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comparison samtools_phase.xml @ 5:2311187710fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:16:22 -0400
parents c21cb56fbbbc
children dd8305e4e58e
comparison
equal deleted inserted replaced
4:ee06ec9cf0a6 5:2311187710fb
1 <tool id="samtools_phase" name="Call and phase" version="2.0"> 1 <tool id="samtools_phase" name="Call and phase" version="2.0.1">
2 <description>heterozygous SNPs</description> 2 <description>heterozygous SNPs</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio"></expand> 7 <expand macro="stdio"/>
8 <expand macro="version_command"></expand> 8 <expand macro="version_command"/>
9 <command>samtools phase -b "phase_wrapper" 9 <command><![CDATA[
10 samtools phase -b phase_wrapper
10 #if str($option_set.option_sets) == 'advanced': 11 #if str($option_set.option_sets) == 'advanced':
11 ${option_set.ignore_chimeras} 12 ${option_set.ignore_chimeras}
12 -k $option_set.block_length 13 -k $option_set.block_length
13 -q $option_set.min_het 14 -q $option_set.min_het
14 -Q $option_set.min_bq 15 -Q $option_set.min_bq
15 -D $option_set.read_depth 16 -D $option_set.read_depth
16 ${option_set.drop_ambiguous} 17 ${option_set.drop_ambiguous}
17 #else 18 #else
18 -k 13 -q 37 -Q 13 -D 256 19 -k 13
20 -q 37
21 -Q 13
22 -D 256
19 #end if 23 #end if
20 "$input_bam" &gt; "$phase_sets" 24 '$input_bam' > '$phase_sets'
21 </command> 25 ]]></command>
22 <inputs> 26 <inputs>
23 <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/> 27 <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
24 <conditional name="option_set"> 28 <conditional name="option_set">
25 <param name="option_sets" type="select" label="Phase parameters"> 29 <param name="option_sets" type="select" label="Phase parameters">
26 <option value="default">Use defaults</option> 30 <option value="default">Use defaults</option>
27 <option value="advanced">Advanced options</option> 31 <option value="advanced">Advanced options</option>
28 </param> 32 </param>
29 <when value="default" /> 33 <when value="default" />
30 <when value="advanced"> 34 <when value="advanced">
31 <param name="block_length" type="integer" value="13" label="Maximum length for local phasing" /> 35 <param name="block_length" argument="-k" type="integer" value="13" label="Maximum length for local phasing" />
32 <param name="min_het" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" /> 36 <param name="min_het" argument="-q" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
33 <param name="min_bq" type="integer" value="13" label="Minimum base quality to be used in het calling" /> 37 <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" />
34 <param name="read_depth" type="integer" value="256" label="Read depth" /> 38 <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" />
35 <param name="ignore_chimeras" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" /> 39 <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
36 <param name="drop_ambiguous" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" /> 40 <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
37 </when> 41 </when>
38 </conditional> 42 </conditional>
39 </inputs> 43 </inputs>
40 <outputs> 44 <outputs>
41 <data format="txt" name="phase_sets" /> 45 <data format="txt" name="phase_sets" />
79 <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" /> 83 <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" />
80 <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" /> 84 <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" />
81 <output name="chimera" file="empty_file.bam" compare="contains" /> 85 <output name="chimera" file="empty_file.bam" compare="contains" />
82 </test> 86 </test>
83 </tests> 87 </tests>
84 <help> 88 <help><![CDATA[
85 **What it does** 89 **What it does**
86 90
87 Call and phase heterozygous SNPs 91 Call and phase heterozygous SNPs.
88 92 ]]></help>
89 ------ 93 <expand macro="citations"/>
90
91 .. list-table:: **Options**
92 :widths: 5 5 40 10
93 :header-rows: 1
94
95 * - Flag
96 - Type
97 - Description
98 - Default
99 * - -k
100 - INT
101 - Block length
102 - 13
103 * - -b
104 - STR
105 - Prefix of BAM file output
106 - *null*
107 * - -q
108 - INT
109 - Minimum het phred-LOD
110 - 37
111 * - -Q
112 - INT
113 - Min base quality in het calling
114 - 13
115 * - -D
116 - INT
117 - Max read depth
118 - 256
119 * - -D
120 - BOOLEAN
121 - Do not attempt to fix chimeras
122 - *off*
123 * - -A
124 - BOOLEAN
125 - Drop reads with ambiguous phase
126 - *off*
127
128 </help>
129 <expand macro="citations"></expand>
130 </tool> 94 </tool>