '$input1' > '$out_file2'
]]></command>
<inputs>
<param name="input1" type="data" label="Input 1"/>
<param name="input2" type="data" label="Input 2"/>
test/functional/tools/for_workflows/cat_list.xml
+6 -6
View File
@@ -1,10 +1,10 @@
<tool id="cat_list" name="Concatenate multiple datasets (for test workflows)">
<description>tail-to-head</description>
<command>
cat #for $q in $input1# $q #end for# > $out_file1
</command>
<tool id="cat_list" name="Concatenate multiple datasets (for test workflows)" version="1.0.0">
<description></description>
<command><![CDATA[
cat #for $q in $input1# '$q' #end for# > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" label="Concatenate Dataset" multiple="true" />
<param name="input1" type="data" multiple="true" label="Concatenate Dataset" />
</inputs>
<outputs>
<data name="out_file1" format="input" metadata_source="input1"/>
test/functional/tools/for_workflows/count_list.xml
+3 -3
View File
@@ -1,10 +1,10 @@
<tool id="count_list" name="count_list">
<tool id="count_list" name="count_list" version="1.0.0">
<description>count the number of items in a list</description>
<command><![CDATA[
echo '${len($input1.keys())}' > '$out_file1'
echo '${len($input1.keys())}' > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data_collection" label="Concatenate Dataset" collection_type="list" />
<param name="input1" type="data_collection" collection_type="list" label="Concatenate Dataset" />
</inputs>
<outputs>
<data name="out_file1" format="txt" />
test/functional/tools/for_workflows/count_multi_file.xml
+3 -3
View File
@@ -1,10 +1,10 @@
<tool id="count_multi_file" name="count_multi_file">
<tool id="count_multi_file" name="count_multi_file" version="1.0.0">
<description>count the number of datasets in a multiple file input</description>
<command><![CDATA[
echo '${len($input1)}' > '$out_file1'
echo '${len($input1)}' > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" label="Concatenate Dataset" multiple="true" />
<param name="input1" type="data" multiple="true" label="Concatenate Dataset" />
</inputs>
<outputs>
<data name="out_file1" format="txt" />
test/functional/tools/for_workflows/head.xml
+16 -12
View File
@@ -1,13 +1,17 @@
<tool id="head" name="Select first">
<description>lines from a dataset</description>
<command>head -n $lineNum '$input' > '$out_file1'</command>
<inputs>
<param name="lineNum" type="integer" value="10" label="Select first" help="lines"/>
<param name="input" type="data" format="txt" label="from"/>
</inputs>
<outputs>
<data name="out_file1" format="input" metadata_source="input"/>
</outputs>
<help>
</help>
<tool id="head" name="Select first" version="1.0.0">
<description>lines from a dataset</description>
<command><![CDATA[
head -n $lineNum '$input' > '$out_file1'
]]></command>
<inputs>
<param name="lineNum" type="integer" value="10" label="Select first" help="lines"/>
<param name="input" type="data" format="txt" label="from"/>
</inputs>
<outputs>
<data name="out_file1" format="input" metadata_source="input"/>
</outputs>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/for_workflows/split.xml
+31 -31
View File
@@ -1,33 +1,33 @@
<tool id="split" name="split" version="0.1.0">
<command detect_errors="exit_code">
bash $script
</command>
<configfiles>
<configfile name="script">
mkdir outputs;
cd outputs;
i=1;
while read -r line || [[ -n "\$line" ]]; do
printf "\$line\n" &gt; \$i ;
i=\$[\$i +1];
done &lt; "$input1";
</configfile>
</configfiles>
<inputs>
<param name="input1" type="data" format="txt" label="Input Text" />
</inputs>
<outputs>
<collection name="output" type="list" label="lines">
<discover_datasets pattern="__name__" directory="outputs" />
</collection>
</outputs>
<tests>
<test>
<param name="input1" value="simple_lines_both.txt" />
<output_collection name="output" type="list">
<element name="1" file="simple_line.txt" />
<element name="2" file="simple_line_alternative.txt" />
</output_collection>
</test>
</tests>
<command detect_errors="exit_code"><![CDATA[
bash '$script'
]]></command>
<configfiles>
<configfile name="script"><![CDATA[
mkdir outputs &&
cd outputs/ &&
i=1 &&
while read -r line || [[ -n "\$line" ]]; do
printf "\$line\n" > \$i ;
i=\$[\$i +1];
done < '$input1'
]]></configfile>
</configfiles>
<inputs>
<param name="input1" type="data" format="txt" label="Input Text" />
</inputs>
<outputs>
<collection name="output" type="list" label="lines">
<discover_datasets pattern="__name__" directory="outputs" />
</collection>
</outputs>
<tests>
<test>
<param name="input1" value="simple_lines_both.txt" />
<output_collection name="output" type="list">
<element name="1" file="simple_line.txt" />
<element name="2" file="simple_line_alternative.txt" />
</output_collection>
</test>
</tests>
</tool>
test/functional/tools/gzipped_inputs.xml
+4 -4
View File
@@ -1,7 +1,7 @@
<tool id="gzipped_inputs" name="Echo Dataset">
<command>
cat $input1 > $out_file1
</command>
<tool id="gzipped_inputs" name="Echo Dataset" version="1.0.0">
<command><![CDATA[
cat '$input1' > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" label="Concatenate Dataset"/>
</inputs>
test/functional/tools/identifier_in_conditional.xml
+3 -3
View File
@@ -1,4 +1,4 @@
<tool id="identifier_in_conditional" name="identifier_in_conditional">
<tool id="identifier_in_conditional" name="identifier_in_conditional" version="1.0.0">
<command><![CDATA[
#if str($outer_cond.multi_input) == 'true':
#for $input in $input1#
@@ -12,10 +12,10 @@
<conditional name="outer_cond">
<param name="multi_input" type="boolean" checked="true" />
<when value="true">
<param type="data" name="input1" label="multi input" multiple="true" />
<param name="input1" type="data" multiple="true" label="multi input" />
</when>
<when value="false">
<param type="data" name="input1" label="single input" multiple="false" />
<param name="input1" type="data" multiple="false" label="single input" />
</when>
</conditional>
</inputs>
test/functional/tools/identifier_multiple.xml
+13 -13
View File
@@ -1,15 +1,15 @@
<tool id="identifier_multiple" name="identifier_multiple">
<command>
#for $input in $input1#
<tool id="identifier_multiple" name="identifier_multiple" version="1.0.0">
<command><![CDATA[
#for $input in $input1#
echo '$input.element_identifier' >> 'output1';
#end for#
</command>
<inputs>
<param type="data" name="input1" label="Input 1" multiple="true" />
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="output1" />
</outputs>
<tests>
</tests>
#end for#
]]></command>
<inputs>
<param name="input1" type="data" multiple="true" label="Input 1" />
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="output1" />
</outputs>
<tests>
</tests>
</tool>
test/functional/tools/identifier_multiple_in_conditional.xml
+22 -22
View File
@@ -1,25 +1,25 @@
<tool id="identifier_multiple_in_conditional" name="identifier_multiple_in_conditional">
<command><![CDATA[
#for $input in $outer_cond.inner_cond.input1#
<tool id="identifier_multiple_in_conditional" name="identifier_multiple_in_conditional" version="1.0.0">
<command><![CDATA[
#for $input in $outer_cond.inner_cond.input1#
echo '$input.element_identifier' >> 'output1';
#end for#
]]></command>
<inputs>
<conditional name="outer_cond">
<param name="cond_param_outer" type="boolean" checked="true" />
<when value="true">
<conditional name="inner_cond">
<param name="cond_param_inner" type="boolean" checked="true" />
<when value="true">
<param type="data" name="input1" label="True Input" multiple="true" />
</when>
#end for#
]]></command>
<inputs>
<conditional name="outer_cond">
<param name="cond_param_outer" type="boolean" checked="true" />
<when value="true">
<conditional name="inner_cond">
<param name="cond_param_inner" type="boolean" checked="true" />
<when value="true">
<param type="data" name="input1" label="True Input" multiple="true" />
</when>
</conditional>
</when>
</conditional>
</when>
</conditional>
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="output1" />
</outputs>
<tests>
</tests>
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="output1" />
</outputs>
<tests>
</tests>
</tool>
test/functional/tools/identifier_multiple_in_repeat.xml
+24 -24
View File
@@ -1,27 +1,27 @@
<tool id="identifier_multiple_in_repeat" name="identifier_multiple_in_repeat">
<command><![CDATA[
#for $repeat_instance in $the_repeat#
#for $input in $repeat_instance.the_data.input1#
<tool id="identifier_multiple_in_repeat" name="identifier_multiple_in_repeat" version="1.0.0">
<command><![CDATA[
#for $repeat_instance in $the_repeat#
#for $input in $repeat_instance.the_data.input1#
echo '$input.element_identifier' >> 'output1';
#end for#
#end for#
]]></command>
<inputs>
<repeat name="the_repeat" title="Repeat Inputs">
<conditional name="the_data">
<param name="cond_param" type="boolean" />
<when value="true">
<param type="data" name="input1" label="True Input" multiple="true" />
</when>
<when value="false">
<param type="data" name="input1" label="False Input" multiple="true" />
</when>
</conditional>
</repeat>
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="output1" />
</outputs>
<tests>
</tests>
#end for#
]]></command>
<inputs>
<repeat name="the_repeat" title="Repeat Inputs">
<conditional name="the_data">
<param name="cond_param" type="boolean" />
<when value="true">
<param name="input1" type="data" multiple="true" label="True Input" />
</when>
<when value="false">
<param name="input1" type="data" multiple="true" label="False Input" />
</when>
</conditional>
</repeat>
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="output1" />
</outputs>
<tests>
</tests>
</tool>
test/functional/tools/identifier_single.xml
+12 -12
View File
@@ -1,13 +1,13 @@
<tool id="identifier_single" name="identifier_single">
<command>
echo '$input1.element_identifier' > 'output1'
</command>
<inputs>
<param type="data" name="input1" label="Input 1" />
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="output1" />
</outputs>
<tests>
</tests>
<tool id="identifier_single" name="identifier_single" version="1.0.0">
<command><![CDATA[
echo '$input1.element_identifier' > 'output1'
]]></command>
<inputs>
<param name="input1" type="data" label="Input 1" />
</inputs>
<outputs>
<data name="output1" format="tabular" from_work_dir="output1" />
</outputs>
<tests>
</tests>
</tool>
test/functional/tools/identifier_single_in_repeat.xml
+3 -3
View File
@@ -1,4 +1,4 @@
<tool id="identifier_single_in_repeat" name="identifier_single_in_repeat">
<tool id="identifier_single_in_repeat" name="identifier_single_in_repeat" version="1.0.0">
<command><![CDATA[
#for $repeat_instance in $the_repeat#
echo '$repeat_instance.the_data.input1.element_identifier' >> 'output1';
@@ -9,10 +9,10 @@
<conditional name="the_data">
<param name="cond_param" type="boolean" />
<when value="true">
<param type="data" name="input1" label="The Input" />
<param name="input1" type="data" label="The Input" />
</when>
<when value="false">
<param type="data" name="input1" label="The Input" />
<param name="input1" type="data" label="The Input" />
</when>
</conditional>
</repeat>
test/functional/tools/identifier_source.xml
+6 -6
View File
@@ -1,11 +1,9 @@
<tool id="identifier_source" name="identifier_source" version="0.1.0">
<description>verifies identifier source can be specified from input</description>
<command>
<![CDATA[
cat '$inputA' '$inputB' >'$outputA' &&
cat '$inputA' '$inputB' > '$outputB'
]]>
</command>
<command><![CDATA[
cat '$inputA' '$inputB' >'$outputA' &&
cat '$inputA' '$inputB' > '$outputB'
]]></command>
<inputs>
<param name="inputA" type="data"/>
<param name="inputB" type="data"/>
@@ -14,6 +12,8 @@
<data name="outputA" default_identifier_source="inputA"/>
<data name="outputB" default_identifier_source="inputB"/>
