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comparison reference.xml @ 0:12744fc315ae draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
author iuc
date Sun, 14 May 2023 20:07:12 +0000
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children 184550cc93fd
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-1:000000000000 0:12744fc315ae
1 <tool id="cnvkit_reference" name="CNVkit Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Compile a copy-number reference from the given files or directory containing normal samples</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 #import re
10 #if str($CNV_reference.CNV_reference_availabel) == "yes"
11 #set $names = []
12 #set $x=1
13 #for $x, $input in enumerate($CNV_reference.input_cnn_file):
14 #set $name_base = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
15 #set $name = $name_base + '_' + str(x)
16 #silent $names.append( $name )
17 ln -s '$input' ${name}.cnn &&
18 #end for
19 #end if
20 #if str($CNV_reference.CNV_reference_availabel) == "no"
21 #if $CNV_reference.antitargets
22 ln -s '$CNV_reference.antitargets' ./antitargets.bed &&
23 #end if
24 ln -s '$CNV_reference.targets' ./targets.bed &&
25 #end if
26 #if $CNV_reference.advanced_settings.reference_source.fasta
27 #if str($CNV_reference.advanced_settings.reference_source.ref_selector) == 'history':
28 ln -s '$CNV_reference.advanced_settings.reference_source.fasta' ./genome.fa &&
29 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
30 #else
31 ln -s '$CNV_reference.advanced_settings.reference_source.fasta.fields.path' ./genome.fa &&
32 ln -s '${CNV_reference.advanced_settings.reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
33 #end if
34 #end if
35 cnvkit.py reference
36 #if str($CNV_reference.CNV_reference_availabel) == "yes"
37 #for $name in $names:
38 ${name}.cnn
39 #end for
40 #end if
41 --output ref-tas.cnn
42 $CNV_reference.advanced_settings.cluster
43 #if str($CNV_reference.advanced_settings.min_cluster_size)
44 --min-cluster-size '$CNV_reference.advanced_settings.min_cluster_size'
45 #end if
46 #if str($CNV_reference.advanced_settings.Sample_sex.sex) == "yes":
47 #if '$CNV_reference.advanced_settings.Sample_sex.sample_sex' == "Male"
48 #set $sample_sex_val = "Male"
49 --sample-sex '$segment_method_val'
50 #else
51 --sample-sex '$CNV_reference.advanced_settings.Sample_sex.sample_sex'
52 #end if
53 #end if
54 $CNV_reference.advanced_settings.male_reference
55 #if str($CNV_reference.CNV_reference_availabel) == "no"
56 --targets ./targets.bed
57 #if $CNV_reference.antitargets
58 --antitargets ./antitargets.bed
59 #end if
60 #end if
61 $CNV_reference.disable_some_of_the_bias_corrections.no_gc
62 $CNV_reference.disable_some_of_the_bias_corrections.no_edge
63 $CNV_reference.disable_some_of_the_bias_corrections.no_rmask
64 ]]></command>
65 <inputs>
66 <conditional name="CNV_reference">
67 <param name="CNV_reference_availabel" type="select" label="Build or reuse a copy number reference file cnn?" help="">
68 <option value="no" selected="True">Build a new copy number reference file</option>
69 <option value="yes">Reuse a copy number reference file</option>
70 </param>
71 <when value="no">
72 <expand macro="construct_CNV_ref_with_natural_expected_number" />
73 <section name="advanced_settings" title="Advanced settings" expanded="false">
74 <expand macro="reference_interface" />
75 <expand macro="reference_optional" />
76 <expand macro="sample_sex_condition" />
77 </section>
78 <section name="disable_some_of_the_bias_corrections" title="Bias corrections settings" expanded="false">
79 <expand macro="disable_specific_automatic_bias_corrections" />
80 </section>
81 </when>
82 <when value="yes">
83 <param name="input_cnn_file" type="data" format="tabular" multiple="true" label="cnn file" help="Normal-sample target or antitarget cnn files, or the directory that contains them" />
84 <section name="advanced_settings" title="Advanced settings" expanded="false">
85 <expand macro="reference_interface" />
86 <expand macro="reference_optional" />
87 <conditional name="Sample_sex">
88 <param name="sex" type="select" label="Sample sex availabel" help="">
89 <option value="yes">Select sample sex</option>
90 </param>
91 <when value="yes">
92 <expand macro="sample_sex" />
93 </when>
94 </conditional>
95 </section>
96 <section name="disable_some_of_the_bias_corrections" title="Bias corrections settings" expanded="false">
97 <expand macro="disable_specific_automatic_bias_corrections" />
98 </section>
99 </when>
100 </conditional>
101 </inputs>
102 <outputs>
103 <data name="out_referene_tas" format="tabular" label="${tool.name} on ${on_string}: TAS-on-target coverage" from_work_dir="ref-tas.cnn" />
104 </outputs>
105 <tests>
106 <test expect_num_outputs="1">
107 <conditional name="reference_source">
108 <param name="ref_selector" value="history"/>
109 <param name="fasta" ftype="fasta" value="genome.fasta" />
110 </conditional>
111 <param name="CNV_reference_availabel" value="yes" />
112 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
113 <param name="no_gc" value="1" />
114 <output name="out_referene_tas" file="ref-tas.cnn" />
115 </test>
116 <test expect_num_outputs="1">
117 <conditional name="reference_source">
118 <param name="ref_selector" value="cached"/>
119 <param name="fasta" value="test_buildid"/>
120 </conditional>
121 <param name="CNV_reference_availabel" value="yes" />
122 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
123 <param name="no_gc" value="1" />
124 <output name="out_referene_tas" file="ref-tas.cnn" />
125 </test>
126 <test expect_num_outputs="1">
127 <conditional name="reference_source">
128 <param name="ref_selector" value="cached"/>
129 <param name="fasta" value="test_buildid"/>
130 </conditional>
131 <param name="CNV_reference_availabel" value="yes" />
132 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,sample.targetcoverage.cnn" />
133 <param name="no_gc" value="1" />
134 <output name="out_referene_tas">
135 <assert_contents><has_text text="chromosome"/></assert_contents>
136 </output>
137 </test>
138 <test expect_num_outputs="1">
139 <conditional name="reference_source">
140 <param name="ref_selector" value="cached"/>
141 <param name="fasta" value="test_buildid"/>
142 </conditional>
143 <param name="CNV_reference_availabel" value="no" />
144 <param name="targets" ftype="bed" value="capture.target.bed" />
145 <param name="no_gc" value="1" />
146 <output name="out_referene_tas">
147 <assert_contents><has_text text="chromosome"/></assert_contents>
148 </output>
149 </test>
150 <test expect_num_outputs="1">
151 <conditional name="reference_source">
152 <param name="ref_selector" value="cached"/>
153 <param name="fasta" value="test_buildid"/>
154 </conditional>
155 <conditional name="Sample_sex">
156 <param name="sex" value="yes" />
157 </conditional>
158 <param name="CNV_reference_availabel" value="no" />
159 <param name="targets" ftype="bed" value="capture.target.bed" />
160 <param name="no_gc" value="1" />
161 <output name="out_referene_tas">
162 <assert_contents><has_text text="chromosome"/></assert_contents>
163 </output>
164 </test>
165 </tests>
166 <help><![CDATA[
167 Compile a copy-number reference from the given files or directory (containing normal samples).
168 If given a reference genome (-f option), also calculate the GC content and repeat-masked
169 proportion of each region.
170
171 The reference .cnn file output contains those columns
172 chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion
173 of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage
174 depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)
175
176 ]]></help>
177 <expand macro="citations" />
178 </tool>