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98 lines
3.8 KiB
XML
98 lines
3.8 KiB
XML
<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.2">
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<description>converts SAM format to BAM format</description>
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<requirements>
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<requirement type="package">samtools</requirement>
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</requirements>
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<command interpreter="python">
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sam_to_bam.py
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--input1=$source.input1
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#if $source.index_source == "history":
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--dbkey=${ref_file.metadata.dbkey}
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--ref_file=$source.ref_file
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#else
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--dbkey=${input1.metadata.dbkey}
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#end if
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--output1=$output1
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--index_dir=${GALAXY_DATA_INDEX_DIR}
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</command>
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<inputs>
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<conditional name="source">
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<param name="index_source" type="select" label="Choose the source for the reference list">
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<option value="cached">Locally cached</option>
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<option value="history">History</option>
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</param>
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<when value="cached">
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<param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert">
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<validator type="unspecified_build" />
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<validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
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</param>
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</when>
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<when value="history">
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<param name="input1" type="data" format="sam" label="Convert SAM file" />
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<param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
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</when>
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</conditional>
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</inputs>
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<outputs>
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<data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM">
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<actions>
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<conditional name="source.index_source">
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<when value="cached">
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<action type="metadata" name="dbkey">
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<option type="from_param" name="source.input1" param_attribute="dbkey" />
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</action>
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</when>
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<when value="history">
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<action type="metadata" name="dbkey">
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<option type="from_param" name="source.ref_file" param_attribute="dbkey" />
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</action>
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</when>
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</conditional>
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</actions>
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</data>
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</outputs>
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<tests>
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<test>
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<!--
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Sam-to-Bam command:
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cp test-data/chr_m.fasta .
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samtools faidx chr_m.fasta
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samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
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samtools sort unsorted.bam sam_to_bam_out1
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chr_m.fasta is the reference file (chrM from equCab2)
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-->
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<param name="index_source" value="history" />
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<param name="input1" value="sam_to_bam_in1.sam" ftype="sam" />
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<param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" />
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<output name="output1" file="sam_to_bam_out1.bam" ftype="bam" />
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</test>
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<test>
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<!--
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Sam-to-Bam command:
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samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam
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samtools sort unsorted.bam sam_to_bam_out2
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chr_m.fasta is the reference file and the index chr_m.fasta.fai
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these should be in the same directory, and chrM is from equCab2
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-->
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<param name="index_source" value="cached" />
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<param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" />
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<output name="output1" file="sam_to_bam_out2.bam" ftype="bam" />
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</test>
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</tests>
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<help>
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**What it does**
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This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file.
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.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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------
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**Citation**
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For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
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</help>
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</tool>
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