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Remove deprecated `interpreter attribute from tools <command>`

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This commit is contained in:
Nicola Soranzo
2020-03-05 12:53:09 +01:00
parent 476b194819
commit ef4f5ccda4
29 changed files with 277 additions and 225 deletions
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test/functional/tools/test_data_source.xml
+3 -1
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@@ -5,7 +5,9 @@
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="test_data_source" id="test_data_source" tool_type="data_source" version="1.0.0">
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get">
<display>go to Ratmine server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" />
tools/data_source/biomart.xml
+12 -10
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@@ -8,11 +8,13 @@
everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
-->
<tool name="BioMart" id="biomart" tool_type="data_source" version="1.0.1">
<description>Ensembl server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://www.ensembl.org/biomart/martview" check_values="false" method="get" target="_top">
<display>go to BioMart Ensembl $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
<description>Ensembl server</description>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://www.ensembl.org/biomart/martview" check_values="false" method="get" target="_top">
<display>go to BioMart Ensembl $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL" remote_name="URL" missing="">
@@ -34,11 +36,11 @@
<request_param galaxy_name="name" remote_name="name" missing="Biomart query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="tabular" />
</outputs>
<options sanitize="False" refresh="True"/>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="tabular" />
</outputs>
<options sanitize="False" refresh="True"/>
<citations>
<citation type="doi">10.1093/database/bar011</citation>
<citation type="doi">10.1093/nar/gkv350</citation>
tools/data_source/biomart_test.xml
+13 -11
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@@ -8,12 +8,14 @@
everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
-->
<tool name="BioMart" id="biomart_test" tool_type="data_source" version="1.0.1">
<description>Test server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://test.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
<display>go to BioMart Central $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
</inputs>
<description>Test server</description>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://test.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
<display>go to BioMart Central $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL" remote_name="URL" missing="">
<append_param separator="&amp;" first_separator="?" join="=">
@@ -34,11 +36,11 @@
<request_param galaxy_name="name" remote_name="name" missing="Biomart test query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="tabular" />
</outputs>
<options sanitize="False" refresh="True"/>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="tabular" />
</outputs>
<options sanitize="False" refresh="True"/>
<citations>
<citation type="doi">10.1093/database/bar011</citation>
<citation type="doi">10.1093/nar/gkv350</citation>
tools/data_source/cbi_rice_mart.xml
+3 -1
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@@ -6,7 +6,9 @@
-->
<tool name="CBI Rice Mart" id="cbi_rice_mart" tool_type="data_source" version="1.0.1">
<description>rice mart</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://ricemart.cbi.edu.cn/biomart/martview/" check_values="false" method="get" target="_top">
<display>go to RMap rice mart $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
tools/data_source/ebi_sra.xml
+3 -1
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@@ -2,7 +2,9 @@
<tool name="EBI SRA" id="ebi_sra_main" tool_type="data_source" version="1.0.1">
<description>ENA SRA</description>
<!-- This paython script imports the file into Galaxy -->
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<!-- The URL where Galaxy will forwards the user when this tool is accessed from the Get Data menu -->
<inputs action="https://www.ebi.ac.uk/ena/data/search" check_values="false" method="get">
<display>go to EBI SRA server $GALAXY_URL</display>
tools/data_source/eupathdb.xml
+3 -1
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@@ -1,6 +1,8 @@
<tool name="EuPathDB" id="eupathdb" tool_type="data_source" url_method="post" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://eupathdb.org/eupathdb/queries_tools.jsp" check_values="false" method="get">
<display>go to EuPathDB server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=eupathdb" />
tools/data_source/fly_modencode.xml
+3 -1
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@@ -1,7 +1,9 @@
<?xml version="1.0"?>
<tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source" version="1.0.1">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://gbrowse.modencode.org/fgb2/gbrowse/fly" check_values="false" target="_top">
