Mercurial > repos > bgruening > deeptools_multi_bigwig_summary
diff multiBigwigSummary.xml @ 28:d580d6acd1df draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5
author | bgruening |
---|---|
date | Fri, 19 May 2023 08:37:10 +0000 |
parents | 6e33cebc6063 |
children | d9ce4897dbb2 |
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--- a/multiBigwigSummary.xml Fri Feb 11 16:20:11 2022 +0000 +++ b/multiBigwigSummary.xml Fri May 19 08:37:10 2023 +0000 @@ -1,17 +1,16 @@ -<tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0"> +<tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.1"> <description>calculates average scores for a list of two or more bigwig files</description> <macros> <token name="@BINARY@">multiBigwigSummary</token> <import>deepTools_macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements" /> <command> <![CDATA[ #set files=[] #set labels=[] @multiple_input_bigwigs@ - @BINARY@ $mode.modeOpt @@ -20,8 +19,10 @@ --outFileName $outFile --bwfiles #echo ' '.join($files)# - --labels #echo ' '.join($labels)# - + + #if $custom_sample_labels_conditional.custom_labels_select == 'Yes' + --labels #echo ' '.join($custom_sample_labels_conditional.labels)# + #end if #if $outRawCounts: --outRawCounts '$outFileRawCounts' #end if @@ -43,7 +44,6 @@ #end if ]]> </command> - <inputs> <expand macro="multiple_input_bigwigs" MIN="2" LABEL="Bigwig files" TITLE="BigWig files"/> <expand macro="custom_sample_labels" /> @@ -70,7 +70,6 @@ help="Correlation is computed for the number of reads that overlap such regions."/> </when> </conditional> - <expand macro="region_limit_operation" /> <param argument="--outRawCounts" type="boolean" label="Save raw counts (scores) to file" help=""/> @@ -91,18 +90,20 @@ <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" /> <param name="modeOpt" value="bins" /> <param name="binSize" value="10" /> - <param name="corMethod" value="spearman" /> <output name="outFile" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" /> </test> - <!--test> + <test> <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" /> - <param name="modeOpt" value="BED-file" /> - <param name="region_file" value="multiBamSummary_regions.bed" /> - <param name="corMethod" value="pearson" /> + <param name="modeOpt" value="bins" /> + <param name="binSize" value="10" /> <param name="outRawCounts" value="True" /> + <conditional name="custom_sample_labels_conditional"> + <param name="custom_labels_select" value="Yes"/> + <param name="labels" value="sample1 sample2"/> + </conditional> <output name="outFileRawCounts" file="multiBigwigSummary_result2.tabular" ftype="tabular" /> - <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" /> - </test--> + <output name="outFile" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" /> + </test> </tests> <help> <![CDATA[