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comparison rd.xml @ 0:8fff33666441 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
author iuc
date Thu, 29 Oct 2020 20:48:48 +0000
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1 <?xml version="1.0"?>
2 <tool id="delly_rd" name="Delly read-depth (rd)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
3 <description>normalization on read-depth profiles</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 rd
12 ## generic options
13 --genome '$generic.genome'
14 --quality '$generic.quality'
15 --mappability '$generic.mappability'
16 --ploidy $generic.ploidy
17 --fragment $generic.fragment
18 #if 'stats' in $oo.out
19 --statsfile 'stats.tsv.gz'
20 #end if
21 --outfile 'result.tsv.gz'
22 $generic.adaptivewindowing
23 ## window options
24 --window-size $window.windowsize
25 --window-offset $window.windowoffset
26 #if $window.bedintervals
27 --bed-intervals '$window.bedintervals'
28 #end if
29 --fraction-window $window.fractionwindow
30 ## gc options
31 --scan-window $gc.scanwindow
32 --fraction-unique $gc.fractionunique
33 #if $gc.scanregions
34 --scan-regions '$gc.scanregions'
35 #end if
36 --mad-cutoff $gc.madcutoff
37 --percentile $gc.percentile
38 $gc.nowindowselection
39 ## samples
40 '$samples' ## input
41
42 ## postprocessing
43 @LOG@
44 ]]></command>
45 <inputs>
46 <expand macro="samples" multiple="false" label="Select file"/>
47 <section name="generic" title="Generic options" expanded="true">
48 <expand macro="genome"/>
49 <param argument="--quality" type="integer" value="10" label="Set minimum mapping quality"/>
50 <param argument="--mappability" type="data" format="fasta" label="Select mappability map file"/>
51 <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
52 <param argument="--fragment" type="float" min="0.0" max="1.0" value="0.97" label="Set minimum fragment uniqueness"/>
53 <param name="adaptivewindowing" type="boolean" truevalue="-a" falsevalue="" label="Use mappable bases for window size?" help="(--adaptive-windowing)"/>
54 </section>
55 <section name="window" title="Window options" expanded="true">
56 <param name="windowsize" type="integer" value="10000" label="Set window size" help="(--window-size)"/>
57 <param name="windowoffset" type="integer" value="10000" label="Set window offset" help="(--window-offset)"/>
58 <param name="bedintervals" type="data" format="BED" optional="true" label="Select input BED file" help="(--bed-intervals)"/>
59 <param name="fractionwindow" type="float" min="0.0" max="1.0" value="0.25" label="Set minimum callable window fraction" help="(--fraction-window)"/>
60 </section>
61 <section name="gc" title="GC options" expanded="true">
62 <param name="scanwindow" type="integer" value="10000" label="Set scan window size" help="(--scan-window)"/>
63 <param name="fractionunique" type="float" min="0.0" max="1.0" value="0.8" label="Set uniqueness filter for scanning windows" help="(--fraction-unique)"/>
64 <param name="scanregions" type="data" format="BED" optional="true" label="Select file with scanning regions" help="(--scan-regions)"/>
65 <param name="madcutoff" type="integer" value="3" label="Set count cutoff" help="(median + 3 * mad) (--mad-cutoff)"/>
66 <param argument="--percentile" type="float" min="0.0" max="1.0" value="0.0005" label="Set threshold to exclude extreme GC fraction"/>
67 <param name="nowindowselection" type="boolean" truevalue="-n" falsevalue="" label="Skip scan window selection?" help="(--no-window-selection)"/>
68 </section>
69 <section name="oo" title="Output options">
70 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
71 <option value="result" selected="true">Result</option>
72 <option value="stats">Statistics (-s)</option>
73 <option value="log">Log</option>
74 </param>
75 </section>
76 </inputs>
77 <outputs>
78 <data name="out_result" format="tabular.gz" from_work_dir="result.tsv.gz" label="${tool.name} on ${on_string}: Result">
79 <filter>'result' in oo['out']</filter>
80 </data>
81 <data name="out_stats" format="tabular.gz" from_work_dir="stats.tsv.gz" label="${tool.name} on ${on_string}: Statistics">
82 <filter>'stats' in oo['out']</filter>
83 </data>
84 <expand macro="log"/>
85 </outputs>
86 <tests>
87 <!-- no test implemented for parameter -b, -r -->
88
89 <!-- #1 default, test data not sufficient -->
90 <test expect_num_outputs="2">
91 <param name="samples" value="normal.bam"/>
92 <section name="generic">
93 <param name="genome" value="genome.fasta"/>
94 <param name="mappability" value="map.fasta"/>
95 </section>
96 <section name="oo">
97 <param name="out" value="result,log"/>
98 </section>
99 <output name="out_result">
100 <assert_contents>
101 <has_n_lines n="0"/>
102 </assert_contents>
103 </output>
104 <output name="out_log">
105 <assert_contents>
106 <has_text_matching expression=".+Scanning Windows"/>
107 </assert_contents>
108 </output>
109 </test>
110 <!-- #2 default, test data not sufficient -->
111 <test expect_num_outputs="3">
112 <param name="samples" value="normal.bam"/>
113 <section name="generic">
114 <param name="genome" value="genome.fasta"/>
115 <param name="quality" value="11"/>
116 <param name="mappability" value="map.fasta"/>
117 <param name="ploidy" value="3"/>
118 <param name="fragment" value="0.96"/>
119 <param name="adaptivewindowing" value="true"/>
120 </section>
121 <section name="window">
122 <param name="windowsize" value="10001"/>
123 <param name="windowoffset" value="9999"/>
124 <param name="fractionwindow" value="0.24"/>
125 </section>
126 <section name="gc">
127 <param name="scanwindow" value="10001"/>
128 <param name="fractionunique" value="0.79"/>
129 <param name="madcutoff" value="2"/>
130 <param name="percentile" value="0.0006"/>
131 <param name="nowindowselection" value="true"/>
132 </section>
133 <section name="oo">
134 <param name="out" value="result,stats,log"/>
135 </section>
136 <output name="out_result">
137 <assert_contents>
138 <has_n_lines n="1"/>
139 </assert_contents>
140 </output>
141 <output name="out_stats">
142 <assert_contents>
143 <has_n_lines n="12"/>
144 </assert_contents>
145 </output>
146 <output name="out_log">
147 <assert_contents>
148 <has_text_matching expression=".+Scanning Windows"/>
149 </assert_contents>
150 </output>
151 </test>
152 </tests>
153 <help><![CDATA[
154 .. class:: infomark
155
156 **What it does**
157
158 @WID@
159
160 Delly *read-depth normalization (rd)* generates read-depth profiles.
161
162 **Input**
163
164 Required inputs are a sample (BAM), a genome (FASTA) and a mappability map (FASTA), which can be downloaded `here <https://gear.embl.de/data/delly/>`_. Optionally intervals (BED) and scanning regions (BED) ca be provided.
165
166 **Output**
167
168 Read-depth profiles (tabular) and optionally statistics (tabular) are created.
169
170 .. class:: infomark
171
172 **References**
173
174 @REFERENCES@
175 ]]></help>
176 <expand macro="citations"/>
177 </tool>