</outputs>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/implicit_default_conds.xml
+9 -9
View File
@@ -1,8 +1,8 @@
<tool id="implicit_default_conds" name="implicit_default_conds">
<command>
echo "$param_group[0].p1.val" >> $out_file1;
echo "$param_group[0].p2.val" >> $out_file1;
</command>
<tool id="implicit_default_conds" name="implicit_default_conds" version="1.0.0">
<command><![CDATA[
echo '$param_group[0].p1.val' > '$out_file1' &&
echo '$param_group[0].p2.val' >> '$out_file1'
]]></command>
<inputs>
<repeat name="param_group" title="Param Group" min="1">
<conditional name="p1">
@@ -11,10 +11,10 @@
<option value="different">A different value</option>
</param>
<when value="default">
<param name="val" value="p1default" type="text" />
<param name="val" type="text" value="p1default" />
</when>
<when value="different">
<param name="val" value="p1different" type="text" />
<param name="val" type="text" value="p1different" />
</when>
</conditional>
<conditional name="p2">
@@ -23,10 +23,10 @@
<option value="different" selected="true">A different value</option>
</param>
<when value="default">
<param name="val" value="p2default" type="text" />
<param name="val" type="text" value="p2default" />
</when>
<when value="different">
<param name="val" value="p2different" type="text" />
<param name="val" type="text" value="p2different" />
</when>
</conditional>
<param name="int_param" type="integer" value="8" />
test/functional/tools/job_environment_default.xml
+11 -9
View File
@@ -1,16 +1,16 @@
<tool id="job_environment_default" name="job_environment_default" version="0.1.0" profile="18.01">
<requirements>
<container type="docker">busybox:ubuntu-14.04</container>
<container type="docker">busybox:ubuntu-14.04</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[
echo 'Writing environment properties to output files.';
(>&2 echo 'Example tool stderr output.');
echo `id -u` > '$user_id';
echo `id -g` > '$group_id';
echo `pwd` > '$pwd';
echo "\$HOME" > '$home';
echo "\$TMP" > '$tmp';
echo "\$SOME_ENV_VAR" > '$some_env_var';
echo 'Writing environment properties to output files.' &&
(>&2 echo 'Example tool stderr output.') &&
echo \$(id -u) > '$user_id' &&
echo \$(id -g) > '$group_id' &&
echo \$(pwd) > '$pwd' &&
echo "\$HOME" > '$home' &&
echo "\$TMP" > '$tmp' &&
echo "\$SOME_ENV_VAR" > '$some_env_var'
]]></command>
<inputs>
</inputs>
@@ -22,6 +22,8 @@
<data name="tmp" format="txt" label="tmp" />
<data name="some_env_var" format="txt" label="env_var" />
</outputs>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/job_environment_default_legacy.xml
+9 -7
View File
@@ -1,14 +1,14 @@
<tool id="job_environment_default_legacy" name="job_environment_default_legacy" version="0.1.0">
<requirements>
<container type="docker">busybox:ubuntu-14.04</container>
<container type="docker">busybox:ubuntu-14.04</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[
echo `id -u` > '$user_id';
echo `id -g` > '$group_id';
echo `pwd` > '$pwd';
echo "\$HOME" > '$home';
echo "\$TMP" > '$tmp';
echo "\$SOME_ENV_VAR" > '$some_env_var';
echo \$(id -u) > '$user_id' &&
echo \$(id -g) > '$group_id' &&
echo \$(pwd) > '$pwd' &&
echo "\$HOME" > '$home' &&
echo "\$TMP" > '$tmp' &&
echo "\$SOME_ENV_VAR" > '$some_env_var'
]]></command>
<inputs>
</inputs>
@@ -20,6 +20,8 @@
<data name="tmp" format="txt" label="tmp" />
<data name="some_env_var" format="txt" label="env_var" />
</outputs>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/job_environment_explicit_isolated_home.xml
+8 -6
View File
@@ -3,12 +3,12 @@
<container type="docker">busybox:ubuntu-14.04</container>
</requirements>
<command use_shared_home="false"><![CDATA[
echo `id -u` > '$user_id';
echo `id -g` > '$group_id';
echo `pwd` > '$pwd';
echo "\$HOME" > '$home';
echo "\$TMP" > '$tmp';
echo "\$SOME_ENV_VAR" > '$some_env_var';
echo \$(id -u) > '$user_id' &&
echo \$(id -g) > '$group_id' &&
echo \$(pwd) > '$pwd' &&
echo "\$HOME" > '$home' &&
echo "\$TMP" > '$tmp' &&
echo "\$SOME_ENV_VAR" > '$some_env_var'
]]></command>
<inputs>
</inputs>
@@ -20,6 +20,8 @@ echo "\$SOME_ENV_VAR" > '$some_env_var';
<data name="tmp" format="txt" label="tmp" />
<data name="some_env_var" format="txt" label="env_var" />
</outputs>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/job_environment_explicit_shared_home.xml
+9 -7
View File
@@ -1,14 +1,14 @@
<tool id="job_environment_explicit_shared_home" name="job_environment_explicit_shared_home" version="0.1.0" profile="18.01">
<requirements>
<container type="docker">busybox:ubuntu-14.04</container>
<container type="docker">busybox:ubuntu-14.04</container>
</requirements>
<command use_shared_home="true"><![CDATA[
echo `id -u` > '$user_id';
echo `id -g` > '$group_id';
echo `pwd` > '$pwd';
echo "\$HOME" > '$home';
echo "\$TMP" > '$tmp';
echo "\$SOME_ENV_VAR" > '$some_env_var';
echo \$(id -u) > '$user_id' &&
echo \$(id -g) > '$group_id' &&
echo \$(pwd) > '$pwd' &&
echo "\$HOME" > '$home' &&
echo "\$TMP" > '$tmp' &&
echo "\$SOME_ENV_VAR" > '$some_env_var'
]]></command>
<inputs>
</inputs>
@@ -20,6 +20,8 @@
<data name="tmp" format="txt" label="tmp" />
<data name="some_env_var" format="txt" label="env_var" />
</outputs>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/job_properties.xml
+18 -17
View File
@@ -1,25 +1,26 @@
<tool id="job_properties" name="Test Job Properties">
<tool id="job_properties" name="Test Job Properties" version="1.0.0">
<stdio>
<exit_code range="127" level="fatal" description="Failing exit code." />
</stdio>
<version_command>echo 'v1.1'</version_command>
<command><![CDATA[
#if $thebool
echo "The bool is true" &&
echo "The bool is really true" 1>&2 &&
echo "This is a line of text." > '$out_file1' &&
cp '$out_file1' '$one' &&
cp '$out_file1' '$two'
#else
echo "The bool is not true" &&
echo "The bool is very not true" 1>&2 &&
echo "This is a different line of text." > '$out_file1' &&
sh -c "exit 2"
#end if
#if $failbool
; sh -c "exit 127"
#end if
#if $thebool
echo 'The bool is true' &&
echo 'The bool is really true' 1>&2 &&
echo 'This is a line of text.' > '$out_file1' &&
cp '$out_file1' '$one' &&
cp '$out_file1' '$two'
#else
echo 'The bool is not true' &&
echo 'The bool is very not true' 1>&2 &&
echo 'This is a different line of text.' > '$out_file1' &&
sh -c 'exit 2'
#end if
#if $failbool
## use ';' to concatenate commands so that the next one is run independently
## of the exit code of the previous one
; exit 127
#end if
]]></command>
<inputs>
<param name="thebool" type="boolean" label="The boolean property" />
test/functional/tools/metadata.xml
+33 -28
View File
@@ -1,29 +1,34 @@
<tool id="metadata" name="metadata" version="1.0.0">
<command>mkdir $output_copy_of_input.extra_files_path; cp $input.extra_files_path/* $output_copy_of_input.extra_files_path; echo "$input.metadata.base_name" > $output_of_input_metadata</command>
<inputs>
<param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
</inputs>
<outputs>
<data format="txt" name="output_of_input_metadata" />
<data format="velvet" name="output_copy_of_input" />
</outputs>
<tests>
<test>
<param name="input" value="velveth_test1/output.html" ftype="velvet" >
<composite_data value="velveth_test1/Sequences" />
<composite_data value="velveth_test1/Roadmaps" />
<composite_data value="velveth_test1/Log"/>
<metadata name="base_name" value="Example Metadata" />
</param>
<!-- This ouptut tests setting input metadata above -->
<output name="output_of_input_metadata" ftype="txt">
<assert_contents>
<has_line line="Example Metadata" />
</assert_contents>
</output>
<!-- This output tests an assertion about output metadata -->
<output name="output_copy_of_input" file="velveth_test1/output.html">
<metadata name="base_name" value="velvet" />
</output>
</test>
</tests></tool>
<command><![CDATA[
mkdir '$output_copy_of_input.extra_files_path' &&
cp '$input.extra_files_path'/* '$output_copy_of_input.extra_files_path' &&
echo '$input.metadata.base_name' > '$output_of_input_metadata'
]]></command>
<inputs>
<param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
</inputs>
<outputs>
<data name="output_of_input_metadata" format="txt" />
<data name="output_copy_of_input" format="velvet" />
</outputs>
<tests>
<test>
<param name="input" value="velveth_test1/output.html" ftype="velvet" >
<composite_data value="velveth_test1/Sequences" />
<composite_data value="velveth_test1/Roadmaps" />
<composite_data value="velveth_test1/Log"/>
<metadata name="base_name" value="Example Metadata" />
</param>
<!-- This ouptut tests setting input metadata above -->
<output name="output_of_input_metadata" ftype="txt">
<assert_contents>
<has_line line="Example Metadata" />
</assert_contents>
</output>
<!-- This output tests an assertion about output metadata -->
<output name="output_copy_of_input" file="velveth_test1/output.html">
<metadata name="base_name" value="velvet" />
</output>
</test>
</tests>
</tool>
test/functional/tools/metadata_bcf.xml
+10 -8
View File
@@ -1,16 +1,18 @@
<tool id="metadata_bcf" name="metadata_BCF" version="1.0.0">
<command>file "${input_bcf.metadata.bcf_index}" &gt; "${output_of_input_metadata}"</command>
<command><![CDATA[
file '${input_bcf.metadata.bcf_index}' > '${output_of_input_metadata}'
]]></command>
<inputs>
<param name="input_bcf" type="data" format="bcf" label="BCF File"/>
<param name="input_bcf" type="data" format="bcf" label="BCF File"/>
</inputs>
<outputs>
<data format="txt" name="output_of_input_metadata" />
<data name="output_of_input_metadata" format="txt" />
</outputs>
<tests>
<test>
<param name="input_bcf" value="bcf_index_metadata_test.bcf" ftype="bcf" />
<!-- Tests whether the .bcf.csi file is of "gzip compressed data, extra field" type -->
<output name="output_of_input_metadata" ftype="txt" file="bcf_index_metadata_test.txt" compare="contains"/>
</test>
<test>
<param name="input_bcf" value="bcf_index_metadata_test.bcf" ftype="bcf" />
<!-- Tests whether the .bcf.csi file is of "gzip compressed data, extra field" type -->
<output name="output_of_input_metadata" ftype="txt" file="bcf_index_metadata_test.txt" compare="contains"/>
</test>
</tests>
</tool>
test/functional/tools/metadata_biom1.xml
+9 -7
View File
@@ -1,5 +1,7 @@
<tool id="metadata_biom1" name="metadata_BIOM1" version="1.0.0">
<command>cp "${input_metadata_values}" "${output_of_input_metadata}"</command>
<command><![CDATA[
cp '${input_metadata_values}' '${output_of_input_metadata}'
]]></command>
<configfiles>
<configfile name="input_metadata_values">table_rows: ${input_biom1.metadata.table_rows}
table_matrix_element_type: ${input_biom1.metadata.table_matrix_element_type}
@@ -14,15 +16,15 @@ table_id: ${input_biom1.metadata.table_id}
table_columns: ${input_biom1.metadata.table_columns}</configfile>
</configfiles>
<inputs>
<param name="input_biom1" type="data" format="biom1" label="BIOM1 File"/>
<param name="input_biom1" type="data" format="biom1" label="BIOM1 File"/>
</inputs>
<outputs>
<data format="txt" name="output_of_input_metadata" />
<data name="output_of_input_metadata" format="txt" />
</outputs>
<tests>
<test>
<param name="input_biom1" value="input_taxonomy.biom1" ftype="biom1" />
<output name="output_of_input_metadata" ftype="txt" file="biom1_metadata_test.txt" lines_diff="4"/>
</test>
<test>
<param name="input_biom1" value="input_taxonomy.biom1" ftype="biom1" />
<output name="output_of_input_metadata" ftype="txt" file="biom1_metadata_test.txt" lines_diff="4"/>
</test>
</tests>
</tool>
test/functional/tools/mulled_example_broken_no_requirements.xml
+6 -6
View File
@@ -10,16 +10,16 @@
<exit_code range="2:" />
</stdio>
<command><![CDATA[
bwa > $output_1 2>&1
bwa > $output_1 2>&1
]]></command>
<inputs>
</inputs>
<outputs>
<data name="output_1" />
<data name="output_1" />
</outputs>
<help><![CDATA[
TODO: Fill in help.
