Mercurial > repos > iuc > samtools_bam_to_cram
diff samtools_bam_to_cram.xml @ 2:3e15f2544a5c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
| author | iuc |
|---|---|
| date | Mon, 29 Jul 2019 08:46:31 -0400 |
| parents | b5dc4f88fb2d |
| children | 3d07b8a6dd8c |
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--- a/samtools_bam_to_cram.xml Sun Oct 14 12:00:54 2018 -0400 +++ b/samtools_bam_to_cram.xml Mon Jul 29 08:46:31 2019 -0400 @@ -9,33 +9,23 @@ <expand macro="version_command"/> <command><![CDATA[ - #if str( $input_alignment.metadata.bam_index ) != "None": - ln - -f - -s - '${input_alignment.metadata.bam_index}' - '${input_alignment}.bai' - && - #end if - - #if $reference_source.reference_source_selector == 'history': - #set ref_fa = 'ref.fa' - ln -s '${reference_source.input_reference}' ref.fa && - #else: - #set ref_fa = str( $reference_source.input_reference.fields.path ) - #end if + @ADDTHREADS@ + @PREPARE_FASTA_IDX@ + @PREPARE_IDX@ samtools view #if $parameter_regions.target_region == "regions_bed_file" -L '${parameter_regions.regions_bed_file}' #end if - -@\${GALAXY_SLOTS:-1} - -C - -T '$ref_fa' + -@ \$addthreads + -C + -h -o '${output_alignment}' - - '${input_alignment}' + -T '$reffa' + -t '$reffai' + --output-fmt-option no_ref + infile #if $parameter_regions.target_region == "region" '${parameter_regions.region_string}' @@ -43,22 +33,22 @@ ]]></command> <inputs> - <param name="input_alignment" type="data" format="bam,sam" label="BAM (or SAM) alignment file"/> - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Load reference genome from"> + <param name="input" type="data" format="bam,sam" label="BAM (or SAM) alignment file"/> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Load reference genome from"> <option value="cached">Local cache</option> <option value="history">History</option> </param> <when value="cached"> - <param name="input_reference" type="select" label="Reference genome"> + <param name="ref" type="select" label="Reference genome"> <options from_data_table="fasta_indexes"> - <filter type="data_meta" ref="input_alignment" key="dbkey" column="1" /> + <filter type="data_meta" ref="input" key="dbkey" column="1" /> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> - <param name="input_reference" type="data" format="fasta" label="Reference FASTA file"/> + <param name="ref" type="data" format="fasta" label="Reference FASTA file"/> </when> </conditional> <conditional name="parameter_regions"> @@ -84,43 +74,43 @@ <tests> <test> - <param name="input_alignment" value="test.bam" ftype="bam" /> - <param name="reference_source_selector" value="history" /> - <param name="input_reference" value="test.fa" /> + <param name="input" value="test.bam" ftype="bam" /> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> <param name="target_region" value="entire_input_file" /> <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> </test> <test> - <param name="input_alignment" value="test.sam" ftype="sam" /> - <param name="reference_source_selector" value="history" /> - <param name="input_reference" value="test.fa" /> + <param name="input" value="test.sam" ftype="sam" /> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> <param name="target_region" value="entire_input_file" /> <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> </test> <test> - <param name="input_alignment" value="test.bam" ftype="bam" /> - <param name="reference_source_selector" value="history" /> - <param name="input_reference" value="test.fa" /> + <param name="input" value="test.bam" ftype="bam" /> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> <param name="target_region" value="region" /> <param name="region_string" value="CHROMOSOME_I" /> <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> </test> <test> - <param name="input_alignment" value="test.bam" ftype="bam" /> - <param name="reference_source_selector" value="history" /> - <param name="input_reference" value="test.fa" /> + <param name="input" value="test.bam" ftype="bam" /> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> <param name="target_region" value="regions_bed_file" /> <param name="regions_bed_file" value="test.bed" ftype="bed" /> <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> </test> <test> - <param name="input_alignment" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" /> - <param name="reference_source_selector" value="cached" /> - <param name="input_reference" value="equCab2chrM" /> + <param name="input" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" /> + <param name="addref_select" value="cached" /> + <param name="ref" value="equCab2chrM" /> <param name="target_region" value="entire_input_file" /> <output name="output_alignment" file="test2.cram" compare="sim_size" delta="250" /> </test>