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un-quotes the region list so chr1 chr2 will not be passed as an inval… #7086

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un-quotes the region list so chr1 chr2 will not be passed as an inval… #7086

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10 changes: 6 additions & 4 deletions tool_collections/samtools/samtools_view/samtools_view.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@
#if str($mode.filter_config.cond_region.select_region) == 'bed':
#set std_filters = $std_filters + " -L '%s'" % str($mode.filter_config.cond_region.bedfile)
#elif str($mode.filter_config.cond_region.select_region) == 'text':
#set $reg_filters = "'%s'" % str($mode.filter_config.cond_region.regions).strip()
#set $reg_filters = "'%s'" % "' '".join(str($mode.filter_config.cond_region.regions).strip().split())
#end if

#if $mode.filter_config.cond_rg.select_rg == 'text':
Expand Down Expand Up @@ -282,7 +282,9 @@
</param>
<when value="no"/>
<when value="text">
<param name="regions" type="text" optional="false" label="Filter by regions" help="One or more space-separated region specifications to restrict output to only those alignments which overlap the specified region(s)."/>
<param name="regions" type="text" optional="false" label="Filter by regions" help="One or more space-separated region specifications to restrict output to only those alignments which overlap the specified region(s).">
<validator type="regex" message="Invalid characters in regions. Only letters, numbers, periods, underscores, hyphens, colons, asterixes, and spaces are allowed.">^[A-Za-z0-9._\-:\*\s]+$</validator>
</param>
</when>
<when value="bed">
<param name="bedfile" format="bed" argument="-L" optional="false" type="data" label="Filter by intervals in a bed file" help="Only output alignments overlapping the intervals in the input bed file." />
Expand Down Expand Up @@ -640,15 +642,15 @@
</conditional>
<output name="outputsam" file="test_17.bam" ftype="bam" lines_diff="4" />
</test>
<!-- 18) -->
<!-- 18) region filtering with multiple regions -> cram -->
<test expect_num_outputs="1">
<param name="input" value="in_test_14.bam" ftype="bam" />
<conditional name="mode">
<param name="outtype" value="selected_reads" />
<section name="filter_config">
<conditional name="cond_region">
<param name="select_region" value="text"/>
<param name="regions" value="CHROMOSOME_I" />
<param name="regions" value="CHROMOSOME_I:1-1 CHROMOSOME_I:2" />
</conditional>
</section>
<conditional name="output_options">
Expand Down