]]></help>
<tests>
</tests>
</tool>
<help><![CDATA[
TODO: Fill in help.
]]></help>
</tool>
test/functional/tools/mulled_example_explicit.xml
+6 -6
View File
@@ -7,16 +7,16 @@
<exit_code range="2:" />
</stdio>
<command><![CDATA[
bwa > $output_1 2>&1
bwa > $output_1 2>&1
]]></command>
<inputs>
</inputs>
<outputs>
<data name="output_1" />
<data name="output_1" />
</outputs>
<help><![CDATA[
TODO: Fill in help.
]]></help>
<tests>
</tests>
</tool>
<help><![CDATA[
TODO: Fill in help.
]]></help>
</tool>
test/functional/tools/mulled_example_invalid_case.xml
+6 -6
View File
@@ -9,16 +9,16 @@
<exit_code range="2:" />
</stdio>
<command><![CDATA[
bwa > $output_1 2>&1
bwa > '$output_1' 2>&1
]]></command>
<inputs>
</inputs>
<outputs>
<data name="output_1" />
<data name="output_1" />
</outputs>
<help><![CDATA[
TODO: Fill in help.
]]></help>
<tests>
</tests>
</tool>
<help><![CDATA[
TODO: Fill in help.
]]></help>
</tool>
test/functional/tools/mulled_example_multi_1.xml
+10 -8
View File
@@ -18,10 +18,10 @@
<requirement type="package" version="2.26.0">bedtools</requirement>
</requirements>
<command><![CDATA[
bedtools --version > '$out_file1' &&
echo "Moo" >> '$out_file1' &&
samtools >> '$out_file1' 2>&1 &&
echo "Cow" >> '$out_file1'
bedtools --version > '$out_file1' &&
echo "Moo" >> '$out_file1' &&
samtools >> '$out_file1' 2>&1 &&
echo "Cow" >> '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" optional="true" />
@@ -29,10 +29,12 @@
<outputs>
<data name="out_file1" format="txt" />
</outputs>
<help>
This is an example mulled tool that combines bedtools and samtools in one
command-line invocation.
</help>
<tests>
</tests>
<help><![CDATA[
This is an example mulled tool that combines bedtools and samtools in one
command-line invocation.
]]></help>
<citations>
<citation type="doi">10.1093/bioinformatics/btq033</citation>
<citation type="bibtex">
test/functional/tools/mulled_example_multi_incomplete.xml
+4 -4
View File
@@ -1,9 +1,9 @@
<tool id="mulled_example_multi_incomplete" name="mulled_example_multi_incomplete" version="0.1.0">
<command><![CDATA[
bedtools --version > $out_file1 ;
echo "Moo" >> $out_file1 ;
samtools >> $out_file1 2>&1 ;
echo "Cow" >> $out_file1 ;
bedtools --version > '$out_file1' &&
echo 'Moo' >> '$out_file1' &&
samtools >> '$out_file1' 2>&1 &&
echo 'Cow' >> '$out_file1'
]]></command>
<requirements>
<requirement type="package" version="1.3.1">samtools</requirement>
test/functional/tools/mulled_example_multi_versionless.xml
+4 -4
View File
@@ -1,9 +1,9 @@
<tool id="mulled_example_multi_versionless" name="mulled_example_multi_versionless" version="0.1.0">
<command><![CDATA[
bedtools --version > $out_file1 ;
echo "Moo" >> $out_file1 ;
samtools >> $out_file1 2>&1 ;
echo "Cow" >> $out_file1 ;
bedtools --version > '$out_file1' &&
echo 'Moo' >> '$out_file1' &&
samtools >> '$out_file1' 2>&1 &&
echo 'Cow' >> '$out_file1'
]]></command>
<requirements>
<requirement type="package">samtools</requirement>
test/functional/tools/mulled_example_simple.xml
+5 -5
View File
@@ -6,16 +6,16 @@
<exit_code range="2:" />
</stdio>
<command><![CDATA[
bwa > $output_1 2>&1
bwa > '$output_1' 2>&1
]]></command>
<inputs>
</inputs>
<outputs>
<data name="output_1" />
<data name="output_1" />
</outputs>
<tests>
</tests>
<help><![CDATA[
TODO: Fill in help.
]]></help>
<tests>
</tests>
</tool>
</tool>
test/functional/tools/multi_repeats.xml
+4 -4
View File
@@ -1,7 +1,7 @@
<tool id="multi_repeats" name="multi_repeats">
<command>
cat $input1 #for $q in $queries# ${q.input2} #end for# #for $q in $more_queries# ${q.more_queries_input} #end for# > $out_file1
</command>
<tool id="multi_repeats" name="multi_repeats" version="1.0.0">
<command><![CDATA[
cat '$input1' #for $q in $queries# '${q.input2}' #end for# #for $q in $more_queries# '${q.more_queries_input}' #end for# > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" label="Concatenate Dataset"/>
<repeat name="queries" title="Dataset">
test/functional/tools/multi_select.xml
+48 -43
View File
@@ -1,45 +1,50 @@
<tool id="multi_select" name="multi_select" version="1.0.0">
<description>multi_select</description>
<configfiles>
<configfile name="config">${select_ex}</configfile>
</configfiles>
<command>cat $config > $output; echo '$select_optional' > $output2</command>
<inputs>
<param name="select_ex" type="select" display="checkboxes" multiple="true">
<option value="--ex1">Ex1</option>
<option value="ex2">Ex2</option>
<option value="--ex3">Ex3</option>
<option value="--ex4">Ex4</option>
<option value="ex5">Ex5</option>
</param>
<param name="select_optional" type="select" optional="true">
<option value="--ex1">Ex1</option>
<option value="ex2">Ex2</option>
<option value="--ex3">Ex3</option>
<option value="--ex4">Ex4</option>
<option value="ex5">Ex5</option>
</param>
</inputs>
<outputs>
<data format="txt" name="output" />
<data format="txt" name="output2" />
</outputs>
<tests>
<test>
<param name="select_ex" value="--ex1,ex2,--ex3" />
<output name="output">
<assert_contents>
<has_line line="--ex1,ex2,--ex3" />
</assert_contents>
</output>
</test>
<test>
<param name="select_ex" value="Ex1" />
<output name="output">
<assert_contents>
<has_line line="--ex1" />
</assert_contents>
</output>
</test>
</tests>
<description>multi_select</description>
<command><![CDATA[
cat '$config' > '$output' &&
echo '$select_optional' > '$output2'
]]></command>
<configfiles>
<configfile name="config">${select_ex}</configfile>
</configfiles>
<inputs>
<param name="select_ex" type="select" display="checkboxes" multiple="true">
<option value="--ex1">Ex1</option>
<option value="ex2">Ex2</option>
<option value="--ex3">Ex3</option>
<option value="--ex4">Ex4</option>
<option value="ex5">Ex5</option>
</param>
<param name="select_optional" type="select" optional="true">
<option value="--ex1">Ex1</option>
<option value="ex2">Ex2</option>
<option value="--ex3">Ex3</option>
<option value="--ex4">Ex4</option>
<option value="ex5">Ex5</option>
</param>
</inputs>
<outputs>
<data name="output" format="txt" />
<data name="output2" format="txt" />
</outputs>
<tests>
<test>
<param name="select_ex" value="--ex1,ex2,--ex3" />
<output name="output">
<assert_contents>
<has_line line="--ex1,ex2,--ex3" />
</assert_contents>
</output>
</test>
<test>
<param name="select_ex" value="Ex1" />
<output name="output">
<assert_contents>
<has_line line="--ex1" />
</assert_contents>
</output>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/output_auto_format.xml
+15 -14
View File
@@ -1,16 +1,17 @@
<tool id="output_auto_format" name="output_auto_format" version="1.0.0">
<command>cp $input 'out'</command>
<inputs>
<param name="input" type="data" format="data" label="An input dataset" help=""/>
</inputs>
<outputs>
<data auto_format="true" name="output" label="Auto Output" from_work_dir="out">
</data>
</outputs>
<tests>
<test>
<param name="input" value="simple_line.txt" ftype="txt" />
<output name="output" file="simple_line.txt" ftype="txt" />
</test>
</tests>
<command><![CDATA[
cp '$input' out
]]></command>
<inputs>
<param name="input" type="data" format="data" label="An input dataset" help=""/>
</inputs>
<outputs>
<data name="output" auto_format="true" label="Auto Output" from_work_dir="out" />
</outputs>
<tests>
<test>
<param name="input" value="simple_line.txt" ftype="txt" />
<output name="output" file="simple_line.txt" ftype="txt" />
</test>
</tests>
</tool>
test/functional/tools/output_filter.xml
+172 -93
View File
@@ -1,95 +1,174 @@
<tool id="output_filter" name="output_filter" version="1.0.0">
<description>test for output filtering and expect_num_outputs</description>
<command>
echo "test" > 1;
echo "test" > 2;
echo "test" > 3;
echo "test" > 4;
echo "test" > 5;
echo "test" > p1.forward;
echo "test" > p1.reverse;
echo "test" > p2.forward;
echo "test" > p2.reverse;
</command>
<inputs>
<param name="produce_out_1" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Do Filter 1" />
<param name="filter_text_1" type="text" value="1" />
<param name="produce_collection" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Collection Filter" />
<param name="produce_paired_collection" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Paired Collection Filter" />
</inputs>
<outputs>
<data format="txt" from_work_dir="1" name="out_1">
<filter>produce_out_1 is True</filter>
</data>
<data format="txt" from_work_dir="2" name="out_2">
<filter>filter_text_1 in ["foo", "bar"]</filter>
<!-- Must pass all filters... -->
<filter>filter_text_1 == "foo"</filter>
</data>
<data format="txt" from_work_dir="3" name="out_3"/>
<collection name="list_output" type="list" label="List">
<discover_datasets pattern="(?P&lt;identifier_0&gt;[45])" ext="txt" visible="true" />
<filter>produce_collection is True</filter>
</collection>
<collection name="paired_list_output" type="list:paired" label="paired list">
<discover_datasets pattern="(?P&lt;identifier_0&gt;p[12])\.(?P&lt;identifier_1&gt;.*)" ext="txt" visible="true" />
<filter>produce_paired_collection is True</filter>
</collection>
</outputs>
<tests>
<test expect_num_outputs="3">
<param name="produce_out_1" value="true" />
<param name="filter_text_1" value="foo" />
<output name="out_1"><assert_contents><has_line line="test" /></assert_contents></output>
<output name="out_2"><assert_contents><has_line line="test" /></assert_contents></output>
<output name="out_3"><assert_contents><has_line line="test" /></assert_contents></output>
</test>
<test expect_num_outputs="2">
<param name="produce_out_1" value="true" />
<param name="filter_text_1" value="bar" /> <!-- fails second filter in out2 -->
<output name="out_1"><assert_contents><has_line line="test" /></assert_contents></output>
<output name="out_3"><assert_contents><has_line line="test" /></assert_contents></output>
</test>
<test expect_num_outputs="1">
<param name="produce_out_1" value="false" />
<param name="filter_text_1" value="not_foo_or_bar" />
<output name="out_3"><assert_contents><has_line line="test" /></assert_contents></output>
</test>
<test expect_num_outputs="4">
<param name="produce_out_1" value="true" />
<param name="filter_text_1" value="foo" />
<param name="produce_collection" value="true" />
<output name="out_1"><assert_contents><has_line line="test" /></assert_contents></output>
<output name="out_2"><assert_contents><has_line line="test" /></assert_contents></output>
<output name="out_3"><assert_contents><has_line line="test" /></assert_contents></output>
<output_collection name="list_output" type="list" count="2">
<element name="4"><assert_contents><has_line line="test" /></assert_contents></element>
<element name="5"><assert_contents><has_line line="test" /></assert_contents></element>
</output_collection>
</test>
<test expect_num_outputs="5">
<param name="produce_out_1" value="true" />
<param name="filter_text_1" value="foo" />
<param name="produce_collection" value="true" />
<param name="produce_paired_collection" value="true" />
<output name="out_1"><assert_contents><has_line line="test" /></assert_contents></output>
<output name="out_2"><assert_contents><has_line line="test" /></assert_contents></output>
