Mercurial > repos > ryanmorin > nextgen_variant_identification
diff SNV/snvmix2.xml @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNV/snvmix2.xml Wed Oct 12 19:50:38 2011 -0400 @@ -0,0 +1,72 @@ +<tool id="snvmix2" name="SNVMix at selected positions" version="0.12.1-rc1"> + <requirements> + <requirement type="package">SNVMix</requirement> + </requirements> + <description>performs SNV calling on a bam file only at the positions provided</description> + <command interpreter="python"> + snvmix.py + -i $input1 + -d ${input1.metadata.dbkey} + -o $output_snvmix + -t $type + -l $pos + -x ${GALAXY_DATA_INDEX_DIR} + -q $q + -Q $Q + -f $full + -R $keep_dups + -c $keep_chastity + </command> + <inputs> + <param name="type" type="select" label="model used"> + <option value="MB">Filter on map quality AND base quality (MB)</option> + <option value="SNVMix1">SNVMix1</option> + <option value="mb">Lowest between map and base quality is used (mb)</option> + <option value="m">Filter on map quality and use as a surrogate for base quality (m)</option> + <option value="b">Filter on base quality and set map quality to 1 (b)</option> + <option value="Mb">Filter on map quality and use both map and base qualities (Mb)</option> + </param> + <conditional name="refOrHistory"> + <param name="reference" type="select" label="Will you select a reference genome from your history or use a built-in index?"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for"> + <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="bam" label="Select the BAM file to generate the pileup file for" /> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> + </when> + </conditional> + <param name="q" type="integer" value="19" label="Cutoff Phred value for Base Quality, anything less than or equal to this value is ignored" /> + <param name="Q" type="integer" value="19" label="Cutoff Phred value for Map Quality, anything less than or equal to this value is ignored" /> + <param name="pos" type="data" format="tabular" label="select the tab-delimited file containing positions" /> + <param name="full" type="select" label="Do you want SNVMix to calculate probabilities for each of these positions? (only works when a set of positions has been provided)"> + <option value="yes">Yes (I know this could generate a huge file)</option> + <option value="no">No, I just want possible variants output</option> + </param> + <param name="keep_dups" type="select" label="Do you want SNVMix to include reads flagged as duplicates? (only works if Picard or some other tool has set this bit in your bam file"> + <option value="no">No (ignore duplicates for variant calling)</option> + <option value="yes">Yes (use all reads)</option> + </param> + <param name="keep_chastity" type="select" label="Do you want SNVMix to include reads flagged as failing the chastity filter? (only works if Picard or some other tool has set this bit in your bam file"> + <option value="no">No (ignore filtered reads for variant calling)</option> + <option value="yes">Yes (use all reads)</option> + </param> +</inputs> + + <outputs> + <data format="tabular" name="output_snvmix" label="${tool.name}: Raw SNVMix calls" /> + </outputs> + <help> + +**What it does** + +This tool uses the SNVMix model (Rodrigo Goya et al, 2010) to call single nucleotide variants (SNVs) from a bam file at a restricted set of positions, similar to samtools pileup -l. This tools is typically used on a matched normal library for the identification of somatic mutations in combination with the SNVMix -f option (report probabilities at all positions). The input must be two columns, the first being the chromosome name and the second being the position. + + </help> +</tool>