<display>go to modENCODE fly server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEfly" />
tools/data_source/flymine.xml
+3 -1
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@@ -6,7 +6,9 @@
-->
<tool name="Flymine" id="flymine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://www.flymine.org" check_values="false" method="get">
<display>go to Flymine server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
tools/data_source/flymine_test.xml
+3 -1
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@@ -6,7 +6,9 @@
-->
<tool name="Flymine test" id="flymine_test" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get">
<display>go to Flymine server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" />
tools/data_source/genbank.xml
+16 -16
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@@ -1,23 +1,23 @@
<tool id="genbank" name="Connect to Genbank" version="1.0.0">
<!-- <description>queries genbank</description> -->
<command interpreter="python">genbank.py $mode "$text" $output</command>
<inputs>
<param name="mode" type="select">
<option value="nucleotide">nucleotide database</option>
<option value="protein">proteins database</option>
<label>Get sequences from the</label>
</param>
<param name="text" type="text" value="6273291" label="with accession ID" />
</inputs>
<outputs>
<data format="fasta" name="output" />
</outputs>
<help>
<!-- <description>queries genbank</description> -->
<command><![CDATA[
python '$__tool_directory__/genbank.py' $mode '$text' '$output'
]]></command>
<inputs>
<param name="mode" type="select" label="Get sequences from the">
<option value="nucleotide">nucleotide database</option>
<option value="protein">proteins database</option>
</param>
<param name="text" type="text" value="6273291" label="with accession ID" />
</inputs>
<outputs>
<data name="output" format="fasta" />
</outputs>
<help><![CDATA[
At the moment this tool allows the following simple searches:
- by GI: **51594135**
- by accession: **CF622840**
- using text: **human hbb1** (this feature is experimental)
</help>
]]></help>
</tool>
tools/data_source/gramene_mart.xml
+3 -1
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@@ -9,7 +9,9 @@
-->
<tool name="GrameneMart" id="gramenemart" tool_type="data_source" version="1.0.1">
<description> Central server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://www.gramene.org/biomart/martview" check_values="false" method="get" target="_top">
<display>go to GrameneMart Central $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
tools/data_source/hapmapmart.xml
+12 -10
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@@ -12,11 +12,13 @@
everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
-->
<tool name="HapMapMart" id="hapmapmart" tool_type="data_source" version="0.0.01">
<description>HapMap Biomart</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://hapmap.ncbi.nlm.nih.gov/biomart/martview" check_values="false" method="get" target="_top">
<display>go to HapMap BioMart $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner/hapmapmart" />
<description>HapMap Biomart</description>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://hapmap.ncbi.nlm.nih.gov/biomart/martview" check_values="false" method="get" target="_top">
<display>go to HapMap BioMart $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner/hapmapmart" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL" remote_name="URL" missing="">
@@ -38,9 +40,9 @@
<request_param galaxy_name="name" remote_name="name" missing="HapMap query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="tabular" />
</outputs>
<options sanitize="False" refresh="True"/>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="tabular" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>
tools/data_source/hbvar.xml
+12 -17
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@@ -1,21 +1,16 @@
<?xml version="1.0"?>
<tool name="HbVar" id="hbvar" tool_type="data_source" version="2.0.0">
<description>Human Hemoglobin Variants and Thalassemias</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3" check_values="false" method="get" target="_top">
<display>go to HbVar database $GALAXY_URL $tool_id</display>
</inputs>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="auto" />
</outputs>
<options sanitize="False" refresh="True"/>
<description>Human Hemoglobin Variants and Thalassemias</description>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3" check_values="false" method="get" target="_top">
<display>go to HbVar database $GALAXY_URL $tool_id</display>
</inputs>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="auto" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>
tools/data_source/import.xml
+27 -25
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@@ -1,27 +1,29 @@
<tool id="Featured datasets4" name="Featured datasets" version="1.0.0">
<description>(PSU prepared queries)</description>
