Mercurial > repos > iuc > samtools_cram_to_bam
comparison samtools_cram_to_bam.xml @ 3:858ada516d8f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 9aed35e37c5bc8ee17a02930c1f2edceb8b0d97b"
| author | iuc |
|---|---|
| date | Sat, 31 Jul 2021 07:26:19 +0000 |
| parents | a744bb7196a2 |
| children | 1551b0dd2d16 |
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| 2:a744bb7196a2 | 3:858ada516d8f |
|---|---|
| 1 <tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@"> | 1 <tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@+galaxy1"> |
| 2 <description>convert CRAM alignments to BAM format</description> | 2 <description>convert CRAM alignments to BAM format</description> |
| 3 | 3 |
| 4 <macros> | 4 <macros> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 8 <expand macro="stdio"/> | 8 <expand macro="stdio"/> |
| 9 <expand macro="version_command"/> | 9 <expand macro="version_command"/> |
| 10 | 10 |
| 11 <command><![CDATA[ | 11 <command><![CDATA[ |
| 12 #set input_cram = "input.cram" | |
| 13 ln -s '${input_alignment}' '${input_cram}' && | |
| 12 #if str( $input_alignment.metadata.cram_index ) != "None": | 14 #if str( $input_alignment.metadata.cram_index ) != "None": |
| 13 ln -f -s '${input_alignment.metadata.cram_index}' '${input_alignment}.crai' && | 15 ln -f -s '${input_alignment.metadata.cram_index}' '${input_cram}.crai' && |
| 14 #end if | 16 #end if |
| 15 | 17 |
| 16 #if $reference_source.reference_source_selector == 'history': | 18 #if $reference_source.reference_source_selector == 'history': |
| 17 #set ref_fa = 'ref.fa' | 19 #set ref_fa = 'ref.fa' |
| 18 ln -s '${reference_source.input_reference}' ref.fa && | 20 ln -s '${reference_source.input_reference}' ref.fa && |
| 26 #end if | 28 #end if |
| 27 -@ \${GALAXY_SLOTS:-2} | 29 -@ \${GALAXY_SLOTS:-2} |
| 28 -b | 30 -b |
| 29 -T '$ref_fa' | 31 -T '$ref_fa' |
| 30 -o '$output_alignment' | 32 -o '$output_alignment' |
| 31 '$input_alignment' | 33 '$input_cram' |
| 32 #if $parameter_regions.target_region == "region" | 34 #if $parameter_regions.target_region == "region" |
| 33 '${parameter_regions.region_string}' | 35 '${parameter_regions.region_string}' |
| 34 #end if | 36 #end if |
| 35 ]]></command> | 37 ]]></command> |
| 36 | 38 |