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comparison bcftools_cnv.xml @ 0:2771c1ba81b1 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 07:01:20 -0400
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-1:000000000000 0:2771c1ba81b1
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
3 <description>Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR)</description>
4 <macros>
5 <token name="@EXECUTABLE@">cnv</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
16 bcftools @EXECUTABLE@
17
18 --output-dir cnv_tmp
19
20 ## General section
21 #set $section = $sec_general
22 #if $section.control_sample:
23 --control-sample "${section.control_sample}"
24 #end if
25 #if $section.query_sample:
26 --query-sample "${section.query_sample}"
27 #end if
28 @AF_FILE@
29
30 #if $section.plot_threshold:
31 --plot-threshold "${section.plot_threshold}"
32 #end if
33
34 ## HMM section
35 #set $section = $sec_hmm
36 #if $section.aberrant_query or $section.aberrant_control:
37 #set $query_val = #if $section.aberrant_query then $section.aberrant_query else '1.0'#
38 #set $control_val = #if $section.aberrant_control then $section.aberrant_control else '1.0'#
39 --aberrant "${query_val},${control_val}"
40 #end if
41 #if $section.BAF_weight:
42 --BAF-weight "${section.BAF_weight}"
43 #end if
44 #if $section.BAF_dev_query or $section.BAF_dev_control:
45 #set $query_val = #if $section.BAF_dev_query then $section.BAF_dev_query else '1.0'#
46 #set $control_val = #if $section.BAF_dev_control then $section.BAF_dev_control else '1.0'#
47 --BAF-dev "${query_val},${control_val}"
48 #end if
49 #if $section.LRR_weight:
50 --LRR-weight "${section.LRR_weight}"
51 #end if
52 #if $section.LRR_dev_query or $section.LRR_dev_control:
53 #set $query_val = #if $section.LRR_dev_query then $section.LRR_dev_query else '1.0'#
54 #set $control_val = #if $section.LRR_dev_control then $section.LRR_dev_control else '1.0'#
55 --LRR-dev "${query_val},${control_val}"
56 #end if
57 #if $section.LRR_smooth_win:
58 --LRR-smooth-win "${section.LRR_smooth_win}"
59 #end if
60 #if $section.optimize:
61 --optimize "${section.optimize}"
62 #end if
63 #if $section.same_prob:
64 --same-prob "${section.same_prob}"
65 #end if
66 #if $section.err_prob:
67 --err-prob "${section.err_prob}"
68 #end if
69 #if $section.xy_prob:
70 --xy-prob "${section.xy_prob}"
71 #end if
72
73 ## Filter section
74 #set $section = $sec_restrict
75 @REGIONS@
76 @TARGETS@
77
78 ## Primary Input/Outputs
79 @INPUT_FILE@
80 && mv $output_dir/cn.*.tab "$output_cn"
81 && mv $output_dir/dat.*.tab "$output_dat"
82 && mv $output_dir/summary.*.tab "$output_summary"
83 ## && python $output_dir/plot.*.py
84 ]]>
85 </command>
86 <inputs>
87 <param name="output_dir" type="hidden" value="cnv_tmp"/>
88 <expand macro="macro_input" />
89 <section name="sec_restrict" expanded="false" title="Restrict to">
90 <expand macro="macro_regions" />
91 <expand macro="macro_targets" />
92 </section>
93 <param name="reference_fasta" type="data" format="fasta" label="Reference Fasta" />
94 <section name="sec_general" expanded="true" title="General Options">
95 <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query samply name" />
96 <param name="control_sample" type="text" label="Control Sample" optional="True" help="Optional control sample name to highlight differences" />
97 <expand macro="macro_AF_file" />
98 <param name="plot_threshold" type="float" label="Plot Threshold" optional="True" help="Plot aberrant chromosomes with quality at least 'float'" />
99 </section>
100 <section name="sec_hmm" expanded="false" title="HMM Options">
101 <param name="err_prob" type="float" value="1e-4" label="Err Prob" optional="True" help="Uniform error probability" />
102 <param name="optimize" type="float" value="" imin="0." max="1." label="Optimize" optional="True" >
103 <help>
104 Iteratively estimate the fraction of aberrant cells, down to the given fraction.
105 Lowering this value from the default 1.0 to say, 0.3, can help discover more events but also increases noise.
106 </help>
107 </param>
108 <param name="same_prob" type="float" value="" min="0." max="1." label="Same Prob" optional="True">
109 <help>
110 The prior probability of the query and the control sample being the same.
111 Setting to 0 calls both independently, setting to 1 forces the same copy number state in both.
112 </help>
113 </param>
114 <param name="xy_prob" type="float" value="" min="0." max="1." label="Xy Prob" default="1e-9" optional="True">
115 <help>
116 The HMM probability of transition to another copy number state.
117 Increasing this value leads to smaller and more frequent calls.
118 </help>
119 </param>
120
121 <param name="aberrant_query" type="float" value="" min="0." max="1." label="Aberrant Query" optional="true"
122 help="Fraction of aberrant cells in query, defaults to 1." />
123 <param name="aberrant_control" type="float" value="" min="0." max="1." label="Aberrant Control" optional="true"
124 help="Fraction of aberrant cells in control, defaults to 1." />
125 <param name="BAF_weight" type="float" value="1." min="0." max="1." label="Baf Weight" optional="True" help="relative contribution from BAF" />
126
127 <param name="BAF_dev_query" type="float" value="" min="0." max="1." label="Baf Query Deviation" optional="true"
128 help="Expected BAF deviation in query, defaults to: 0.04" />
129 <param name="BAF_dev_control" type="float" value="" min="0." max="1." label="Baf Control Deviation" optional="true"
130 help="Expected BAF deviation in control, defaults to: 0.04" />
131
132 <param name="LRR_weight" type="float" default="" label="LRR Weight" optional="True" >
133 <help>
134 Relative contribution from LRR.
135 With noisy data, this option can have big effect on the number of calls produced.
136 In truly random noise (such as in simulated data), the value should be set high (1.0), i
137 but in the presence of systematic noise when LRR are not informative, lower values result in cleaner calls (0.2).
138 </help>
139 </param>
140 <param name="LRR_dev_query" type="float" value="" min="0." max="1." label="LRR Query Deviation"
141 help="Expected LRR deviation in query, default is: 0.2" />
142 <param name="LRR_dev_control" type="float" value="" min="0." max="1." label="LRR Control Deviation"
143 help="Expected LRR deviation in control, default is: 0.2" />
144 <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" default="10" optional="True"
145 help="Window of LRR moving average smoothing" />
146
147 </section>
148 </inputs>
149 <outputs>
150 <data name="output_cn" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.cn"/>
151 <data name="output_dat" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.dat"/>
152 <data name="output_summary" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.summary"/>
153 <!-- add plot output -->
154 <!-- script has png per chr, html of images or collect into pdf?
155 <data name="output_plots" format="" />
156 -->
157 </outputs>
158 <tests />
159 <help><![CDATA[
160 =====================================
161 bcftools @EXECUTABLE@
162 =====================================
163
164 Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R Ratio intensity (LRR).
165 The HMM considers the following copy number states: CN 2 (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain)
166
167 @REGIONS_HELP@
168 @TARGETS_HELP@
169
170 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
171
172 @BCFTOOLS_WIKI@
173 ]]>
174 </help>
175 <expand macro="citations" />
176 </tool>