<command interpreter="python">import.py $data $output</command>
<inputs>
<display>$data</display>
<param name="data" type="select" display="radio">
<option value="eryth">Erythroid predicted cis-regulatory modules</option>
<option value="exons">Exons of protein-coding genes in the mouse genome, assembly mm3</option>
<option value="cishg16 ">Known cis-regulatory modules in the human HBB gene complex (hg16)</option>
<option value="cishg17">Known cis-regulatory modules in the human HBB gene complex (hg17)</option>
<option value="krhg16">Known regulatory regions (hg16)</option>
<option value="krhg17">Known regulatory regions (hg17)</option>
<option value="tARhg16mmc">Human (hg16) evolutionary cold region (vs mouse)</option>
<option value="tARhg16mmm">Human (hg16) evolutionary medium region (vs mouse)</option>
<option value="tARhg16mmh">Human (hg16) evolutionary hot region (vs mouse)</option>
<option value="tARhg16rnc">Human (hg16) evolutionary cold region (vs rat)</option>
<option value="tARhg16rnm">Human (hg16) evolutionary medium region (vs rat)</option>
<option value="tARhg16rnh">Human (hg16) evolutionary hot region (vs rat)</option>
<option value="phastConsHg16">phastCons hg16 (stringent, top ~5%) from UCSC</option>
<option value="omimhg16">OMIM disorders (hg16)</option>
<option value="omimhg17">OMIM disorders (hg17)</option>
</param>
</inputs>
<outputs>
<data format="bed" name="output" />
</outputs>
<description>(PSU prepared queries)</description>
<command><![CDATA[
python '$__tool_directory__/import.py' $data '$output'
]]></command>
<inputs>
<display>$data</display>
<param name="data" type="select" display="radio">
<option value="eryth">Erythroid predicted cis-regulatory modules</option>
<option value="exons">Exons of protein-coding genes in the mouse genome, assembly mm3</option>
<option value="cishg16 ">Known cis-regulatory modules in the human HBB gene complex (hg16)</option>
<option value="cishg17">Known cis-regulatory modules in the human HBB gene complex (hg17)</option>
<option value="krhg16">Known regulatory regions (hg16)</option>
<option value="krhg17">Known regulatory regions (hg17)</option>
<option value="tARhg16mmc">Human (hg16) evolutionary cold region (vs mouse)</option>
<option value="tARhg16mmm">Human (hg16) evolutionary medium region (vs mouse)</option>
<option value="tARhg16mmh">Human (hg16) evolutionary hot region (vs mouse)</option>
<option value="tARhg16rnc">Human (hg16) evolutionary cold region (vs rat)</option>
<option value="tARhg16rnm">Human (hg16) evolutionary medium region (vs rat)</option>
<option value="tARhg16rnh">Human (hg16) evolutionary hot region (vs rat)</option>
<option value="phastConsHg16">phastCons hg16 (stringent, top ~5%) from UCSC</option>
<option value="omimhg16">OMIM disorders (hg16)</option>
<option value="omimhg17">OMIM disorders (hg17)</option>
</param>
</inputs>
<outputs>
<data name="output" format="bed" />
</outputs>
</tool>
tools/data_source/intermine.xml
+3 -1
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@@ -6,7 +6,9 @@
-->
<tool name="InterMine" id="intermine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://registry.intermine.org/im-to-galaxy" check_values="false" method="get">
<display>go to InterMine server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=intermine" />
tools/data_source/metabolicmine.xml
+3 -1
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@@ -1,7 +1,9 @@
<?xml version="1.0"?>
<tool name="metabolicMine" id="metabolicmine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://www.metabolicmine.org/beta/begin.do" check_values="false" method="get">
<display>go to metabolicMine server $GALAXY_URL</display>
</inputs>
tools/data_source/microbial_import.xml
+92 -88
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@@ -1,91 +1,95 @@
<tool id="microbial_import1" name="Get Microbial Data" version="1.0.0">
<command interpreter="python">microbial_import.py $CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3 $output ${GALAXY_DATA_INDEX_DIR}/microbial_data.loc</command>
<inputs>
<param name="kingdom" type="select" label="Select the Desired Kingdom">
<options from_file="microbial_data.loc" startswith="ORG">
<column name="name" index="3"/>
<column name="value" index="3"/>
<filter type="unique_value" name="unique" column="3"/>
</options>
</param>
<param name="org" type="select" label="Select the Desired Organism">
<options from_file="microbial_data.loc" startswith="ORG">
<column name="name" index="2"/>
<column name="value" index="1"/>
<filter type="param_value" ref="kingdom" name="kingdom" column="3"/>
<filter type="sort_by" column="2"/>
</options>
</param>
<param name="CDS" type="select" label="Select Desired Coding Sequences" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="CDS" column="4"/>
</options>
</param>
<param name="tRNA" type="select" label="Select Desired tRNA" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="tRNA" column="4"/>
</options>
</param>
