Mercurial > repos > devteam > sam_to_bam
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author | devteam |
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date | Tue, 20 Aug 2013 11:59:47 -0400 |
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children | 7095d651c95f |
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<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.2"> <description>converts SAM format to BAM format</description> <requirements> <requirement type="package" version="0.1.18">samtools</requirement> </requirements> <command interpreter="python"> sam_to_bam.py --input1=$source.input1 #if $source.index_source == "history": --dbkey=${ref_file.metadata.dbkey} --ref_file=$source.ref_file #else --dbkey=${input1.metadata.dbkey} #end if --output1=$output1 --index_dir=${GALAXY_DATA_INDEX_DIR} </command> <inputs> <conditional name="source"> <param name="index_source" type="select" label="Choose the source for the reference list"> <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert"> <validator type="unspecified_build" /> <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" /> </param> </when> <when value="history"> <param name="input1" type="data" format="sam" label="Convert SAM file" /> <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" /> </when> </conditional> </inputs> <outputs> <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM"> <actions> <conditional name="source.index_source"> <when value="cached"> <action type="metadata" name="dbkey"> <option type="from_param" name="source.input1" param_attribute="dbkey" /> </action> </when> <when value="history"> <action type="metadata" name="dbkey"> <option type="from_param" name="source.ref_file" param_attribute="dbkey" /> </action> </when> </conditional> </actions> </data> </outputs> <tests> <test> <!-- Sam-to-Bam command: cp test-data/chr_m.fasta . samtools faidx chr_m.fasta samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam samtools sort unsorted.bam sam_to_bam_out1 chr_m.fasta is the reference file (chrM from equCab2) --> <param name="index_source" value="history" /> <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" /> <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> <output name="output1" file="sam_to_bam_out1.bam" ftype="bam" /> </test> <test> <!-- Sam-to-Bam command: samtools view -hbt chr_m.fasta.fai -o unsorted.bam test-data/sam_to_bam_in1.sam samtools sort unsorted.bam sam_to_bam_out2 chr_m.fasta is the reference file and the index chr_m.fasta.fai these should be in the same directory, and chrM is from equCab2 --> <param name="index_source" value="cached" /> <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" /> <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" /> </test> </tests> <help> **What it does** This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml ------ **Citation** 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>`_ </help> </tool>