Mercurial > repos > iuc > featurecounts
changeset 17:8ce1e2c7ee72 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
| author | iuc |
|---|---|
| date | Wed, 20 Jun 2018 05:32:55 -0400 |
| parents | 92808b865dfb |
| children | d60b1c4e0347 |
| files | featurecounts.xml test-data/output.bam |
| diffstat | 2 files changed, 26 insertions(+), 3 deletions(-) [+] |
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--- a/featurecounts.xml Thu Jun 14 04:33:21 2018 -0400 +++ b/featurecounts.xml Wed Jun 20 05:32:55 2018 -0400 @@ -1,7 +1,8 @@ -<tool id="featurecounts" name="featureCounts" version="1.6.0.6" profile="16.04"> +<tool id="featurecounts" name="featureCounts" version="1.6.0.7" profile="16.04"> <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> <requirements> <requirement type="package" version="1.6.0">subread</requirement> + <requirement type="package" version="1.7">samtools</requirement> </requirements> <version_command>featureCounts -v 2>&1 | grep .</version_command> @@ -58,7 +59,9 @@ $extended_parameters.read_reduction $extended_parameters.primary $extended_parameters.ignore_dup - + #if $extended_parameters.R: + $extended_parameters.R + #end if #if str($extended_parameters.read_extension_5p) != "0": --readExtension5 $extended_parameters.read_extension_5p #end if @@ -108,6 +111,9 @@ && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}' #end if + #if $extended_parameters.R: + && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} *.featureCounts.bam + #end if && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}' ]]></command> <inputs> @@ -389,6 +395,13 @@ label="Ignore reads marked as duplicate" help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." /> + <param type="boolean" + truevalue="-R BAM" + falsevalue="" + argument="-R" + label="Annotates the alignment file with 'XS:Z:'-tags to described per read or read-pair the corresponding assigned feature(s)." + help="" /> + <param name="count_split_alignments_only" type="boolean" truevalue=" --countSplitAlignmentsOnly" @@ -408,6 +421,12 @@ </actions> </data> + <data format="bam" + name="output_bam" + label="${tool.name} on ${on_string}: Alignment file"> + <filter>extended_parameters['R']</filter> + </data> + <data format="tabular" name="output_short" label="${tool.name} on ${on_string}"> @@ -500,14 +519,18 @@ </output> </test> <!-- Ensure featureCounts built-in annotation works --> - <test expect_num_outputs="2"> + <test expect_num_outputs="3"> <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" /> <param name="anno_select" value="builtin"/> <param name="format" value="tabdel_short" /> + <section name="extended_parameters"> + <param name="R" value="true" /> + </section> <output name="output_short" file="output_builtin_hg19.tab"> <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> </output> <output name="output_summary" file="output_summary_builtin_hg19.tab"/> + <output name="output_bam" file="output.bam" ftype="bam"/> </test> <!-- Ensure cached GTFs work --> <test expect_num_outputs="3">