<output name="out_3"><assert_contents><has_line line="test" /></assert_contents></output>
<output_collection name="list_output" type="list" count="2">
<element name="4"><assert_contents><has_line line="test" /></assert_contents></element>
<element name="5"><assert_contents><has_line line="test" /></assert_contents></element>
</output_collection>
<output_collection name="paired_list_output" type="list:paired" count="2">
<element name="p1">
<element name="forward"><assert_contents><has_line line="test" /></assert_contents></element>
<element name="reverse"><assert_contents><has_line line="test" /></assert_contents></element>
</element>
<element name="p2">
<element name="forward"><assert_contents><has_line line="test" /></assert_contents></element>
<element name="reverse"><assert_contents><has_line line="test" /></assert_contents></element>
</element>
</output_collection>
</test>
</tests>
<description>test for output filtering and expect_num_outputs</description>
<command><![CDATA[
echo 'test' > 1 &&
echo 'test' > 2 &&
echo 'test' > 3 &&
echo 'test' > 4 &&
echo 'test' > 5 &&
echo 'test' > p1.forward &&
echo 'test' > p1.reverse &&
echo 'test' > p2.forward &&
echo 'test' > p2.reverse
]]></command>
<inputs>
<param name="produce_out_1" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Do Filter 1" />
<param name="filter_text_1" type="text" value="1" />
<param name="produce_collection" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Collection Filter" />
<param name="produce_paired_collection" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Paired Collection Filter" />
</inputs>
<outputs>
<data name="out_1" format="txt" from_work_dir="1">
<filter>produce_out_1 is True</filter>
</data>
<data name="out_2" format="txt" from_work_dir="2">
<filter>filter_text_1 in ["foo", "bar"]</filter>
<!-- Must pass all filters... -->
<filter>filter_text_1 == "foo"</filter>
</data>
<data name="out_3" format="txt" from_work_dir="3"/>
<collection name="list_output" type="list" label="List">
<discover_datasets pattern="(?P&lt;identifier_0&gt;[45])" ext="txt" visible="true" />
<filter>produce_collection is True</filter>
</collection>
<collection name="paired_list_output" type="list:paired" label="paired list">
<discover_datasets pattern="(?P&lt;identifier_0&gt;p[12])\.(?P&lt;identifier_1&gt;.*)" ext="txt" visible="true" />
<filter>produce_paired_collection is True</filter>
</collection>
</outputs>
<tests>
<test expect_num_outputs="3">
<param name="produce_out_1" value="true" />
<param name="filter_text_1" value="foo" />
<output name="out_1">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output name="out_2">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output name="out_3">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
</test>
<test expect_num_outputs="2">
<param name="produce_out_1" value="true" />
<param name="filter_text_1" value="bar" /> <!-- fails second filter in out2 -->
<output name="out_1">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output name="out_3">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
</test>
<test expect_num_outputs="1">
<param name="produce_out_1" value="false" />
<param name="filter_text_1" value="not_foo_or_bar" />
<output name="out_3">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
</test>
<test expect_num_outputs="4">
<param name="produce_out_1" value="true" />
<param name="filter_text_1" value="foo" />
<param name="produce_collection" value="true" />
<output name="out_1">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output name="out_2">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output name="out_3">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output_collection name="list_output" type="list" count="2">
<element name="4">
<assert_contents>
<has_line line="test" />
</assert_contents>
</element>
<element name="5">
<assert_contents>
<has_line line="test" />
</assert_contents>
</element>
</output_collection>
</test>
<test expect_num_outputs="5">
<param name="produce_out_1" value="true" />
<param name="filter_text_1" value="foo" />
<param name="produce_collection" value="true" />
<param name="produce_paired_collection" value="true" />
<output name="out_1">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output name="out_2">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output name="out_3">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output_collection name="list_output" type="list" count="2">
<element name="4">
<assert_contents>
<has_line line="test" />
</assert_contents>
</element>
<element name="5">
<assert_contents>
<has_line line="test" />
</assert_contents>
</element>
</output_collection>
<output_collection name="paired_list_output" type="list:paired" count="2">
<element name="p1">
<element name="forward">
<assert_contents>
<has_line line="test" />
</assert_contents>
</element>
<element name="reverse">
<assert_contents>
<has_line line="test" />
</assert_contents>
</element>
</element>
<element name="p2">
<element name="forward">
<assert_contents>
<has_line line="test" />
</assert_contents>
</element>
<element name="reverse">
<assert_contents>
<has_line line="test" />
</assert_contents>
</element>
</element>
</output_collection>
</test>
</tests>
</tool>
test/functional/tools/output_filter_exception_1.xml
+38 -34
View File
@@ -1,35 +1,39 @@
<tool id="output_filter_exception_1" name="output_filter_exception_1" version="1.0.0">
<command>
echo "test" > 1;
echo "test" > 2;
echo "test" > 3;
echo "test" > 4;
echo "test" > 5;
</command>
<inputs>
<conditional name="options">
<param help="" label="Options" name="options" type="select">
<option selected="True" value="default">Use defaults</option>
<option value="advanced">Specify advanced options</option>
</param>
<when value="default" />
<when value="advanced">
<param falsevalue="" truevalue="--adv_opt1" help="" name="adv_opt1" type="boolean" />
</when>
</conditional>
</inputs>
<outputs>
<data format="txt" from_work_dir="1" name="out_1">
</data>
<data format="txt" from_work_dir="2" name="out_2">
<filter>options['adv_opt1'] is True</filter>
</data>
</outputs>
<tests>
<!-- Filter condition throws exception, filter "fails" and so output is produced. -->
<test expect_num_outputs="2">
<output name="out_1"><assert_contents><has_line line="test" /></assert_contents></output>
<output name="out_2"><assert_contents><has_line line="test" /></assert_contents></output>
</test>
</tests>
</tool>
<command><![CDATA[
echo 'test' > 1 &&
echo 'test' > 2
]]></command>
<inputs>
<conditional name="options">
<param help="" label="Options" name="options" type="select">
<option selected="True" value="default">Use defaults</option>
<option value="advanced">Specify advanced options</option>
</param>
<when value="default" />
<when value="advanced">
<param falsevalue="" truevalue="--adv_opt1" help="" name="adv_opt1" type="boolean" />
</when>
</conditional>
</inputs>
<outputs>
<data name="out_1" format="txt" from_work_dir="1" />
<data name="out_2" format="txt" from_work_dir="2">
<filter>options['adv_opt1'] is True</filter>
</data>
</outputs>
<tests>
<!-- Filter condition throws exception, filter "fails" and so output is produced. -->
<test expect_num_outputs="2">
<output name="out_1">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output name="out_2">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
</test>
</tests>
</tool>
test/functional/tools/output_filter_with_input.xml
+27 -29
View File
@@ -1,31 +1,29 @@
<tool id="output_filter_with_input" name="output_filter_with_input" version="1.0.0">
<!-- output_filter.xml but with an input -->
<command>
echo "test" > 1;
echo "test" > 2;
echo "test" > 3;
echo "test" > 4;
echo "test" > 5;
</command>
<inputs>
<param name="input_1" type="data" />
<param name="produce_out_1" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Do Filter 1" />
<param name="filter_text_1" type="text" value="1" />
</inputs>
<outputs>
<data format="txt" from_work_dir="1" name="out_1">
<filter>produce_out_1 is True</filter>
</data>
<data format="txt" from_work_dir="2" name="out_2">
<filter>filter_text_1 in ["foo", "bar"]</filter>
<!-- Must pass all filters... -->
<filter>filter_text_1 == "foo"</filter>
</data>
<data format="txt" from_work_dir="3" name="out_3">
<!-- always produce out_3 -->
<filter>input_1.ext != 'xyz'</filter>
</data>
</outputs>
<tests>
</tests>
<!-- output_filter.xml but with an input -->
<command><![CDATA[
echo 'test' > 1 &&
echo 'test' > 2 &&
echo 'test' > 3
]]></command>
<inputs>
<param name="input_1" type="data" />
<param name="produce_out_1" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Do Filter 1" />
<param name="filter_text_1" type="text" value="1" />
</inputs>
<outputs>
<data name="out_1" format="txt" from_work_dir="1">
<filter>produce_out_1 is True</filter>
</data>
<data name="out_2" format="txt" from_work_dir="2">
<filter>filter_text_1 in ["foo", "bar"]</filter>
<!-- Must pass all filters... -->
<filter>filter_text_1 == "foo"</filter>
</data>
<data name="out_3" format="txt" from_work_dir="3">
<!-- always produce out_3 -->
<filter>input_1.ext != 'xyz'</filter>
</data>
</outputs>
<tests>
</tests>
</tool>
test/functional/tools/output_format.xml
+86 -72
View File
@@ -1,74 +1,88 @@
<tool id="output_format" name="output_format" version="1.0.0">
<command>
echo "test" > 1;
echo "test" > 2;
echo "test" > 3;
echo "test" > 4;
echo "test" > 5;
</command>
<inputs>
<param name="input_data_1" type="data" format="data" label="input_data_1" />
<param name="input_data_2" type="data" format="data" label="input_data_2" />
<param name="input_text" type="text" value="1" label="input_text" />
</inputs>
<outputs>
<data format="txt" from_work_dir="1" name="direct_output" />
<!-- TODO: fixme, following input gets random type fastqsanger or
fastqsolexa. -->
<data format="input" from_work_dir="2" name="input_based_output" />
<data format="txt" from_work_dir="3" name="format_source_1_output" format_source="input_data_1" />
<data format="txt" from_work_dir="4" name="format_source_2_output" format_source="input_data_2" />
<data format="txt" from_work_dir="5" name="change_format_output">
<change_format>
<when input="input_text" value="foo" format="fastqsolexa" />
<when input="input_text" value="bar" format="fastqillumina" />
</change_format>
</data>
</outputs>
<tests>
<test>
<param name="input_data_1" value="1.fastqsanger" ftype="fastqsanger" />
<param name="input_data_2" value="1.fastqsolexa" ftype="fastqsolexa" />
<param name="input_text" value="foo" />
<output name="direct_output" ftype="txt">
<assert_contents><has_line line="test" /></assert_contents>
<metadata name="created_from_basename" value="1" />
</output>
<!-- In this case input_based_output ftype is "randomly" either
fastqsanger or fastqsolexa -->
<output name="format_source_1_output" ftype="fastqsanger">
<assert_contents><has_line line="test" /></assert_contents>
<metadata name="created_from_basename" value="3" />
</output>
<output name="format_source_2_output" ftype="fastqsolexa">
