Mercurial > repos > iuc > sniffles
diff sniffles.xml @ 3:09f5c6f3088a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
| author | iuc |
|---|---|
| date | Thu, 26 Sep 2024 11:44:13 +0000 |
| parents | 3f6f028f418f |
| children |
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--- a/sniffles.xml Wed Sep 25 13:25:31 2024 +0000 +++ b/sniffles.xml Thu Sep 26 11:44:13 2024 +0000 @@ -16,6 +16,13 @@ <![CDATA[ ln -f -s '${input}' input.bam && ln -f -s '${input.metadata.bam_index}' input.bam.bai && +#if $reference_genome.genome_type_select != "None": + #if $reference_genome.genome_type_select == "indexed": + ln -f -s '${reference_genome.genome.fields.path}' 'reference.fa' && + #else: + ln -f -s '${reference_genome.genome}' 'reference.fa' && + #end if +#end if sniffles -t \${GALAXY_SLOTS:-2} -i 'input.bam' @@ -23,11 +30,7 @@ ## must set allow-overwrite since the new output vcf file exists --allow-overwrite #if $reference_genome.genome_type_select != "None": - #if $reference_genome.genome_type_select == "indexed": - --reference '${reference_genome.genome.fields.path}' - #else: - --reference '${reference_genome.genome}' - #end if + --reference 'reference.fa' #end if ## general_options --minsupport '$general_options.minsupport' @@ -109,6 +112,15 @@ <param name="mosaic" value="--mosaic"/> <output name="output" file="expected_outcome5.vcf" lines_diff="4"/> </test> + <test> <!-- test 6 - reference --> + <param name="input" value="reads_region.bam"/> + <conditional name="reference_genome"> + <param name="genome_type_select" value="history"/> + <param name="genome" value="humsamp.fa"/> + <param name="genome.ext" value="fasta"/> + </conditional> + <output name="output" file="expected_outcome6.vcf" lines_diff="4"/> + </test> </tests> <help> <![CDATA[