| Previous changeset 1:56781a718729 (2021-12-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6 |
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modified:
cnv.xml macros.xml |
| b |
| diff -r 56781a718729 -r 8ad49c4272ea cnv.xml --- a/cnv.xml Tue Dec 14 19:06:35 2021 +0000 +++ b/cnv.xml Mon Jun 27 18:18:05 2022 +0000 |
| [ |
| @@ -8,12 +8,16 @@ <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ +@SINGLE_BAM@ +@FASTA@ +ln -s '$generic.mappability' mappability.fa && + ## run delly cnv ## generic options ---genome '$generic.genome' +--genome genome.fa --quality '$generic.quality' ---mappability '$generic.mappability' +--mappability mappability.fa --ploidy $generic.ploidy --outfile 'result.bcf' --covfile 'result.gz' @@ -46,7 +50,7 @@ --percentile $gc.percentile $gc.nowindowselection ## input -'$input' +'input.bam' ## postprocessing @LOG@ @@ -162,7 +166,7 @@ </section> <output name="out_cnv"> <assert_contents> - <has_size value="700" delta="10"/> + <has_size value="645" delta="10"/> </assert_contents> </output> <output name="out_coverage"> |
| b |
| diff -r 56781a718729 -r 8ad49c4272ea macros.xml --- a/macros.xml Tue Dec 14 19:06:35 2021 +0000 +++ b/macros.xml Mon Jun 27 18:18:05 2022 +0000 |
| [ |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">0.9.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">delly</requirement> @@ -23,12 +23,20 @@ </xml> <!-- command --> + <token name="@SINGLE_BAM@"><![CDATA[ +ln -s '$input' 'input.bam' && +ln -s '$input.metadata.bam_index' 'input.bam.bai' && + ]]></token> <token name="@BAM@"><![CDATA[ #for $i, $current in enumerate($input) ln -s '${current}' 'input_${i}.bam' && ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' && #end for ]]></token> + <!-- fasta needs to be linked, because .fai file is created --> + <token name="@FASTA@"><![CDATA[ +ln -s '$generic.genome' genome.fa && + ]]></token> <token name="@DUMP@"><![CDATA[ #if 'dump' in $oo.out && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.' |