<assert_contents><has_line line="test" /></assert_contents>
</output>
<!-- input_text == foo => format set to fastsolexa -->
<output name="change_format_output" ftype="fastqsolexa">
<assert_contents><has_line line="test" /></assert_contents>
</output>
</test>
<test>
<param name="input_data_1" value="1.fastqsanger" ftype="fastqsanger" />
<param name="input_data_2" value="1.fastqsanger" ftype="fastqsanger" />
<param name="input_text" value="bar" />
<output name="input_based_output" ftype="fastqsanger">
<assert_contents><has_line line="test" /></assert_contents>
</output>
<!-- input_text == bar => format set to fastqillumina -->
<output name="change_format_output" ftype="fastqillumina">
<assert_contents><has_line line="test" /></assert_contents>
</output>
</test>
<test>
<param name="input_data_1" value="1.fastqsanger" ftype="fastqsanger" />
<param name="input_data_2" value="1.fastqsanger" ftype="fastqsanger" />
<param name="input_text" value="not_foo_or_bar" />
<!-- input_text doesn't match any when, default to explicitly declared
type. -->
<output name="change_format_output" ftype="txt">
<assert_contents><has_line line="test" /></assert_contents>
</output>
</test>
</tests>
<command><![CDATA[
echo 'test' > 1 &&
echo 'test' > 2 &&
echo 'test' > 3 &&
echo 'test' > 4 &&
echo 'test' > 5
]]></command>
<inputs>
<param name="input_data_1" type="data" format="data" label="input_data_1" />
<param name="input_data_2" type="data" format="data" label="input_data_2" />
<param name="input_text" type="text" value="1" label="input_text" />
</inputs>
<outputs>
<data name="direct_output" format="txt" from_work_dir="1" />
<!-- TODO: fixme, following input gets random type fastqsanger or
fastqsolexa. -->
<data name="input_based_output" format="input" from_work_dir="2" />
<data name="format_source_1_output" format_source="input_data_1" from_work_dir="3" />
<data name="format_source_2_output" format_source="input_data_2" from_work_dir="4" />
<data name="change_format_output" format="txt" from_work_dir="5">
<change_format>
<when input="input_text" value="foo" format="fastqsolexa" />
<when input="input_text" value="bar" format="fastqillumina" />
</change_format>
</data>
</outputs>
<tests>
<test>
<param name="input_data_1" value="1.fastqsanger" ftype="fastqsanger" />
<param name="input_data_2" value="1.fastqsolexa" ftype="fastqsolexa" />
<param name="input_text" value="foo" />
<output name="direct_output" ftype="txt">
<assert_contents>
<has_line line="test" />
</assert_contents>
<metadata name="created_from_basename" value="1" />
</output>
<!-- In this case input_based_output ftype is "randomly" either
fastqsanger or fastqsolexa -->
<output name="format_source_1_output" ftype="fastqsanger">
<assert_contents>
<has_line line="test" />
</assert_contents>
<metadata name="created_from_basename" value="3" />
</output>
<output name="format_source_2_output" ftype="fastqsolexa">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<!-- input_text == foo => format set to fastsolexa -->
<output name="change_format_output" ftype="fastqsolexa">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
</test>
<test>
<param name="input_data_1" value="1.fastqsanger" ftype="fastqsanger" />
<param name="input_data_2" value="1.fastqsanger" ftype="fastqsanger" />
<param name="input_text" value="bar" />
<output name="input_based_output" ftype="fastqsanger">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<!-- input_text == bar => format set to fastqillumina -->
<output name="change_format_output" ftype="fastqillumina">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
</test>
<test>
<param name="input_data_1" value="1.fastqsanger" ftype="fastqsanger" />
<param name="input_data_2" value="1.fastqsanger" ftype="fastqsanger" />
<param name="input_text" value="not_foo_or_bar" />
<!-- input_text doesn't match any when, default to explicitly declared
type. -->
<output name="change_format_output" ftype="txt">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
</test>
</tests>
</tool>
test/functional/tools/output_format_collection.xml
+33 -33
View File
@@ -1,35 +1,35 @@
<tool id="output_format_collection" name="output_format_collection" version="1.0.0">
<command>
echo "test" > 1;
echo "test" > 2;
</command>
<inputs>
<param name="input_collection" type="data_collection" format="data" />
</inputs>
<outputs>
<!-- Access by element name (for paired data) -->
<data from_work_dir="1" name="format_source_1_output" format_source="input_collection['forward']" />
<!-- Access by element index (for any collection) -->
<data from_work_dir="2" name="format_source_2_output" format_source="input_collection[0]" />
</outputs>
<tests>
<test>
<param name="input_collection">
<collection type="paired">
<element name="forward" value="simple_line.txt" />
<element name="reverse" value="simple_line_alternative.txt" />
</collection>
</param>
<output name="format_source_1_output" ftype="txt">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output name="format_source_2_output" ftype="txt">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
</test>
</tests>
<command><![CDATA[
echo "test" > 1 &&
echo "test" > 2
]]></command>
<inputs>
<param name="input_collection" type="data_collection" format="data" />
</inputs>
<outputs>
<!-- Access by element name (for paired data) -->
<data name="format_source_1_output" format_source="input_collection['forward']" from_work_dir="1" />
<!-- Access by element index (for any collection) -->
<data name="format_source_2_output" format_source="input_collection[0]" from_work_dir="2" />
</outputs>
<tests>
<test>
<param name="input_collection">
<collection type="paired">
<element name="forward" value="simple_line.txt" />
<element name="reverse" value="simple_line_alternative.txt" />
</collection>
</param>
<output name="format_source_1_output" ftype="txt">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
<output name="format_source_2_output" ftype="txt">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
</test>
</tests>
</tool>
test/functional/tools/output_format_deprecated_when.xml
+32 -28
View File
@@ -1,30 +1,34 @@
<tool id="output_format_deprecated_when" name="output_format_deprecated_when" version="1.0.0">
<command>
echo "test" > 5;
</command>
<inputs>
<param name="input_data_1" type="data" format="data" label="input_data_1" />
</inputs>
<outputs>
<data format="txt" from_work_dir="5" name="change_format_deprecated">
<change_format>
<when input_dataset="input_data_1" attribute="extension" value="fastq" format="fastq" />
</change_format>
</data>
</outputs>
<tests>
<test>
<param name="input_data_1" value="1.fastqsanger" ftype="fastq" />
<output name="change_format_deprecated" ftype="fastq">
<assert_contents><has_line line="test" /></assert_contents>
</output>
</test>
<test>
<param name="input_data_1" value="1.fastqsanger" ftype="fastqsanger" />
<output name="change_format_deprecated" ftype="txt">
<!-- Fails to check subclasses, use format_soure if possible -->
<assert_contents><has_line line="test" /></assert_contents>
</output>
</test>
</tests>
<command><![CDATA[
echo "test" > 5
]]></command>
<inputs>
<param name="input_data_1" type="data" format="data" label="input_data_1" />
</inputs>
<outputs>
<data name="change_format_deprecated" format="txt" from_work_dir="5">
<change_format>
<when input_dataset="input_data_1" attribute="extension" value="fastq" format="fastq" />
</change_format>
</data>
</outputs>
<tests>
<test>
<param name="input_data_1" value="1.fastqsanger" ftype="fastq" />
<output name="change_format_deprecated" ftype="fastq">
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
</test>
<test>
<param name="input_data_1" value="1.fastqsanger" ftype="fastqsanger" />
<output name="change_format_deprecated" ftype="txt">
<!-- Fails to check subclasses, use format_soure if possible -->
<assert_contents>
<has_line line="test" />
</assert_contents>
</output>
</test>
</tests>
</tool>
test/functional/tools/output_order.xml
+26 -23
View File
@@ -1,25 +1,28 @@
<tool id="output_order" name="output_order" version="0.1.0">
<command>echo $pa > $output_a; echo $pb > $output_b</command>
<inputs>
<param name="pa" type="integer" value="1" />
<param name="pb" type="integer" value="2" />
</inputs>
<outputs>
<data format="txt" name="output_a" />
<data format="txt" name="output_b" />
</outputs>
<tests>
<test>
<output name="output_b">
<assert_contents>
<has_line line="2" />
</assert_contents>
</output>
<output name="output_a">
<assert_contents>
<has_line line="1" />
</assert_contents>
</output>
</test>
</tests>
<command><![CDATA[
echo $pa > '$output_a' &&
echo $pb > '$output_b'
]]></command>
<inputs>
<param name="pa" type="integer" value="1" />
<param name="pb" type="integer" value="2" />
</inputs>
<outputs>
<data name="output_a" format="txt" />
<data name="output_b" format="txt" />
</outputs>
<tests>
<test>
<output name="output_b">
<assert_contents>
<has_line line="2" />
</assert_contents>
</output>
<output name="output_a">
<assert_contents>
<has_line line="1" />
</assert_contents>
</output>
</test>
</tests>
</tool>
test/functional/tools/parallelism.xml
+4 -4
View File
@@ -1,8 +1,8 @@
<tool id="parallelism" name="Split file line-by-line and rebuild dataset">
<tool id="parallelism" name="Split file line-by-line and rebuild dataset" version="1.0.0">
<parallelism method="multi" split_inputs="input1" split_mode="to_size" split_size="1" merge_outputs="out_file1" />
<command detect_errors="exit_code">
cat '$input1' > '$out_file1'
</command>
<command detect_errors="exit_code"><![CDATA[
cat '$input1' > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" label="Dataset"/>
</inputs>
test/functional/tools/parallelism_optional.xml
+5 -5
View File
@@ -1,11 +1,11 @@
<tool id="parallelism_optional" name="Split file line-by-line and rebuild dataset (with optional dataset)">
<tool id="parallelism_optional" name="Split file line-by-line and rebuild dataset (with optional dataset)" version="1.0.0">
<parallelism method="multi" split_inputs="input1" split_mode="to_size" split_size="1" merge_outputs="out_file1" />
<command detect_errors="exit_code">
cat '$input1' > '$out_file1'
</command>
<command detect_errors="exit_code"><![CDATA[
cat '$input1' > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" label="Dataset"/>
<param name="input2" type="data" label="Optional Dataset" optional="true" />
<param name="input2" type="data" optional="true" label="Optional Dataset" />
</inputs>
<outputs>
<data name="out_file1" format="txt" />
test/functional/tools/param_text_option.xml
+3 -3
View File
@@ -1,7 +1,7 @@
<tool id="param_text_option" name="param_text_option" version="1.0.0">
<command>
echo "$text_param" > $out_file1;
</command>
<command><![CDATA[
echo "$text_param" > $out_file1;
]]></command>
<inputs>
<param name="text_param" type="text" value="foo 1">
<option value="foo 1">Foo 1</option>
test/functional/tools/python_environment_problem.xml
+3 -3
View File
@@ -3,9 +3,9 @@
This script imports galaxy.eggs which is no longer available to tools
by default. Only declared legacy tools have this available.
