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comparison bcftools_roh.xml @ 5:45091d60320f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author iuc
date Thu, 13 Apr 2017 17:41:53 -0400
parents 33454033cdf6
children b0d39ef600a7
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4:33454033cdf6 5:45091d60320f
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
3 <description>HMM model for detecting runs of autozygosity</description> 3 <description>HMM model for detecting runs of homo/autozygosity</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">roh</token> 5 <token name="@EXECUTABLE@">roh</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@ 11 @PREPARE_ENV@
12 @PREPARE_INPUT_FILE@ 12 @PREPARE_INPUT_FILE@
13 #set $section = $sec_restrict 13 #set $section = $sec_restrict
14 @PREPARE_TARGETS_FILE@ 14 @PREPARE_TARGETS_FILE@
15 @PREPARE_REGIONS_FILE@
15 ## General section 16 ## General section
16 #set $section = $sec_general 17 #set $section = $sec_general
17 @PREPARE_AF_FILE@ 18 @PREPARE_AF_FILE@
18 19
19 bcftools @EXECUTABLE@ 20 bcftools @EXECUTABLE@
37 --genetic-map "${section.genetic_map}" 38 --genetic-map "${section.genetic_map}"
38 #end if 39 #end if
39 #if $section.rec_rate: 40 #if $section.rec_rate:
40 --rec-rate "${section.rec_rate}" 41 --rec-rate "${section.rec_rate}"
41 #end if 42 #end if
43 #if $section.buffer_size:
44 #if $section.buffer_overlap:
45 --buffer-size "${section.buffer_size},${section.buffer_overlap}"
46 #else:
47 --buffer-size "${section.buffer_size}"
48 #end if
49 #end if
42 50
43 ## HMM section 51 ## HMM section
44 #set $section = $sec_hmm 52 #set $section = $sec_hmm
45 #if $section.hw_to_az: 53 #if $section.hw_to_az:
46 --hw-to-az "${section.hw_to_az}" 54 --hw-to-az "${section.hw_to_az}"
52 60
53 ## General section 61 ## General section
54 #set $section = $sec_restrict 62 #set $section = $sec_restrict
55 @REGIONS@ 63 @REGIONS@
56 @TARGETS@ 64 @TARGETS@
65 @SAMPLES@
66
67 #if str($output_type) in ('r','s'):
68 --output-type $output_type
69 #end if
57 70
58 ## Primary Input/Outputs 71 ## Primary Input/Outputs
59 @INPUT_FILE@ 72 @INPUT_FILE@
60 > "$output_file" 73 > '$output_file'
61 ]]> 74 ]]>
62 </command> 75 </command>
63 <inputs> 76 <inputs>
64 <expand macro="macro_input" /> 77 <expand macro="macro_input" />
65 <section name="sec_restrict" expanded="false" title="Restrict to"> 78 <section name="sec_restrict" expanded="false" title="Restrict to">
66 <expand macro="macro_regions" /> 79 <expand macro="macro_regions" />
67 <expand macro="macro_targets" /> 80 <expand macro="macro_targets" />
81 <expand macro="macro_samples" />
68 </section> 82 </section>
69 <section name="sec_general" expanded="true" title="Roh General Options"> 83 <section name="sec_general" expanded="true" title="Roh General Options">
70 <expand macro="macro_sample" /> 84 <expand macro="macro_sample" />
71 <param name="AF_tag" type="text" value="" label="AF TAG" optional="True" 85 <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." /> 86 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." />
75 <expand macro="macro_estimate_AF" /> 89 <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." /> 90 <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" /> 91 <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" /> 92 <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" /> 93 <param name="rec_rate" type="float" label="Rec Rate" optional="True" help="Constant recombination rate per bp" />
94 <param name="buffer_size" type="integer" label="Sliding Buffer Size" optional="True">
95 <help>
96 Use when the entire many-sample file cannot fit into memory.
97 The number of sites to keep in memory.
98 If negative, it is interpreted as the maximum memory to use, in MB.
99 </help>
100 </param>
101 <param name="buffer_overlap" type="integer" min="0" label="Sliding Buffer Overlap" optional="True">
102 <help>
103 The number of overlapping sites for the sliding buffer. The default overlap is set to roughly 1% of the buffer size.
104 </help>
105 </param>
80 </section> 106 </section>
81 <section name="sec_hmm" expanded="true" title="HMM Options"> 107 <section name="sec_hmm" expanded="true" title="HMM Options">
82 <param name="hw_to_az" type="float" label="Hw To Az" value="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" /> 108 <param name="hw_to_az" type="float" label="Hw To Az" value="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" value="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" /> 109 <param name="az_to_hw" type="float" label="Az To Hw" value="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" /> 110 <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" />
85 </section> 111 </section>
112 <param name="output_type" type="select" optional="true" label="limit output">
113 <option value="s">s:per-site</option>
114 <option value="r">r:regions</option>
115 </param>
86 </inputs> 116 </inputs>
87 <outputs> 117 <outputs>
88 <data name="output_file" format="tabular"/> 118 <data name="output_file" format="tabular"/>
89 </outputs> 119 </outputs>
90 <tests> 120 <tests>
91 <!-- Need an actual test input file -->
92 <test> 121 <test>
93 <param name="input_file" ftype="vcf" value="mpileup.vcf" /> 122 <param name="input_file" ftype="vcf" value="roh.vcf" />
94 <param name="sample" value="HG00100" /> 123 <param name="AF_dflt" value="0.4" />
124 <param name="GTs_only" value="30" />
95 <output name="output_file"> 125 <output name="output_file">
96 <assert_contents> 126 <assert_contents>
97 <has_text text="HG00100"/> 127 <has_text_matching expression="ST\tsample\t1"/>
98 <has_text text="State "/> 128 <has_text_matching expression="RG\tsample\t1"/>
129 </assert_contents>
130 </output>
131 </test>
132 <test>
133 <param name="input_file" ftype="vcf" value="roh.vcf" />
134 <param name="AF_dflt" value="0.4" />
135 <param name="GTs_only" value="30" />
136 <param name="output_type" value="r" />
137 <output name="output_file">
138 <assert_contents>
139 <not_has_text text="ST"/>
140 <has_text_matching expression="RG\tsample\t1"/>
99 </assert_contents> 141 </assert_contents>
100 </output> 142 </output>
101 </test> 143 </test>
102 </tests> 144 </tests>
103 <help><![CDATA[ 145 <help><![CDATA[