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comparison samtools_phase.xml @ 0:cba1944e3ed0 draft

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Uploaded tool and dependency definition.
author devteam
date Thu, 27 Mar 2014 15:26:17 -0400
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-1:000000000000 0:cba1944e3ed0
1 <tool id="samtools_phase" name="Call and phase" version="1.0.0">
2 <description>heterozygous SNPs</description>
3 <requirements>
4 <requirement type="package" version="0.1.19">samtools</requirement>
5 </requirements>
6 <command>samtools phase -b "phase_wrapper"
7 #if str($option_set.option_sets) == 'advanced':
8 ${option_set.ignore_chimeras}
9 -k $option_set.block_length
10 -q $option_set.min_het
11 -Q $option_set.min_bq
12 -D $option_set.read_depth
13 ${option_set.drop_ambiguous}
14 #else
15 -k 13 -q 37 -Q 13 -D 256
16 #end if
17 "$input_bam" &gt; "$phase_sets"
18 </command>
19 <stdio>
20 <exit_code range="1:" level="fatal" description="Error" />
21 </stdio>
22 <inputs>
23 <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
24 <conditional name="option_set">
25 <param name="option_sets" type="select" label="Phase parameters">
26 <option value="default">Use defaults</option>
27 <option value="advanced">Advanced options</option>
28 </param>
29 <when value="default" />
30 <when value="advanced">
31 <param name="block_length" type="integer" value="13" label="Maximum length for local phasing" />
32 <param name="min_het" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
33 <param name="min_bq" type="integer" value="13" label="Minimum base quality to be used in het calling" />
34 <param name="read_depth" type="integer" value="256" label="Read depth" />
35 <param name="ignore_chimeras" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
36 <param name="drop_ambiguous" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
37 </when>
38 </conditional>
39 </inputs>
40 <outputs>
41 <data format="txt" name="phase_sets" />
42 <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" />
43 <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" />
44 <data format="bam" from_work_dir="phase_wrapper.chimeras.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" />
45 </outputs>
46 <tests>
47 <test>
48 <param name="option_sets" value="default" />
49 <param name="input_bam" value="samtools_phase_in_1.bam" />
50 <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" />
51 <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" />
52 <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" />
53 <output name="chimera" file="empty_file.bam" compare="contains" />
54 </test>
55 <test>
56 <param name="input_bam" value="samtools_phase_in_2.bam" />
57 <param name="option_sets" value="advanced" />
58 <param name="option_set|block_length" value="13" />
59 <param name="option_set|min_het" value="37" />
60 <param name="option_set|min_bq" value="13" />
61 <param name="option_set|read_depth" value="256" />
62 <param name="option_set|ignore_chimeras" value="false" />
63 <param name="option_set|drop_ambiguous" value="true" />
64 <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" />
65 <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" />
66 <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" />
67 <output name="chimera" file="empty_file.bam" compare="contains" />
68 </test>
69 <test>
70 <param name="input_bam" value="samtools_phase_in_2.bam" />
71 <param name="option_sets" value="advanced" />
72 <param name="option_set|block_length" value="13" />
73 <param name="option_set|min_het" value="37" />
74 <param name="option_set|min_bq" value="13" />
75 <param name="option_set|read_depth" value="256" />
76 <param name="option_set|ignore_chimeras" value="true" />
77 <param name="option_set|drop_ambiguous" value="false" />
78 <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" />
79 <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" />
81 <output name="chimera" file="empty_file.bam" compare="contains" />
82 </test>
83 </tests>
84 <help>
85 **What it does**
86
87 Call and phase heterozygous SNPs
88
89 ------
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 ------
129
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>