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comparison cnv.xml @ 0:d402af96808e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
author iuc
date Fri, 22 Jan 2021 14:31:18 +0000
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children 56781a718729
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-1:000000000000 0:d402af96808e
1 <?xml version="1.0"?>
2 <tool id="delly_cnv" name="Delly cnv" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
3 <description>discover and genotype copy-number variants</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="version_command"/>
9 <command detect_errors="exit_code"><![CDATA[
10 ## run
11 delly cnv
12 ## generic options
13 --genome '$generic.genome'
14 --quality '$generic.quality'
15 --mappability '$generic.mappability'
16 --ploidy $generic.ploidy
17 --outfile 'result.bcf'
18 --covfile 'result.gz'
19 ## cnv calling options
20 --sdrd $cnv.sdrd
21 --cn-offset $cnv.cnoffset
22 --cnv-size $cnv.cnvsize
23 #if $cnv.svfile
24 --svfile $cnv.svfile
25 #end if
26 #if $cnv.vcffile
27 --vcffile '$cnv.vcffile'
28 #end if
29 $cnv.segmentation
30 ## read-depth window options
31 --window-size $read.windowsize
32 --window-offset $read.windowoffset
33 #if $read.bedintervals
34 --bed-intervals '$read.bedintervals'
35 #end if
36 --fraction-window $read.fractionwindow
37 $read.adaptivewindowing
38 ## gc fragment normalization options
39 --scan-window $gc.scanwindow
40 --fraction-unique $gc.fractionunique
41 #if $gc.scanregions
42 --scan-regions '$gc.scanregions'
43 #end if
44 --mad-cutoff $gc.madcutoff
45 --percentile $gc.percentile
46 $gc.nowindowselection
47 ## input
48 '$input'
49
50 ## postprocessing
51 @LOG@
52 ]]></command>
53 <inputs>
54 <expand macro="input" format="bam" label="Select input file"/>
55 <section name="generic" title="Generic options" expanded="true">
56 <expand macro="genome"/>
57 <param argument="--quality" type="integer" value="10" label="Set minimum mapping quality"/>
58 <param argument="--mappability" type="data" format="fasta" label="Select mappability map file"/>
59 <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
60 </section>
61 <section name="cnv" title="CNV calling options" expanded="true">
62 <param argument="--sdrd" type="integer" value="2" label="Set minimum SD read-depth shift"/>
63 <expand macro="cnoffset" default="0.1"/>
64 <param name="cnvsize" type="integer" value="1000" label="Set minimum CNV size" help="(--cnv-size)"/>
65 <param argument="--svfile" type="data" format="bcf" optional="true" label="Select delly SV file for breakpoint refinement"/> <!-- filetype sv.bcf not supported by galaxy -->
66 <expand macro="vcffile"/>
67 <param argument="--segmentation" type="boolean" truevalue="--segmentation" falsevalue="" label="Use copy-number segmentation?"/>
68 </section>
69 <section name="read" title="Read-depth window options" expanded="true">
70 <param name="windowsize" type="integer" value="10000" label="Set window size" help="(--window-size)"/>
71 <param name="windowoffset" type="integer" value="10000" label="Set window offset" help="(--window-offset)"/>
72 <param name="bedintervals" type="data" format="bed" optional="true" label="Select input BED file" help="(--bed-intervals)"/>
73 <param name="fractionwindow" type="float" min="0.0" max="1.0" value="0.25" label="Set minimum callable window fraction" help="(--fraction-window)"/>
74 <param name="adaptivewindowing" type="boolean" truevalue="-a" falsevalue="" label="Use mappable bases for window size?" help="(--adaptive-windowing)"/>
75 </section>
76 <section name="gc" title="GC fragment normalization options" expanded="true">
77 <param name="scanwindow" type="integer" value="10000" label="Set scan window size" help="(--scan-window)"/>
78 <param name="fractionunique" type="float" min="0.0" max="1.0" value="0.8" label="Set uniqueness filter for scan windows" help="(--fraction-unique)"/>
79 <param name="scanregions" type="data" format="bed" optional="true" label="Select file with scanning regions" help="(--scan-regions)"/>
