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Add missing single-quotes in tools Cheetah

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This commit is contained in:
Nicola Soranzo
2020-11-10 19:29:22 +00:00
parent be1e21bffc
commit 1e9f83b53e
4 changed files with 39 additions and 41 deletions
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test/functional/tools/for_workflows/mapper.xml
+3 -3
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@@ -1,7 +1,7 @@
<tool id="mapper" name="Mapper" version="0.1.0">
<command>
cp $__tool_directory__/1.bam $out_file1
</command>
<command><![CDATA[
cp '$__tool_directory__/1.bam' '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" format="fastq" label="Fastq Input"/>
<param name="reference" type="data" format="fasta" label="Fasta Input"/>
test/functional/tools/for_workflows/mapper2.xml
+22 -22
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@@ -1,29 +1,29 @@
<tool id="mapper2" name="mapper2" version="0.1.0">
<command>
cp $__tool_directory__/1.bam $out_file1
</command>
<command><![CDATA[
cp '$__tool_directory__/1.bam' '$out_file1'
]]></command>
<inputs>
<!-- Conditional input block loosely based on bwa-mem. -->
<conditional name="fastq_input">
<param name="fastq_input_selector" type="select" label="Single or Paired-end reads">
<option value="paired">Paired</option>
<option value="single">Single</option>
<option value="paired_collection">Paired Collection</option>
<option value="paired_iv">Paired Interleaved</option>
</param>
<when value="paired">
<param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" />
<param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" />
</when>
<when value="single">
<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset"/>
</when>
<when value="paired_collection">
<param name="fastq_input1" format="fastq" type="data_collection" collection_type="paired" label="Select a paired collection" />
</when>
<when value="paired_iv">
<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" />
</when>
<param name="fastq_input_selector" type="select" label="Single or Paired-end reads">
<option value="paired">Paired</option>
<option value="single">Single</option>
<option value="paired_collection">Paired Collection</option>
<option value="paired_iv">Paired Interleaved</option>
</param>
<when value="paired">
<param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" />
<param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" />
</when>
<when value="single">
<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset"/>
</when>
<when value="paired_collection">
<param name="fastq_input1" type="data_collection" collection_type="paired" format="fastq" label="Select a paired collection" />
</when>
<when value="paired_iv">
<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" />
</when>
</conditional>
<param name="reference" type="data" format="fasta" label="Fasta Input"/>
</inputs>
test/functional/tools/for_workflows/pileup.xml
+4 -4
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@@ -1,9 +1,9 @@
<tool id="pileup" name="Pileup" version="0.1.0">
<command>
printf "Summary" > $out_file1
</command>
<command><![CDATA[
printf 'Summary' > '$out_file1'
]]></command>
<inputs>
<param name="input1" type="data" format="bam" multiple="true" label="BAM Inputs" min="1">
<param name="input1" type="data" format="bam" multiple="true" min="1" label="BAM Inputs">
<validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
</param>
<param name="reference" type="data" format="fasta" label="Fasta Input"/>
tools/filters/catWrapper.xml
+10 -12
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@@ -1,13 +1,13 @@
<tool id="cat1" name="Concatenate datasets" version="1.0.0">
<description>tail-to-head</description>
<command interpreter="python">
catWrapper.py
$out_file1
$input1
#for $q in $queries
${q.input2}
#end for
</command>
<command interpreter="python"><![CDATA[
catWrapper.py
'$out_file1'
'$input1'
#for $q in $queries
'${q.input2}'
#end for
]]></command>
<inputs>
<param name="input1" type="data" label="Concatenate Dataset"/>
<repeat name="queries" title="Dataset">
@@ -33,8 +33,7 @@
</test>
-->
</tests>
<help>
<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.
@@ -74,6 +73,5 @@ will result in the following::
chr1 151278832 151279227 Z 0 -
chr2 100000030 200000955 P 0 +
chr2 100000015 200000999 Q 0 +
</help>
]]></help>
</tool>