-->
<command>
python $__tool_directory__/python_environment_problem.py '$out_file1'
</command>
<command><![CDATA[
python '$__tool_directory__/python_environment_problem.py' '$out_file1'
]]></command>
<inputs>
</inputs>
<outputs>
test/functional/tools/qc_stdout.xml
+5 -5
View File
@@ -3,11 +3,11 @@
<regex match="Quality of sample is .*%\." source="stdout" level="qc" />
</stdio>
<command detect_errors="exit_code"><![CDATA[
cp $input $output;
echo "Some example stdout........";
echo "Quality of sample is ${int($quality) * 10}%.";
echo "Some more example stdout........";
>&2 echo "my standard error"
cp '$input' '$output' &&
echo "Some example stdout........" &&
echo "Quality of sample is ${int($quality) * 10}%." &&
echo "Some more example stdout........" &&
>&2 echo "my standard error"
]]></command>
<inputs>
<param name="input" type="data" format="txt" label="Input data" />
test/functional/tools/sam_to_bam.xml
+3 -3
View File
@@ -1,7 +1,7 @@
<tool id="sam_to_conversion" name="Test sam to bam conversion">
<command>
cat '$input1' > '$out_file1'
</command>
<command><![CDATA[
cat '$input1' > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" format="bam" label="Concatenate Dataset"/>
</inputs>
test/functional/tools/section.xml
+5 -5
View File
@@ -1,8 +1,8 @@
<tool id="section" name="section">
<command>
echo "$int.inttest" >> $out_file1;
echo "$float.floattest" >> $out_file1;
</command>
<tool id="section" name="section" version="1.0.0">
<command><![CDATA[
echo $int.inttest > '$out_file1' &&
echo $float.floattest >> '$out_file1'
]]></command>
<inputs>
<section name="int" title="Integer Section" expanded="true">
<param name="inttest" value="1" type="integer" />
test/functional/tools/select_from_dataset.xml
+19 -20
View File
@@ -1,39 +1,39 @@
<tool id="select_from_dataset" name="select_from_dataset" version="0.1.0">
<description>Create dynamic options from data sets</description>
<command><![CDATA[
echo select_single $select_single > '$output' &&
echo select_multiple $select_multiple >> '$output' &&
echo select_collection $select_collection >> '$output'
echo select_single '$select_single' > '$output' &&
echo select_multiple '$select_multiple' >> '$output' &&
echo select_collection '$select_collection' >> '$output'
]]></command>
<inputs>
<param name="single" type="data" format="tabular" label="single"/>
<param name="select_single" type="select" label="select_single">
<options from_dataset="single">
<column name="name" index="0"/>
<column name="value" index="0"/>
<validator type="no_options" message="No data is available in single" />
</options>
<options from_dataset="single">
<column name="name" index="0"/>
<column name="value" index="0"/>
<validator type="no_options" message="No data is available in single" />
</options>
</param>
<param name="multiple" type="data" format="tabular" multiple="true" label="multiple"/>
<param name="select_multiple" type="select" multiple="true" label="select_multiple">
<options from_dataset="multiple">
<column name="name" index="0"/>
<column name="value" index="0"/>
<validator type="no_options" message="No data is available in single" />
</options>
<options from_dataset="multiple">
<column name="name" index="0"/>
<column name="value" index="0"/>
<validator type="no_options" message="No data is available in single" />
</options>
</param>
<param name="collection" type="data_collection" format="tabular" collection_type="list" label="collection"/>
<param name="select_collection" type="select" multiple="true" label="select_collection">
<options from_dataset="collection">
<column name="name" index="0"/>
<column name="value" index="0"/>
<validator type="no_options" message="No data is available in single" />
</options>
<options from_dataset="collection">
<column name="name" index="0"/>
<column name="value" index="0"/>
<validator type="no_options" message="No data is available in single" />
</options>
</param>
</inputs>
<outputs>
<data format="txt" name="output" />
<data name="output" format="txt" />
</outputs>
<tests>
@@ -58,7 +58,6 @@
</output>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/simple_constructs.xml
+12 -12
View File
@@ -1,16 +1,16 @@
<tool id="simple_constructs" name="simple_constructs" version="1.0.0">
<command>
echo "$p1.p1val" >> $out_file1;
echo "$booltest" >> $out_file1;
echo "$inttest" >> $out_file1;
echo "$floattest" >> $out_file1;
echo "$radio_select" >> $out_file1;
echo "$check_select" >> $out_file1;
echo "$drop_select" >> $out_file1;
#if len($files) > 0
cat "$files[0].file" >> $out_file1;
#end if
</command>
<command><![CDATA[
echo '$p1.p1val' > '$out_file1' &&
echo $booltest >> '$out_file1' &&
echo $inttest >> '$out_file1' &&
echo $floattest >> '$out_file1' &&
echo $radio_select >> '$out_file1' &&
echo $check_select >> '$out_file1' &&
echo $drop_select >> '$out_file1' &&
#if len($files) > 0
cat '$files[0].file' >> '$out_file1'
#end if
]]></command>
<inputs>
<conditional name="p1">
<param type="boolean" name="p1use" />
test/functional/tools/special_params.xml
+42 -34
View File
@@ -1,36 +1,44 @@
<tool id="special_params" name="special_params" version="1.0.0">
<command>echo $__root_dir__ > out_root_dir;
echo $__datatypes_config__ > out_datatypes_config;
echo $__admin_users__ > out_admin_users;
echo $__user_email__ > out_user_email
</command>
<inputs>
<param name="ignored" type="integer" value="0" />
</inputs>
<outputs>
<data format="txt" name="out_root_dir" from_work_dir="out_root_dir" />
<data format="txt" name="out_datatypes_config" from_work_dir="out_datatypes_config" />
<data format="txt" name="out_admin_users" from_work_dir="out_admin_users" />
<data format="txt" name="out_user_email" from_work_dir="out_user_email" />
</outputs>
<tests>
<test>
<output name="out_root_dir">
<!-- Is an absolute path. -->
<assert_contents><has_line_matching expression="^\/.*$" /></assert_contents>
</output>
<output name="out_datatypes_config">
<!-- Is an absolute path. -->
<assert_contents><has_line_matching expression="^\/.*$" /></assert_contents>
</output>
<output name="out_admin_users">
<!-- Has at least on e-mail address. -->
<assert_contents><has_text text="@" /></assert_contents>
</output>
<output name="out_user_email">
<!-- Looks like an e-mail address. -->
<assert_contents><has_line_matching expression="[^@]+@[^@]+\.[^@]+" /></assert_contents>
</output>
</test>
</tests>
<command><![CDATA[
echo '$__root_dir__' > out_root_dir &&
echo '$__datatypes_config__' > out_datatypes_config &&
echo '$__admin_users__' > out_admin_users &&
echo '$__user_email__' > out_user_email
]]></command>
<inputs>
</inputs>
<outputs>
<data name="out_root_dir" format="txt" from_work_dir="out_root_dir" />
<data name="out_datatypes_config" format="txt" from_work_dir="out_datatypes_config" />
<data name="out_admin_users" format="txt" from_work_dir="out_admin_users" />
<data name="out_user_email" format="txt" from_work_dir="out_user_email" />
</outputs>
<tests>
<test>
<output name="out_root_dir">
<!-- Is an absolute path. -->
<assert_contents>
<has_line_matching expression="^\/.*$" />
</assert_contents>
</output>
<output name="out_datatypes_config">
<!-- Is an absolute path. -->
<assert_contents>
<has_line_matching expression="^\/.*$" />
</assert_contents>
</output>
<output name="out_admin_users">
<!-- Has at least on e-mail address. -->
<assert_contents>
<has_text text="@" />
</assert_contents>
</output>
<output name="out_user_email">
<!-- Looks like an e-mail address. -->
<assert_contents>
<has_line_matching expression="[^@]+@[^@]+\.[^@]+" />
</assert_contents>
</output>
</test>
</tests>
</tool>
test/functional/tools/strict_shell.xml
+5 -5
View File
@@ -1,9 +1,9 @@
<tool id="strict_shell" name="strict_shell" version="1.0.0">
<command strict="true" detect_errors="exit_code">
echo "Hello" > $out_file1
; sh -c "exit $exit_code"
; sh -c "exit 0"
</command>
<command strict="true" detect_errors="exit_code"><![CDATA[
echo "Hello" > '$out_file1';
sh -c 'exit $exit_code';
sh -c 'exit 0'
]]></command>
<inputs>
<param name="exit_code" type="integer" value="0" label="exit code"/>
</inputs>
test/functional/tools/strict_shell_default_off.xml
+5 -5
View File
@@ -1,9 +1,9 @@
<tool id="strict_shell_default_off" name="strict_shell_default_off" version="1.0.0">
<command detect_errors="exit_code">
echo "Hello" > $out_file1
; sh -c "exit $exit_code"
; sh -c "exit 0"
</command>
<command detect_errors="exit_code"><![CDATA[
echo 'Hello' > '$out_file1'
; sh -c 'exit $exit_code'
; sh -c 'exit 0'
]]></command>
<inputs>
<param name="exit_code" type="integer" value="0" label="exit code"/>
</inputs>
test/functional/tools/strict_shell_profile.xml
+5 -5
View File
@@ -1,9 +1,9 @@
<tool id="strict_shell_profile" name="strict_shell_profile" version="1.0.0" profile="20.09">
<command detect_errors="exit_code">
echo "Hello" > $out_file1
; sh -c "exit $exit_code"
; sh -c "exit 0"
</command>
<command detect_errors="exit_code"><![CDATA[
echo 'Hello' > '$out_file1'
; sh -c 'exit $exit_code'
; sh -c 'exit 0'
]]></command>
<inputs>
<param name="exit_code" type="integer" value="0" label="exit code"/>
</inputs>
test/functional/tools/tool_directory.xml
+18 -19
View File
@@ -1,20 +1,19 @@
<tool id="tool_directory" name="tool_directory">
<command>
cp $__tool_directory__/tool_directory.xml output1
</command>
<inputs>
<param type="integer" name="ignored" label="Ignored" value="0" />
</inputs>
<outputs>
<data name="output1" format="xml" from_work_dir="output1" />
</outputs>
<tests>
<test>
<output name="output1">
<assert_contents>
<has_text text="QUINE" />
</assert_contents>
</output>
</test>
</tests>
<tool id="tool_directory" name="tool_directory" version="1.0.0">
<command><![CDATA[
cp '$__tool_directory__/tool_directory.xml' output1
]]></command>
<inputs>
</inputs>
<outputs>
<data name="output1" format="xml" from_work_dir="output1" />
</outputs>
<tests>
<test>
<output name="output1">
<assert_contents>
<has_text text="QUINE" />
</assert_contents>
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_1.xml
+15 -17
View File
@@ -1,30 +1,28 @@
<tool id="tool_provided_metadata_1" name="tool_provided_metadata_1">
<tool id="tool_provided_metadata_1" name="tool_provided_metadata_1" version="1.0.0">
<!-- Demonstrate setting simple dataset metadata for output datasets via galaxy.json for legacy tools (galaxy.json structure changes for profile >= 17.09 tools). -->
<command>
echo "This is a line of text." > $out1;
cp $c1 galaxy.json;
</command>
<command><![CDATA[
echo 'This is a line of text.' > '$out1' &&
cp '$c1' galaxy.json
]]></command>
<configfiles>
<configfile name="c1">{"type": "dataset", "dataset_id": $out1.dataset.dataset.id, "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", "dbkey": "cust1"}</configfile>
<configfile name="c1">{"type": "dataset", "dataset_id": $out1.dataset.dataset.id, "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", "dbkey": "cust1"}</configfile>
</configfiles>
<inputs>
<param name="input1" type="data" label="Input Dataset"/>
</inputs>
<outputs>
<!-- Set format="auto" to read from galaxy.json, use auto_format="true"
to sniff. -->
<data name="out1" format="auto" />
</outputs>
<tests>
<test>
<output name="out1" file="simple_line.txt" ftype="txt">
<metadata name="name" value="my dynamic name" />
<metadata name="info" value="my dynamic info" />
<metadata name="dbkey" value="cust1" />
</output>
</test>
</tests>
<help>
</help>
<tests>
<test>
<param name="input1" value="simple_line.txt" />
<output name="out1" file="simple_line.txt" ftype="txt">
<metadata name="name" value="my dynamic name" />
<metadata name="info" value="my dynamic info" />
<metadata name="dbkey" value="cust1" />
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_10.xml
+31 -31
View File
@@ -1,38 +1,38 @@
<tool id="tool_provided_metadata_10" name="tool_provided_metadata_10" profile="17.09" version="1.0.0">
<!-- Demonstrate setting datatype defined metadata for discovered datasets via galaxy.json for
profile >= 17.09 tools (see tool_provided_metadata_3 for legacy version of this test). -->
<command>
echo "1" > sample1.report.tsv;
cp $c1 galaxy.json;
</command>
<configfiles>
<configfile name="c1">{"sample": {
<!-- Demonstrate setting datatype defined metadata for discovered datasets via galaxy.json for
profile >= 17.09 tools (see tool_provided_metadata_3 for legacy version of this test). -->
<command><![CDATA[
echo '1' > sample1.report.tsv &&
cp '$c1' galaxy.json
]]></command>
<configfiles>
<configfile name="c1">{"sample": {
"datasets": [
{"filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "metadata": {"data_lines": 10}}
]
}}
</configfile>
</configfiles>
<inputs>
<param name="input" type="data" />
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<param name="input" ftype="txt" value="simple_line.txt"/>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents><has_line line="1" /></assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
<metadata name="data_lines" value="10" />
</discovered_dataset>
</output>
</test>
</tests>
</configfiles>
<inputs>
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents>
