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comparison samtools_phase.xml @ 1:8bfe0d1616d2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_phase commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:53:49 -0500
parents cba1944e3ed0
children 6166013090c0
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0:cba1944e3ed0 1:8bfe0d1616d2
1 <tool id="samtools_phase" name="Call and phase" version="1.0.0"> 1 <tool id="samtools_phase" name="Call and phase" version="2.0">
2 <description>heterozygous SNPs</description> 2 <description>heterozygous SNPs</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.1.19">samtools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <expand macro="version_command"></expand>
6 <command>samtools phase -b "phase_wrapper" 9 <command>samtools phase -b "phase_wrapper"
7 #if str($option_set.option_sets) == 'advanced': 10 #if str($option_set.option_sets) == 'advanced':
8 ${option_set.ignore_chimeras} 11 ${option_set.ignore_chimeras}
9 -k $option_set.block_length 12 -k $option_set.block_length
10 -q $option_set.min_het 13 -q $option_set.min_het
14 #else 17 #else
15 -k 13 -q 37 -Q 13 -D 256 18 -k 13 -q 37 -Q 13 -D 256
16 #end if 19 #end if
17 "$input_bam" &gt; "$phase_sets" 20 "$input_bam" &gt; "$phase_sets"
18 </command> 21 </command>
19 <stdio>
20 <exit_code range="1:" level="fatal" description="Error" />
21 </stdio>
22 <inputs> 22 <inputs>
23 <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/> 23 <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
24 <conditional name="option_set"> 24 <conditional name="option_set">
25 <param name="option_sets" type="select" label="Phase parameters"> 25 <param name="option_sets" type="select" label="Phase parameters">
26 <option value="default">Use defaults</option> 26 <option value="default">Use defaults</option>
123 * - -A 123 * - -A
124 - BOOLEAN 124 - BOOLEAN
125 - Drop reads with ambiguous phase 125 - Drop reads with ambiguous phase
126 - *off* 126 - *off*
127 127
128 ------ 128 </help>
129 129 <expand macro="citations"></expand>
130 **Citation**
131
132 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
133
134
135 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
136
137 </help>
138 </tool> 130 </tool>