Mercurial > repos > iuc > samtools_bam_to_cram
diff samtools_bam_to_cram.xml @ 0:b5dc4f88fb2d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author | iuc |
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date | Tue, 09 May 2017 11:18:16 -0400 |
parents | |
children | 3e15f2544a5c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_bam_to_cram.xml Tue May 09 11:18:16 2017 -0400 @@ -0,0 +1,137 @@ +<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@TOOL_VERSION@"> + <description>convert BAM alignments to CRAM format</description> + + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <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 + + samtools view + #if $parameter_regions.target_region == "regions_bed_file" + -L '${parameter_regions.regions_bed_file}' + #end if + + -@\${GALAXY_SLOTS:-1} + -C + -T '$ref_fa' + -o '${output_alignment}' + + '${input_alignment}' + + #if $parameter_regions.target_region == "region" + '${parameter_regions.region_string}' + #end if + ]]></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"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="input_reference" type="select" label="Reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input_alignment" 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"/> + </when> + </conditional> + <conditional name="parameter_regions"> + <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)"> + <option value="entire_input_file">Entire BAM alignment file</option> + <option value="region">Specific region</option> + <option value="regions_bed_file">List of specific regions (BED file)</option> + </param> + <when value="entire_input_file" /> + <when value="region"> + <param name="region_string" type="text" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:start-end" /> + </when> + <when value="regions_bed_file"> + <param name="regions_bed_file" argument="-L" type="data" format="bed" + label="Only include reads overlapping this BED file" /> + </when> + </conditional> + </inputs> + + <outputs> + <data name="output_alignment" format="cram" label="$tool.name on ${on_string}.cram"></data> + </outputs> + + <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="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="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="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="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="target_region" value="entire_input_file" /> + <output name="output_alignment" file="test2.cram" compare="sim_size" delta="250" /> + </test> + </tests> + + <help><![CDATA[ +**What this tool does** + +Converts alignments from the BAM format to the CRAM format using the ``samtools view`` command. +The CRAM format does additional compression relative to the reference genome which makes the compression in terms of file size more efficient. + ]]></help> + + <expand macro="citations" /> +</tool>