80 <param name="madcutoff" type="integer" value="3" label="Set count cutoff" help="(median + 3 * mad) (--mad-cutoff)"/>
81 <param argument="--percentile" type="float" min="0.0" max="1.0" value="0.0005" label="Set threshold for excluding extreme GC fraction"/>
82 <param name="nowindowselection" type="boolean" truevalue="-n" falsevalue="" label="Skip scan window selection?" help="(--no-window-selection)"/>
83 </section>
84 <section name="oo" title="Output options" expanded="true">
85 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
86 <option value="cnv" selected="true">CNV</option>
87 <option value="coverage">Coverage</option>
88 <option value="log">Log</option>
89 </param>
90 </section>
91 </inputs>
92 <outputs>
93 <data name="out_cnv" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: CNV">
94 <filter>'cnv' in oo['out']</filter>
95 </data>
96 <data name="out_coverage" format="tabular.gz" from_work_dir="result.gz" label="${tool.name} on ${on_string}: Coverage">
97 <filter>'coverage' in oo['out']</filter>
98 </data>
99 <expand macro="log"/>
100 </outputs>
101 <tests>
102 <!-- no test implemented for vcffile, svfile, bed-intervals, scanregions -->
103
104 <!-- #1 default; test data to small, results are empty -->
105 <test expect_num_outputs="3">
106 <param name="input" value="normal.bam"/>
107 <section name="generic">
108 <param name="genome" value="genome.fasta"/>
109 <param name="mappability" value="map.fasta"/>
110 </section>
111 <section name="oo">
112 <param name="out" value="cnv,coverage,log"/>
113 </section>
114 <output name="out_cnv">
115 <assert_contents>
116 <has_size value="0"/>
117 </assert_contents>
118 </output>
119 <output name="out_coverage">
120 <assert_contents>
121 <has_size value="0"/>
122 </assert_contents>
123 </output>
124 <output name="out_log">
125 <assert_contents>
126 <has_text_matching expression=".+Scanning Windows"/>
127 <has_line line="***************************************************"/>
128 </assert_contents>
129 </output>
130 </test>
131 <!-- #2 -->
132 <test expect_num_outputs="3">
133 <param name="input" value="normal.bam"/>
134 <section name="generic">
135 <param name="genome" value="genome.fasta"/>
136 <param name="quality" value="11"/>
137 <param name="mappability" value="map.fasta"/>
138 <param name="ploidy" value="3"/>
139 </section>
140 <section name="cnv">
141 <param name="sdrd" value="3"/>
142 <param name="cnoffset" value="0.2"/>
143 <param name="cnvsize" value="1001"/>
144 <param name="segmentation" value="true"/>
145 </section>
146 <section name="read">
147 <param name="windowsize" value="10001"/>
148 <param name="windowoffset" value="9999"/>
149 <param name="fractionwindow" value="0.24"/>
150 <param name="adaptivewindowing" value="true"/>
151 </section>
152 <section name="gc">
153 <param name="scanwindow" value="10001"/>
154 <param name="fractionunique" value="0.79"/>
155 <param name="madcutoff" value="2"/>
156 <param name="percentile" value="0.0006"/>
157 <param name="nowindowselection" value="true"/>
158 </section>
159 <section name="oo">
160 <param name="out" value="cnv,coverage,log"/>
161 </section>
162 <output name="out_cnv">
163 <assert_contents>
164 <has_size value="700" delta="10"/>
165 </assert_contents>
166 </output>
167 <output name="out_coverage">
168 <assert_contents>
169 <has_size value="61"/>
170 </assert_contents>
171 </output>
172 <output name="out_log">
173 <assert_contents>
174 <has_text_matching expression=".+Done.+"/>
175 </assert_contents>
176 </output>
177 </test>
178 </tests>
179 <help><![CDATA[
180 .. class:: infomark
181
182 **What it does**
183
184 @WID@
185
186 **Input**
187
188 Delly *cnv* requires are a sample (BAM), a genome (FASTA) and a mappability map (FASTA), which is available `here <https://gear.embl.de/data/delly/>`_. Intervals (BED), scanning regions (BED) and a delly SV file for breakpoint refinement (BCF) can be provided optionally.
189
190 **Output**
191
192 CNV (BCF) and coverage (compressed tabular) files are created.
193
194 .. class:: infomark
195
196 **References**
197
198 @REFERENCES@
199 ]]></help>
200 <expand macro="citations"/>
201 </tool>