Mercurial > repos > nilesh > rseqc
diff bam2wig.xml @ 13:a7f9084572fe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
| author | iuc |
|---|---|
| date | Sat, 10 Dec 2022 11:21:47 +0000 |
| parents | 57fad5deeb8e |
| children |
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--- a/bam2wig.xml Sat Dec 18 19:40:16 2021 +0000 +++ b/bam2wig.xml Sat Dec 10 11:21:47 2022 +0000 @@ -1,11 +1,12 @@ -<tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@"> +<tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description> converts all types of RNA-seq data from .bam to .wig </description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + + <expand macro="bio_tools"/> <expand macro="requirements" /> @@ -14,9 +15,8 @@ <version_command><![CDATA[bam2wig.py --version]]></version_command> <command><![CDATA[ - ln -sf '${input}' 'input.bam' && - ln -sf '${input.metadata.bam_index}' 'input.bam.bai' && - bam2wig.py -i 'input.bam' -s '${chromsize}' -o outfile + @BAM_SAM_INPUTS@ + bam2wig.py -i 'input.${extension}' -s '${chromsize}' -o outfile #if str($strand_type.strand_specific) == "pair" -d @@ -64,10 +64,10 @@ <data format="wig" name="output" from_work_dir="outfile.wig"> <filter>strand_type['strand_specific'] == 'none'</filter> </data> - <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)"> + <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string}: forward reads"> <filter>strand_type['strand_specific'] != 'none'</filter> </data> - <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)"> + <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string}: reverse reads"> <filter>strand_type['strand_specific'] != 'none'</filter> </data> </outputs>