<has_line line="1" />
</assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
<metadata name="data_lines" value="10" />
</discovered_dataset>
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_11.xml
+43 -39
View File
@@ -1,41 +1,45 @@
<tool id="tool_provided_metadata_11" name="tool_provided_metadata_11">
<!-- Demonstrate setting simple dataset metadata for discovered datasets via galaxy.json for legacy tools (galaxy.json structure changes for profile >= 17.09 tools). -->
<command>
mkdir sample1data;
echo "1" > sample1.report.tsv;
echo "foo line" > sample1data/foo;
echo "moo cow bar" > sample1data/bar;
cp $c1 galaxy.json;
</command>
<configfiles>
<configfile name="c1">{"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "extra_files": "sample1data"}
<tool id="tool_provided_metadata_11" name="tool_provided_metadata_11" version="1.0.0">
<!-- Demonstrate setting simple dataset metadata for discovered datasets via galaxy.json for legacy tools (galaxy.json structure changes for profile >= 17.09 tools). -->
<command><![CDATA[
mkdir sample1data &&
echo '1' > sample1.report.tsv &&
echo 'foo line' > sample1data/foo &&
echo 'moo cow bar' > sample1data/bar &&
cp '$c1' galaxy.json
]]></command>
<configfiles>
<configfile name="c1">{"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "extra_files": "sample1data"}
</configfile>
</configfiles>
<inputs>
<param name="input" type="data" />
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<param name="input" ftype="txt" value="simple_line.txt"/>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents><has_line line="1" /></assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
<extra_files type="file" name="foo">
<assert_contents><has_line line="foo line" /></assert_contents>
</extra_files>
<extra_files type="file" name="bar">
<assert_contents><has_line line="moo cow bar" /></assert_contents>
</extra_files>
</discovered_dataset>
</output>
</test>
</tests>
</configfiles>
<inputs>
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents>
<has_line line="1" />
</assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
<extra_files type="file" name="foo">
<assert_contents>
<has_line line="foo line" />
</assert_contents>
</extra_files>
<extra_files type="file" name="bar">
<assert_contents>
<has_line line="moo cow bar" />
</assert_contents>
</extra_files>
</discovered_dataset>
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_12.xml
+44 -38
View File
@@ -1,45 +1,51 @@
<tool id="tool_provided_metadata_12" name="tool_provided_metadata_12" profile="17.09" version="1.0.0">
<!-- Demonstrate setting extra_files for discovered primary datasets in profile >= 17.09 tools. -->
<command>
mkdir sample1data;
echo "1" > sample1.report.tsv;
echo "foo line" > sample1data/foo;
echo "moo cow bar" > sample1data/bar;
cp $c1 galaxy.json;
</command>
<configfiles>
<configfile name="c1">{"sample": {
<!-- Demonstrate setting extra_files for discovered primary datasets in profile >= 17.09 tools. -->
<command><![CDATA[
mkdir sample1data &&
echo '1' > sample1.report.tsv &&
echo 'foo line' > sample1data/foo &&
echo 'moo cow bar' > sample1data/bar &&
cp '$c1' galaxy.json
]]></command>
<configfiles>
<configfile name="c1">{"sample": {
"datasets": [
{"filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "extra_files": "sample1data"}
]
}}
</configfile>
</configfiles>
<inputs>
<param name="input" type="data" />
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<param name="input" ftype="txt" value="simple_line.txt"/>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents><has_line line="1" /></assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
<extra_files type="file" name="foo">
<assert_contents><has_line line="foo line" /></assert_contents>
</extra_files>
<extra_files type="file" name="bar">
<assert_contents><has_line line="moo cow bar" /></assert_contents>
</extra_files>
</discovered_dataset>
</output>
</test>
</tests>
</configfiles>
<inputs>
<param name="input" type="data" />
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<param name="input" ftype="txt" value="simple_line.txt"/>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents>
<has_line line="1" />
</assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
<extra_files type="file" name="foo">
<assert_contents>
<has_line line="foo line" />
</assert_contents>
</extra_files>
<extra_files type="file" name="bar">
<assert_contents>
<has_line line="moo cow bar" />
</assert_contents>
</extra_files>
</discovered_dataset>
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_2.xml
+38 -36
View File
@@ -1,39 +1,41 @@
<tool id="tool_provided_metadata_2" name="tool_provided_metadata_2">
<!-- Demonstrate setting simple dataset metadata for discovered datasets via galaxy.json for legacy tools (galaxy.json structure changes for profile >= 17.09 tools). -->
<command>
echo "1" > sample1.report.tsv;
echo "2" > sample2.report.tsv;
cp $c1 galaxy.json;
</command>
<configfiles>
<configfile name="c1">{"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19"}
<tool id="tool_provided_metadata_2" name="tool_provided_metadata_2" version="1.0.0">
<!-- Demonstrate setting simple dataset metadata for discovered datasets via galaxy.json for legacy tools (galaxy.json structure changes for profile >= 17.09 tools). -->
<command><![CDATA[
echo '1' > sample1.report.tsv &&
echo '2' > sample2.report.tsv &&
cp '$c1' galaxy.json
]]></command>
<configfiles>
<configfile name="c1">{"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19"}
{"type": "new_primary_dataset", "filename": "sample2.report.tsv", "name": "cool name 2", "ext": "txt", "info": "cool 2 info", "dbkey": "hg19"}
</configfile>
</configfiles>
<inputs>
<param name="input" type="data" />
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<param name="input" ftype="txt" value="simple_line.txt"/>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents><has_line line="1" /></assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
</discovered_dataset>
<discovered_dataset designation="sample2" ftype="txt">
<assert_contents><has_line line="2" /></assert_contents>
<metadata name="name" value="cool name 2" />
<metadata name="info" value="cool 2 info" />
</discovered_dataset>
</output>
</test>
</tests>
</configfiles>
<inputs>
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents>
<has_line line="1" />
</assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
</discovered_dataset>
<discovered_dataset designation="sample2" ftype="txt">
<assert_contents>
<has_line line="2" />
</assert_contents>
<metadata name="name" value="cool name 2" />
<metadata name="info" value="cool 2 info" />
</discovered_dataset>
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_3.xml
+43 -41
View File
@@ -1,44 +1,46 @@
<tool id="tool_provided_metadata_3" name="tool_provided_metadata_3">
<!-- Demonstrate setting datatype defined metadata for discovered datasets via galaxy.json for legacy tools (galaxy.json structure changes for profile >= 17.09 tools). -->
<command>
echo "1" > sample1.report.tsv;
echo "2" > sample2.report.tsv;
cp $c1 galaxy.json;
</command>
<configfiles>
<configfile name="c1">{"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "metadata": {"data_lines": 10, "foo": "bar"}}
<tool id="tool_provided_metadata_3" name="tool_provided_metadata_3" version="1.0.0">
<!-- Demonstrate setting datatype defined metadata for discovered datasets via galaxy.json for legacy tools (galaxy.json structure changes for profile >= 17.09 tools). -->
<command><![CDATA[
echo '1' > sample1.report.tsv &&
echo '2' > sample2.report.tsv &&
cp '$c1' galaxy.json
]]></command>
<configfiles>
<configfile name="c1">{"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "metadata": {"data_lines": 10, "foo": "bar"}}
{"type": "new_primary_dataset", "filename": "sample2.report.tsv", "name": "cool name 2", "ext": "txt", "info": "cool 2 info", "dbkey": "hg19", "metadata": {"data_lines": 20, "foo": "bar"}}
</configfile>
</configfiles>
<inputs>
<param name="input" type="data" />
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<param name="input" ftype="txt" value="simple_line.txt"/>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents><has_line line="1" /></assert_contents>
<!-- Datatype defined metadata can be overridden/specified directly.
-->
<metadata name="data_lines" value="10" />
<!-- Non-datatype defined metadata values are ignored by the framework.
Uncommenting the following test will break this test.
-->
<!--
<metadata name="foo" value="bar" />
-->
</discovered_dataset>
<discovered_dataset designation="sample2" ftype="txt">
<assert_contents><has_line line="2" /></assert_contents>
<metadata name="data_lines" value="20" />
</discovered_dataset>
</output>
</test>
</tests>
</configfiles>
<inputs>
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents>
<has_line line="1" />
</assert_contents>
<!-- Datatype defined metadata can be overridden/specified directly.
-->
<metadata name="data_lines" value="10" />
<!-- Non-datatype defined metadata values are ignored by the framework.
Uncommenting the following test will break this test.
-->
<!--
<metadata name="foo" value="bar" />
-->
</discovered_dataset>
<discovered_dataset designation="sample2" ftype="txt">
<assert_contents>
<has_line line="2" />
</assert_contents>
<metadata name="data_lines" value="20" />
</discovered_dataset>
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_4.xml
+14 -16
View File
@@ -1,31 +1,29 @@
<tool id="tool_provided_metadata_4" name="tool_provided_metadata_4" version="1.0.0">
<!-- Demonstrate indexing dataset metadata by dataset basename instead of dataset id in galaxy.json for legacy tools (galaxy.json structure changes for profile >= 17.09 tools). -->
<command>
echo "This is a line of text." > '$out1';
cp $c1 galaxy.json;
</command>
<command><![CDATA[
echo 'This is a line of text.' > '$out1' &&
cp '$c1' galaxy.json
]]></command>
<configfiles>
<configfile name="c1">#import os
<configfile name="c1">#import os
{"type": "dataset", "dataset": "${os.path.basename(str($out1))}", "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", "dbkey": "cust1"}</configfile>
</configfiles>
<inputs>
<param name="input1" type="data" label="Input Dataset"/>
</inputs>
<outputs>
<!-- Set format="auto" to read from galaxy.json, use auto_format="true"
to sniff. -->
<data name="out1" format="auto" />
</outputs>
<tests>
<test>
<output name="out1" file="simple_line.txt" ftype="txt">
<metadata name="name" value="my dynamic name" />
<metadata name="info" value="my dynamic info" />
<metadata name="dbkey" value="cust1" />
</output>
</test>
</tests>
<help>
</help>
<tests>
<test>
<param name="input1" value="simple_line.txt" />
<output name="out1" file="simple_line.txt" ftype="txt">
<metadata name="name" value="my dynamic name" />
<metadata name="info" value="my dynamic info" />
<metadata name="dbkey" value="cust1" />
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_5.xml
+13 -15
View File
@@ -1,9 +1,9 @@
<tool id="tool_provided_metadata_5" name="tool_provided_metadata_5" profile="17.09" version="1.0.0">
<!-- Demonstrate setting simple output dataset metadata via galaxy.json for profile >= 17.09 tools. -->
<command>
echo "This is a line of text." > $out1;
cp $c1 galaxy.json;
</command>
<command><![CDATA[
echo 'This is a line of text.' > '$out1' &&
cp '$c1' galaxy.json
]]></command>
<configfiles>
<configfile name="c1">{"out1": {
"name": "my dynamic name",
@@ -14,23 +14,21 @@
</configfile>
</configfiles>
<inputs>
<param name="input1" type="data" label="Input Dataset"/>
</inputs>
<outputs>
<!-- Set format="auto" to read from galaxy.json, use auto_format="true"
j to sniff. -->
<data name="out1" format="auto" />
</outputs>
<tests>
<test>
<output name="out1" file="simple_line.txt" ftype="txt">
<metadata name="name" value="my dynamic name" />
<metadata name="info" value="my dynamic info" />
<metadata name="dbkey" value="cust1" />
</output>
</test>
</tests>
<help>
</help>
<tests>
<test>
<param name="input1" value="simple_line.txt" />
<output name="out1" file="simple_line.txt" ftype="txt">
<metadata name="name" value="my dynamic name" />
<metadata name="info" value="my dynamic info" />
<metadata name="dbkey" value="cust1" />
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_6.xml
+35 -33
View File
@@ -1,10 +1,10 @@
<tool id="tool_provided_metadata_6" name="tool_provided_metadata_6" profile="17.09" version="1.0.0">
<!-- Demonstrate setting discovered dataset metadata via galaxy.json for profile >= 17.09 tools. -->
<command>
echo "1" > sample1.report.tsv;
echo "2" > sample2.report.tsv;
cp $c1 galaxy.json;
</command>
<!-- Demonstrate setting discovered dataset metadata via galaxy.json for profile >= 17.09 tools. -->
<command><![CDATA[
echo '1' > sample1.report.tsv &&
echo '2' > sample2.report.tsv &&
cp '$c1' galaxy.json
]]></command>
<configfiles>
<configfile name="c1">{"sample": {
"datasets": [
@@ -13,31 +13,33 @@
]
}}
</configfile>
</configfiles>
<inputs>
<param name="input" type="data" />
