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comparison SNV/snvmix2.xml @ 0:74f5ea818cea

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author ryanmorin
date Wed, 12 Oct 2011 19:50:38 -0400
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1 <tool id="snvmix2" name="SNVMix at selected positions" version="0.12.1-rc1">
2 <requirements>
3 <requirement type="package">SNVMix</requirement>
4 </requirements>
5 <description>performs SNV calling on a bam file only at the positions provided</description>
6 <command interpreter="python">
7 snvmix.py
8 -i $input1
9 -d ${input1.metadata.dbkey}
10 -o $output_snvmix
11 -t $type
12 -l $pos
13 -x ${GALAXY_DATA_INDEX_DIR}
14 -q $q
15 -Q $Q
16 -f $full
17 -R $keep_dups
18 -c $keep_chastity
19 </command>
20 <inputs>
21 <param name="type" type="select" label="model used">
22 <option value="MB">Filter on map quality AND base quality (MB)</option>
23 <option value="SNVMix1">SNVMix1</option>
24 <option value="mb">Lowest between map and base quality is used (mb)</option>
25 <option value="m">Filter on map quality and use as a surrogate for base quality (m)</option>
26 <option value="b">Filter on base quality and set map quality to 1 (b)</option>
27 <option value="Mb">Filter on map quality and use both map and base qualities (Mb)</option>
28 </param>
29 <conditional name="refOrHistory">
30 <param name="reference" type="select" label="Will you select a reference genome from your history or use a built-in index?">
31 <option value="indexed">Use a built-in index</option>
32 <option value="history">Use one from the history</option>
33 </param>
34 <when value="indexed">
35 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for">
36 <validator type="unspecified_build" />
37 <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" />
38 </param>
39 </when>
40 <when value="history">
41 <param name="input1" type="data" format="bam" label="Select the BAM file to generate the pileup file for" />
42 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" />
43 </when>
44 </conditional>
45 <param name="q" type="integer" value="19" label="Cutoff Phred value for Base Quality, anything less than or equal to this value is ignored" />
46 <param name="Q" type="integer" value="19" label="Cutoff Phred value for Map Quality, anything less than or equal to this value is ignored" />
47 <param name="pos" type="data" format="tabular" label="select the tab-delimited file containing positions" />
48 <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)">
49 <option value="yes">Yes (I know this could generate a huge file)</option>
50 <option value="no">No, I just want possible variants output</option>
51 </param>
52 <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">
53 <option value="no">No (ignore duplicates for variant calling)</option>
54 <option value="yes">Yes (use all reads)</option>
55 </param>
56 <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">
57 <option value="no">No (ignore filtered reads for variant calling)</option>
58 <option value="yes">Yes (use all reads)</option>
59 </param>
60 </inputs>
61
62 <outputs>
63 <data format="tabular" name="output_snvmix" label="${tool.name}: Raw SNVMix calls" />
64 </outputs>
65 <help>
66
67 **What it does**
68
69 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.
70
71 </help>
72 </tool>