| Previous changeset 19:5ec526530725 (2025-11-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_view commit ec877e3c25274c76a3794ec614d896cb7f28a973 |
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modified:
samtools_view.xml |
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| diff -r 5ec526530725 -r 5cf9fcc93508 samtools_view.xml --- a/samtools_view.xml Wed Nov 12 12:59:47 2025 +0000 +++ b/samtools_view.xml Mon Mar 23 21:01:10 2026 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> +<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>- reformat, filter, or subsample SAM, BAM or CRAM</description> <macros> <import>macros.xml</import> @@ -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 $mode.filter_config.cond_rg.select_rg == 'text': @@ -282,7 +282,9 @@ </param> <when value="no"/> <when value="text"> - <param name="regions" type="text" optional="false" label="Filter by regions" help="One or more space-separated region specifications to restrict output to only those alignments which overlap the specified region(s)."/> + <param name="regions" type="text" optional="false" label="Filter by regions" help="One or more space-separated region specifications to restrict output to only those alignments which overlap the specified region(s)."> + <validator type="regex" message="Invalid characters in regions. Only letters, numbers, periods, underscores, hyphens, colons, asterixes, and spaces are allowed.">^[A-Za-z0-9._\-:\*\s]+$</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." /> @@ -637,7 +639,7 @@ </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"> @@ -645,7 +647,7 @@ <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"> |