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<param name="input" ftype="txt" value="simple_line.txt"/>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents><has_line line="1" /></assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
</discovered_dataset>
<discovered_dataset designation="sample2" ftype="txt">
<assert_contents><has_line line="2" /></assert_contents>
<metadata name="name" value="cool name 2" />
<metadata name="info" value="cool 2 info" />
</discovered_dataset>
</output>
</test>
</tests>
</configfiles>
<inputs>
</inputs>
<outputs>
<data name="sample">
<discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" visible="true" />
</data>
</outputs>
<tests>
<test>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents>
<has_line line="1" />
</assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
</discovered_dataset>
<discovered_dataset designation="sample2" ftype="txt">
<assert_contents>
<has_line line="2" />
</assert_contents>
<metadata name="name" value="cool name 2" />
<metadata name="info" value="cool 2 info" />
</discovered_dataset>
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_7.xml
+37 -35
View File
@@ -1,43 +1,45 @@
<tool id="tool_provided_metadata_7" name="tool_provided_metadata_7" profile="17.09" version="1.0.0">
<!-- Demonstrate setting discovered dataset metadata via galaxy.json for profile >= 17.09 tools. -->
<command>
echo "1" > sample1.report.tsv;
echo "2" > sample2.report.tsv;
cp $c1 galaxy.json;
</command>
<configfiles>
<configfile name="c1">{"sample": {
<!-- Demonstrate setting discovered dataset metadata via galaxy.json for profile >= 17.09 tools. -->
<command><![CDATA[
echo '1' > sample1.report.tsv &&
echo '2' > sample2.report.tsv &&
cp '$c1' galaxy.json
]]></command>
<configfiles>
<configfile name="c1">{"sample": {
"datasets": [
{"filename": "sample1.report.tsv", "designation": "sample1", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19"},
{"filename": "sample2.report.tsv", "designation": "sample2", "name": "cool name 2", "ext": "txt", "info": "cool 2 info", "dbkey": "hg19"}
]
}}
</configfile>
</configfiles>
<inputs>
<param name="input" type="data" />
</inputs>
<outputs>
<data name="sample">
<discover_datasets from_provided_metadata="true" visible="true" />
</data>
</outputs>
<tests>
<test>
<param name="input" ftype="txt" value="simple_line.txt"/>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents><has_line line="1" /></assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
</discovered_dataset>
<discovered_dataset designation="sample2" ftype="txt">
<assert_contents><has_line line="2" /></assert_contents>
<metadata name="name" value="cool name 2" />
<metadata name="info" value="cool 2 info" />
</discovered_dataset>
</output>
</test>
</tests>
</configfiles>
<inputs>
</inputs>
<outputs>
<data name="sample">
<discover_datasets from_provided_metadata="true" visible="true" />
</data>
</outputs>
<tests>
<test>
<output name="sample">
<discovered_dataset designation="sample1" ftype="txt">
<assert_contents>
<has_line line="1" />
</assert_contents>
<metadata name="name" value="cool name 1" />
<metadata name="dbkey" value="hg19" />
<metadata name="info" value="cool 1 info" />
</discovered_dataset>
<discovered_dataset designation="sample2" ftype="txt">
<assert_contents>
<has_line line="2" />
</assert_contents>
<metadata name="name" value="cool name 2" />
<metadata name="info" value="cool 2 info" />
</discovered_dataset>
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_8.xml
+14 -16
View File
@@ -1,31 +1,29 @@
<tool id="tool_provided_metadata_8" name="tool_provided_metadata_8" version="1.0.0" profile="17.09">
<!-- Demonstrate reverting tools with new profiles to older galaxy.json style
using provided_metadata_style attribute on outputs. -->
<command>
echo "This is a line of text." > $out1;
cp $c1 galaxy.json;
</command>
<command><![CDATA[
echo 'This is a line of text.' > '$out1' &&
cp '$c1' galaxy.json;
]]></command>
<configfiles>
<configfile name="c1">{"type": "dataset", "dataset_id": $out1.dataset.dataset.id, "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", "dbkey": "cust1"}</configfile>
<configfile name="c1">{"type": "dataset", "dataset_id": $out1.dataset.dataset.id, "name": "my dynamic name", "ext": "txt", "info": "my dynamic info", "dbkey": "cust1"}</configfile>
</configfiles>
<inputs>
<param name="input1" type="data" label="Input Dataset"/>
</inputs>
<outputs provided_metadata_style="legacy">
<!-- Set format="auto" to read from galaxy.json, use auto_format="true"
to sniff. -->
<data name="out1" format="auto" />
</outputs>
<tests>
<test>
<output name="out1" file="simple_line.txt" ftype="txt">
<metadata name="name" value="my dynamic name" />
<metadata name="info" value="my dynamic info" />
<metadata name="dbkey" value="cust1" />
</output>
</test>
</tests>
<help>
</help>
<tests>
<test>
<param name="input1" value="simple_line.txt" />
<output name="out1" file="simple_line.txt" ftype="txt">
<metadata name="name" value="my dynamic name" />
<metadata name="info" value="my dynamic info" />
<metadata name="dbkey" value="cust1" />
</output>
</test>
</tests>
</tool>
test/functional/tools/tool_provided_metadata_9.xml
+15 -17
View File
@@ -1,12 +1,12 @@
<tool id="tool_provided_metadata_9" name="tool_provided_metadata_9" profile="17.09" version="1.0.0">
<!-- Demonstrate overriding the location of the tool provided metadata file to
be something other than galaxy.json. -->
<command>
echo "This is a line of text." > $out1;
cp $c1 not_galaxy.json;
</command>
<command><![CDATA[
echo 'This is a line of text.' > '$out1' &&
cp '$c1' not_galaxy.json
]]></command>
<configfiles>
<configfile name="c1">{"out1": {
<configfile name="c1">{"out1": {
"name": "my dynamic name",
"ext": "txt",
"info": "my dynamic info",
@@ -16,22 +16,20 @@
</configfile>
</configfiles>
<inputs>
<param name="input1" type="data" label="Input Dataset"/>
</inputs>
<outputs provided_metadata_file="not_galaxy.json">
<data name="out1" format="auto" />
</outputs>
<tests>
<test>
<output name="out1" file="simple_line.txt" ftype="txt">
<metadata name="name" value="my dynamic name" />
<metadata name="info" value="my dynamic info" />
<metadata name="dbkey" value="cust1" />
<metadata name="created_from_basename" value="my name.txt" />
</output>
</test>
</tests>
<help>
</help>
<tests>
<test>
<param name="input1" value="simple_line.txt" />
<output name="out1" file="simple_line.txt" ftype="txt">
<metadata name="name" value="my dynamic name" />
<metadata name="info" value="my dynamic info" />
<metadata name="dbkey" value="cust1" />
<metadata name="created_from_basename" value="my name.txt" />
</output>
</test>
</tests>
</tool>
test/functional/tools/top_level_data.xml
+32 -32
View File
@@ -1,34 +1,34 @@
<tool id="top_level_data" name="top_level_data" version="0.1.0">
<command>
cat '${f1}' >> $out1;
echo '${library.f2}' >> $out2; <!-- cannot use just f2 here -->
</command>
<inputs>
<conditional name="library">
<param name="type" type="select" label="Parameter Settings">
<option value="no">Use defaults</option>
<option value="yes">Full parameter list</option>
</param>
<when value="yes">
<param name="f1" type="data" format="txt" label="Data 1" />
<param name="f2" type="text" label="Text 1" />
</when>
<when value="no">
<param name="f1" type="data" format="txt" label="Data 1" />
<param name="f2" type="text" label="TExt 1" />
</when>
</conditional>
</inputs>
<outputs>
<data format="txt" name="out1" />
<data format="txt" name="out2" />
</outputs>
<tests>
<test>
<param name="f1" value="simple_line.txt" />
<param name="f2" value="This is a line of text." />
<output name="out1" file="simple_line.txt" />
<output name="out2" file="simple_line.txt" />
</test>
</tests>
<command><![CDATA[
cat '${f1}' >> '$out1' &&
echo '${library.f2}' >> '$out2' ## cannot use just f2 here
]]></command>
<inputs>
<conditional name="library">
<param name="type" type="select" label="Parameter Settings">
<option value="no">Use defaults</option>
<option value="yes">Full parameter list</option>
</param>
<when value="yes">
<param name="f1" type="data" format="txt" label="Data 1" />
<param name="f2" type="text" label="Text 1" />
</when>
<when value="no">
<param name="f1" type="data" format="txt" label="Data 1" />
<param name="f2" type="text" label="Text 1" />
</when>
</conditional>
</inputs>
<outputs>
<data name="out1" format="txt" />
<data name="out2" format="txt" />
</outputs>
<tests>
<test>
<param name="f1" value="simple_line.txt" />
<param name="f2" value="This is a line of text." />
<output name="out1" file="simple_line.txt" />
<output name="out2" file="simple_line.txt" />
</test>
</tests>
</tool>
test/functional/tools/unicode_stream.xml
+10 -8
View File
@@ -1,23 +1,25 @@
<tool id="unicode_stream" name="unicode_stream" version="0.1.0">
<description>
</description>
<version_command>echo "\x00"</version_command>
<version_command><![CDATA[
echo "\x00"
]]></version_command>
<command detect_errors="exit_code"><![CDATA[
#if $include_null:
echo "\x00" > $out_file1;
echo "\x00" > '$out_file1' &&
#end if
echo '$input1' >> '$out_file1';
cat '$cf';
echo "\x00";
>&2 cat '$cf';
sh -c "exit $exit"
echo '$input1' >> '$out_file1' &&
cat '$cf' &&
echo "\x00" &&
>&2 cat '$cf' &&
sh -c 'exit $exit'
]]></command>
<configfiles>
<configfile name="cf">ვეპხის ტყაოსანი შოთა რუსთაველი</configfile>
</configfiles>
<inputs>
<param name="input1" type="text" label="Input">
<sanitizer sanitize="False" />
<sanitizer sanitize="false" />
</param>
<param name="exit" type="integer" value="0" label="Exit Code" />
<param name="include_null" type="boolean" label="Include unicode null in output?"/>
test/functional/tools/validation_default.xml
+37 -37
View File
@@ -1,39 +1,39 @@
<tool id="validation_default" name="Validation (default)" version="0.1">
<command>
echo '$input1' > out1;
echo $float_param > out2;
echo $select_param > out3;
</command>
<inputs>
<param name="input1" type="text" label="text input" />
<param name="float_param" type="float" label="float input" value="8.0" />
<param name="select_param" type="select" label="select_param">
<option value="opt1">Option 1</option>
<option value="opt2">Option 2</option>
</param>
</inputs>
<outputs>
<data name="out_file1" from_work_dir="out1" />
<data name="out_file2" from_work_dir="out2" />
<data name="out_file3" from_work_dir="out3" />
</outputs>
<tests>
<test>
<param name="input1" value="&quot; ; echo &quot;moo" />
<param name="float_param" value="5" />
<param name="select_param" value="opt1" />
<output name="out_file1">
<assert_contents>
<has_line line="__dq__ X echo __dq__moo" />
<has_line line="__dq__ X echo __dq__moo" n="1" />
<has_text text="o" n="3" />
<has_n_lines n="1" />
<has_size value="24"/>
<has_size value="20" delta="5"/>
</assert_contents>
</output>
</test>
</tests>
<help>
</help>
<command><![CDATA[
echo '$input1' > out1 &&
echo $float_param > out2 &&
echo $select_param > out3
]]></command>
<inputs>
<param name="input1" type="text" label="text input" />
<param name="float_param" type="float" label="float input" value="8.0" />
<param name="select_param" type="select" label="select_param">
<option value="opt1">Option 1</option>
<option value="opt2">Option 2</option>
</param>
</inputs>
<outputs>
<data name="out_file1" from_work_dir="out1" />
<data name="out_file2" from_work_dir="out2" />
<data name="out_file3" from_work_dir="out3" />
</outputs>
<tests>
<test>
<param name="input1" value="&quot; ; echo &quot;moo" />
<param name="float_param" value="5" />
<param name="select_param" value="opt1" />
<output name="out_file1">
<assert_contents>
<has_line line="__dq__ X echo __dq__moo" />
<has_line line="__dq__ X echo __dq__moo" n="1" />
<has_text text="o" n="3" />
<has_n_lines n="1" />
<has_size value="24"/>
<has_size value="20" delta="5"/>
</assert_contents>
</output>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/validation_empty_dataset.xml
+16 -16
View File
@@ -1,17 +1,17 @@
<tool id="validation_empty_dataset" name="validation_empty_dataset">
<command>
echo "Hello World" > out1;
</command>
<inputs>
<param name="input1" type="data" label="non-empty input">
<validator type="empty_dataset" />
</param>
</inputs>
<outputs>
<data name="out_file1" from_work_dir="out1" />
</outputs>
<tests>
</tests>
<help>
</help>
<tool id="validation_empty_dataset" name="validation_empty_dataset" version="1.0.0">
<command><![CDATA[
echo 'Hello World' > out1
]]></command>
<inputs>
<param name="input1" type="data" label="non-empty input">
<validator type="empty_dataset" />
</param>
</inputs>
<outputs>
<data name="out_file1" from_work_dir="out1" />
</outputs>
<tests>
</tests>
<help>
</help>
</tool>
test/functional/tools/validation_hdf5.xml
+3 -3
View File
@@ -1,7 +1,7 @@
<tool id="validation_hdf5" name="Validation (hdf5)" version="1.0">
<command>
cp '$input' '$output'
</command>
<command><![CDATA[
cp '$input' '$output'
]]></command>
<inputs>
<param name="input" type="data" format="cool" />
</inputs>

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