Mercurial > repos > iuc > samtools_coverage
changeset 3:c4ff13d2aab3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
| author | iuc |
|---|---|
| date | Thu, 29 Jun 2023 10:40:07 +0000 |
| parents | 8a477224dfee |
| children | |
| files | samtools_coverage.xml test-data/results_4.tabular test-data/results_5.tabular |
| diffstat | 3 files changed, 33 insertions(+), 7 deletions(-) [+] |
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--- a/samtools_coverage.xml Wed May 31 17:15:17 2023 +0000 +++ b/samtools_coverage.xml Thu Jun 29 10:40:07 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>computes the depth at each position or region</description> <macros> <import>macros.xml</import> @@ -8,16 +8,18 @@ <expand macro="version_command"/> <command><![CDATA[ #if $condition_input.input_pooling == "No": + #set $input = $condition_input.input @PREPARE_IDX@ #else: + #set $input_bams = $condition_input.input_bams @PREPARE_IDX_MULTIPLE@ #end if samtools coverage #if $condition_input.input_pooling == "Yes": - ${ ' '.join( [ "'%s'" % $x for $x in $condition_input.input_bams] ) } + ${ ' '.join( [ "'%s'" % $i for $i, $x in enumerate($condition_input.input_bams)]) } #else - '$condition_input.input' + infile #end if -l $additional_options.min_read_length @@ -32,12 +34,13 @@ @FLAGS@ --ff $flags + #if $additional_options.region != "": + -r '$additional_options.region' + #end if + #if $condition_histogram.histogram_select == "yes" -m -w $condition_histogram.n_bins - #if $condition_histogram.region != "": - -r '$condition_histogram.region' - #end if #end if -o '$output' @@ -68,6 +71,15 @@ <param name="skipped_flags" argument="--ff" type="select" multiple="True" label="Exclude reads with any of the following flags set"> <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/> </param> + <param name="region" argument="-r" type="text" value="" label="Show specified region" help="Show specified region. Format: chr:start-end." > + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits"> + <add value=":" /> + <add value="-" /> + <add value="_" /> + </valid> + </sanitizer> + </param> </section> <conditional name="condition_histogram"> @@ -77,7 +89,6 @@ </param> <when value="yes"> <param name="n_bins" argument="-w" type="integer" min="1" value="100" label="Number of bins in histogram" help="Number of bins in histogram" /> - <param name="region" argument="-r" type="text" value="" label="Show specified region" help="Show specified region. Format: chr:start-end." /> </when> <when value="no" /> </conditional> @@ -105,6 +116,17 @@ <param name="n_bins" value="100" /> <output name="output" file="results_3.txt" ftype="tabular" /> </test> + <test><!-- test with a region (requires index) --> + <param name="input" value="test_1.bam" ftype="bam" /> + <param name="region" value="ref1" /> + <output name="output" file="results_4.tabular" ftype="tabular" /> + </test> + <test><!-- test with pooled BAMs and a region --> + <param name="input_pooling" value="Yes" /> + <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" /> + <param name="region" value="ref2" /> + <output name="output" file="results_5.tabular" ftype="tabular" /> + </test> </tests> <help><![CDATA[ **What it does**