Mercurial > repos > iuc > delly_lr
changeset 4:7bd397ff21a2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
| author | iuc |
|---|---|
| date | Mon, 27 Jun 2022 18:17:41 +0000 |
| parents | d30785dbe6b7 |
| children | 97f649646cc1 |
| files | lr.xml macros.xml |
| diffstat | 2 files changed, 21 insertions(+), 13 deletions(-) [+] |
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--- a/lr.xml Tue Dec 14 19:06:16 2021 +0000 +++ b/lr.xml Mon Jun 27 18:17:41 2022 +0000 @@ -10,13 +10,13 @@ <command detect_errors="exit_code"><![CDATA[ ## initialize @BAM@ - +@FASTA@ ## run delly lr ## generic options --svtype $generic.svtype --technology $generic.technology ---genome '$generic.genome' +--genome genome.fa #if $generic.exclude --exclude '$generic.exclude' #end if @@ -99,12 +99,12 @@ </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> @@ -120,7 +120,7 @@ </section> <output name="out_bcf"> <assert_contents> - <has_size value="1189" delta="10"/> + <has_size value="1131" delta="10"/> </assert_contents> </output> <output name="out_log"> @@ -130,7 +130,7 @@ </output> <output name="out_vcf"> <assert_contents> - <has_size value="3667" delta="10"/> + <has_n_lines valuen="42"/> </assert_contents> </output> </test> @@ -146,7 +146,7 @@ </section> <output name="out_bcf"> <assert_contents> - <has_size value="1186" delta="10"/> + <has_size value="1127" delta="10"/> </assert_contents> </output> <output name="out_dump"> @@ -161,7 +161,7 @@ </output> <output name="out_vcf"> <assert_contents> - <has_size value="3661" delta="10"/> + <has_n_lines n="46"/> </assert_contents> </output> </test> @@ -195,7 +195,7 @@ </section> <output name="out_bcf"> <assert_contents> - <has_size value="1182" delta="10"/> + <has_size value="1127" delta="10"/> </assert_contents> </output> <output name="out_dump"> @@ -210,7 +210,7 @@ </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> @@ -227,7 +227,7 @@ </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> @@ -244,7 +244,7 @@ </section> <output name="out_bcf"> <assert_contents> - <has_size value="1182" delta="10"/> + <has_size value="1127" delta="10"/> </assert_contents> </output> </test>
--- a/macros.xml Tue Dec 14 19:06:16 2021 +0000 +++ b/macros.xml Mon Jun 27 18:17:41 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.'