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comparison bcftools_roh.xml @ 0:b221ee100d2c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:08:58 -0400
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children 6ed9d03452ad
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-1:000000000000 0:b221ee100d2c
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
3 <description>HMM model for detecting runs of autozygosity</description>
4 <macros>
5 <token name="@EXECUTABLE@">roh</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="version_command" />
10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@
12 @PREPARE_INPUT_FILE@
13 #set $section = $sec_restrict
14 @PREPARE_TARGETS_FILE@
15 ## General section
16 #set $section = $sec_general
17 @PREPARE_AF_FILE@
18
19 bcftools @EXECUTABLE@
20
21 ## General section
22 #set $section = $sec_general
23 @SAMPLE@
24 @AF_FILE@
25 #if $section.AF_tag:
26 --AF-tag "${section.AF_tag}"
27 #end if
28 #if $section.AF_dflt:
29 --AF-dflt "${section.AF_dflt}"
30 #end if
31 @ESTIMATE_AF@
32 #if $section.GTs_only:
33 --GTs-only "${section.GTs_only}"
34 #end if
35 ${section.skip_indels}
36 #if $section.genetic_map:
37 --genetic-map "${section.genetic_map}"
38 #end if
39 #if $section.rec_rate:
40 --rec-rate "${section.rec_rate}"
41 #end if
42
43 ## HMM section
44 #set $section = $sec_hmm
45 #if $section.hw_to_az:
46 --hw-to-az "${section.hw_to_az}"
47 #end if
48 #if $section.az_to_hw:
49 --az-to-hw "${section.az_to_hw}"
50 #end if
51 ${section.viterbi_training}
52
53 ## General section
54 #set $section = $sec_restrict
55 @REGIONS@
56 @TARGETS@
57
58 ## Primary Input/Outputs
59 @INPUT_FILE@
60 > "$output_file"
61 ]]>
62 </command>
63 <inputs>
64 <expand macro="macro_input" />
65 <section name="sec_restrict" expanded="false" title="Restrict to">
66 <expand macro="macro_regions" />
67 <expand macro="macro_targets" />
68 </section>
69 <section name="sec_general" expanded="true" title="Roh General Options">
70 <expand macro="macro_sample" />
71 <param name="AF_tag" type="text" value="" label="AF TAG" optional="True"
72 help="Use the specified INFO tag TAG as an allele frequency estimate instead of the defaul AC and AN tags. Sites which do not have TAG will be skipped." />
73 <param name="AF_dflt" type="float" value="" min="0." max="1." label="AF Default" optional="True" help="If AF is not known, use this allele frequency" />
74 <expand macro="macro_AF_file" />
75 <expand macro="macro_estimate_AF" />
76 <param name="GTs_only" type="float" label="Gts Only" optional="True" help="Use GTs, ignore PLs, use &lt;float&gt; for PL of unseen genotypes. Safe value to use is 30 to account for GT errors." />
77 <param name="skip_indels" type="boolean" truevalue="--skip-indels" falsevalue="" label="Skip Indels" help="Skip indels as their genotypes are enriched for errors" />
78 <param name="genetic_map" type="data" format="data" label="Genetic Map" optional="True" help="Genetic map in IMPUTE2 format, single file or mask, where string &quot;{CHROM}&quot; is replaced with chromosome name" />
79 <param name="rec_rate" type="float" label="Rec Rate" optional="True" help="Constant recombination rate per bp" />
80 </section>
81 <section name="sec_hmm" expanded="true" title="HMM Options">
82 <param name="hw_to_az" type="float" label="Hw To Az" default="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" />
83 <param name="az_to_hw" type="float" label="Az To Hw" default="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" />
84 <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" />
85 </section>
86 </inputs>
87 <outputs>
88 <data name="output_file" format="tabular"/>
89 </outputs>
90 <tests>
91 <!-- Need an actual test input file -->
92 <test>
93 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
94 <param name="sample" value="HG00100" />
95 <output name="output_file">
96 <assert_contents>
97 <has_text text="HG00100"/>
98 <has_text text="State "/>
99 </assert_contents>
100 </output>
101 </test>
102 </tests>
103 <help><![CDATA[
104 =====================================
105 bcftools @EXECUTABLE@
106 =====================================
107
108 HMM model for detecting runs of autozygosity.
109
110 @REGIONS_HELP@
111 @TARGETS_HELP@
112
113 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
114
115 @BCFTOOLS_WIKI@
116 ]]>
117 </help>
118 <expand macro="citations" />
119 </tool>