| Previous changeset 3:6f383714149d (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:
call.xml macros.xml |
| b |
| diff -r 6f383714149d -r c34eab9d5134 call.xml --- a/call.xml Tue Dec 14 19:05:58 2021 +0000 +++ b/call.xml Mon Jun 27 18:17:19 2022 +0000 |
| [ |
| @@ -10,12 +10,12 @@ <command detect_errors="exit_code"><![CDATA[ ## initialize @BAM@ - +@FASTA@ ## run delly call ## generic options --svtype $generic.svtype ---genome '$generic.genome' +--genome genome.fa #if $generic.exclude --exclude '$generic.exclude' #end if @@ -95,12 +95,12 @@ </section> <output name="out_bcf"> <assert_contents> - <has_size value="1184" delta="10"/> + <has_size value="1127" delta="10"/> </assert_contents> </output> <output name="out_vcf"> <assert_contents> - <has_size value="3661" delta="10"/> + <has_n_lines n="46"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> </assert_contents> </output> @@ -185,7 +185,7 @@ </section> <output name="out_vcf"> <assert_contents> - <has_size value="3661" delta="10"/> + <has_n_lines n="46"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> </assert_contents> </output> @@ -202,7 +202,7 @@ </section> <output name="out_bcf"> <assert_contents> - <has_size value="1183" delta="10"/> + <has_size value="1127" delta="10"/> </assert_contents> </output> </test> @@ -250,7 +250,7 @@ </section> <output name="out_vcf"> <assert_contents> - <has_size value="3661" delta="10"/> + <has_n_lines n="46"/> <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> </assert_contents> </output> |
| b |
| diff -r 6f383714149d -r c34eab9d5134 macros.xml --- a/macros.xml Tue Dec 14 19:05:58 2021 +0000 +++ b/macros.xml Mon Jun 27 18:17:19 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.' |