<param name="rRNA" type="select" label="Select Desired rRNA" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="rRNA" column="4"/>
</options>
</param>
<param name="sequence" type="select" label="Select Desired DNA Sequences" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="sequence" column="4"/>
</options>
</param>
<param name="GeneMark" type="select" label="Select Desired GeneMark Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="GeneMark" column="4"/>
</options>
</param>
<param name="GeneMarkHMM" type="select" label="Select Desired GeneMarkHMM Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="GeneMarkHMM" column="4"/>
</options>
</param>
<param name="Glimmer3" type="select" label="Select Desired Glimmer3 Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="Glimmer3" column="4"/>
</options>
</param>
</inputs>
<outputs>
<data format="bed" name="output"/>
</outputs>
<code file="microbial_import_code.py"/>
<help>
<command><![CDATA[
python '$__tool_directory__/microbial_import.py'
$CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3
'$output'
'${GALAXY_DATA_INDEX_DIR}/microbial_data.loc'
]]></command>
<inputs>
<param name="kingdom" type="select" label="Select the Desired Kingdom">
<options from_file="microbial_data.loc" startswith="ORG">
<column name="name" index="3"/>
<column name="value" index="3"/>
<filter type="unique_value" name="unique" column="3"/>
</options>
</param>
<param name="org" type="select" label="Select the Desired Organism">
<options from_file="microbial_data.loc" startswith="ORG">
<column name="name" index="2"/>
<column name="value" index="1"/>
<filter type="param_value" ref="kingdom" name="kingdom" column="3"/>
<filter type="sort_by" column="2"/>
</options>
</param>
<param name="CDS" type="select" label="Select Desired Coding Sequences" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="CDS" column="4"/>
</options>
</param>
<param name="tRNA" type="select" label="Select Desired tRNA" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="tRNA" column="4"/>
</options>
</param>
<param name="rRNA" type="select" label="Select Desired rRNA" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="rRNA" column="4"/>
</options>
</param>
<param name="sequence" type="select" label="Select Desired DNA Sequences" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="sequence" column="4"/>
</options>
</param>
<param name="GeneMark" type="select" label="Select Desired GeneMark Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="GeneMark" column="4"/>
</options>
</param>
<param name="GeneMarkHMM" type="select" label="Select Desired GeneMarkHMM Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="GeneMarkHMM" column="4"/>
</options>
</param>
<param name="Glimmer3" type="select" label="Select Desired Glimmer3 Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="Glimmer3" column="4"/>
</options>
</param>
</inputs>
<outputs>
<data name="output" format="bed"/>
</outputs>
<code file="microbial_import_code.py"/>
<help><![CDATA[
This tool will allow you to obtain various genomic datasets for any completed Microbial Genome Project as listed at NCBI_.
.. _NCBI: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1
@@ -102,5 +106,5 @@ Current datasets available include
-----
Organisms in **bold** are available at the UCSC Browser.
</help>
]]></help>
</tool>
tools/data_source/modmine.xml
+3 -1
View File
@@ -6,7 +6,9 @@
-->
<tool name="modENCODE modMine" id="modmine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://intermine.modencode.org/" check_values="false" method="get">
<display>go to modENCODE modMine server $GALAXY_URL</display>
</inputs>
tools/data_source/mousemine.xml
+3 -1
View File
@@ -6,7 +6,9 @@
-->
<tool name="MouseMine" id="mousemine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://www.mousemine.org/mousemine/begin.do" check_values="false" method="get">
<display>go to MouseMine server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=mousemine" />
tools/data_source/ratmine.xml
+3 -1
View File
@@ -6,7 +6,9 @@
-->
<tool name="Ratmine" id="ratmine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get">
<display>go to Ratmine server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" />
tools/data_source/ucsc_tablebrowser.xml
+3 -1
View File
@@ -6,7 +6,9 @@
-->
<tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source" version="1.0.0">
<description>table browser</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="https://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
<display>go to UCSC Table Browser $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
tools/data_source/ucsc_tablebrowser_archaea.xml
+3 -1
View File
@@ -6,7 +6,9 @@
-->
<tool name="UCSC Archaea" id="ucsc_table_direct_archaea1" tool_type="data_source" version="1.0.0">
<description>table browser</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://archaea.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
<display>go to UCSC Table Browser $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
tools/data_source/ucsc_tablebrowser_test.xml
+3 -1
View File
@@ -6,7 +6,9 @@
-->
<tool name="UCSC Test" id="ucsc_table_direct_test1" tool_type="data_source" version="1.0.1">
<description>table browser</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://genome-test.gi.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
<display>go to UCSC Table Browser $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
tools/data_source/worm_modencode.xml
+3 -1
View File
@@ -1,7 +1,9 @@
<?xml version="1.0"?>
<tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source" version="1.0.1">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://gbrowse.modencode.org/fgb2/gbrowse/worm" check_values="false" target="_top">
<display>go to modENCODE worm server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEworm" />
tools/data_source/wormbase.xml
+3 -1
View File
@@ -1,7 +1,9 @@
<?xml version="1.0"?>
<tool name="WormBase" id="wormbase" tool_type="data_source" version="1.0.1">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://www.wormbase.org/tools/genome/gbrowse/c_elegans/" check_values="false" target="_top">
<display>go to Wormbase server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase" />
tools/data_source/wormbase_test.xml
+3 -1
View File
@@ -1,7 +1,9 @@
<?xml version="1.0"?>
<tool name="Wormbase" id="wormbase_test" tool_type="data_source" version="1.0.0">
<description>test server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" target="_top">
<display>go to Wormbase test server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase_test" />
tools/data_source/yeastmine.xml
+3 -1
View File
@@ -1,7 +1,9 @@
<?xml version="1.0"?>
<tool name="YeastMine" id="yeastmine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get">
<display>go to yeastMine server $GALAXY_URL</display>
</inputs>
tools/data_source/zebrafishmine.xml
+3 -1
View File
@@ -1,7 +1,9 @@
<?xml version="1.0"?>
<tool name="ZebrafishMine" id="zebrafishmine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<command><![CDATA[
python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
]]></command>
<inputs action="http://zebrafishmine.org/begin.do" check_values="false" method="get">
<display>go to ZebrafishMine server $GALAXY_URL</display>
</inputs>
tools/visualization/LAJ.xml
+30 -27
View File
@@ -1,20 +1,25 @@
<tool id="laj_1" name="LAJ" version="1.0.0">
<description>Pairwise Alignment Viewer</description>
<command interpreter="python">LAJ.py $maf_input $out_file1</command>
<inputs>
<param name="maf_input" type="data" format="lav" label="Alignment File" optional="False"/>
<param name="seq_file1" type="data" format="fasta" label="First Sequence File" optional="True"/>
<param name="seq_file2" type="data" format="fasta" label="Second Sequence File" optional="True"/>
<param name="exonfile" type="data" format="txt" label="Exon File" optional="True"/>
<param name="repeatfile" type="data" format="txt" label="Repeat File" optional="True"/>
<param name="annotationfile" type="data" format="txt" label="Annotation File" optional="True"/>
<param name="underlayfile" type="data" format="txt" label="Underlay File" optional="True"/>
<param name="highlightfile" type="data" format="txt" label="Highlight File" optional="True"/>
</inputs>
<outputs>
<data name="out_file1" format="laj"/>
</outputs>
<help>
<code file="LAJ_code.py"/>
<command><![CDATA[
python '$__tool_directory__/LAJ.py' '$maf_input' '$out_file1'
]]></command>
<inputs>
<param name="maf_input" type="data" format="lav" label="Alignment File"/>
<param name="seq_file1" type="data" format="fasta" optional="true" label="First Sequence File"/>
<param name="seq_file2" type="data" format="fasta" optional="true" label="Second Sequence File"/>
<param name="exonfile" type="data" format="txt" optional="true" label="Exon File"/>
<param name="repeatfile" type="data" format="txt" optional="true" label="Repeat File"/>
<param name="annotationfile" type="data" format="txt" optional="true" label="Annotation File"/>
<param name="underlayfile" type="data" format="txt" optional="true" label="Underlay File"/>
<param name="highlightfile" type="data" format="txt" optional="true" label="Highlight File"/>
</inputs>
<outputs>
<data name="out_file1" format="laj"/>
</outputs>
<tests>
</tests>
<help><![CDATA[
You can use this tool to view a set of LAV alignments. You may include FASTA formatted sequences for both species.
For detailed information on LAJ, click here_.
@@ -26,17 +31,15 @@ Laj is a tool for viewing and manipulating the output from pairwise alignment pr
.. class:: infomark
**Note:** If you save output from the applet, you will need to manually refresh your history.
</help>
<code file="LAJ_code.py"/>
<citations>
<citation type="bibtex">
@misc{Miller2005,
author = {Miller Lab},
year = {2005},
title = {Laj},
url = {http://globin.bx.psu.edu/dist/laj/},
]]></help>
<citations>
<citation type="bibtex">
@misc{Miller2005,
author = {Miller Lab},
year = {2005},
title = {Laj},
url = {http://globin.bx.psu.edu/dist/laj/},
}
</citation>
</citations>
</citation>
</citations>
</tool>