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comparison call.xml @ 0:04793bafe25a 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 20:04:08 +0000
parents
children d17420823d11
comparison
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-1:000000000000 0:04793bafe25a
1 <tool id="cnvkit_call" name="CNVkit Call" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Call copy number variants from segmented log2 ratios</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 ln -s '$input_sample_file' ./tumor.cns &&
10 #if $additional_SNP_allelic_process.vcf
11 ln -s '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
12 #end if
13 cnvkit.py call
14 ./tumor.cns
15 #if $advanced_settings.method == "threshold"
16 #set $method_val = "threshold"
17 --method '$method_val'
18 #else
19 --method '$advanced_settings.method'
20 #end if
21 #if $advanced_settings.center == "median"
22 #set $center_val = "median"
23 --center '$center_val'
24 #else
25 --center '$advanced_settings.center'
26 #end if
27 #if str($advanced_settings.thresholds)
28 --thresholds'$advanced_settings.thresholds'
29 #end if
30 #if str($advanced_settings.center_at)
31 --center-at '$advanced_settings.center_at'
32 #end if
33 #if str($advanced_settings.add_filter.Filter) == "yes":
34 #if '$advanced_settings.add_filter.filter' == "ampdel"
35 #set $filter_val = "ampdel"
36 --filter '$filter_val'
37 #else
38 --filter '$advanced_settings.add_filter.filter'
39 #end if
40 #end if
41 #if str($advanced_settings.ploidy)
42 --ploidy $advanced_settings.ploidy
43 #end if
44 #if str($advanced_settings.purity)
45 --purity $advanced_settings.purity
46 #end if
47 $advanced_settings.drop_low_coverage
48 #if str($advanced_settings.Sample_sex.sex) == "yes":
49 #if '$advanced_settings.Sample_sex.sample_sex' == "Male"
50 #set $sample_sex_val = "Male"
51 --sample-sex '$segment_method_val'
52 #else
53 --sample-sex '$advanced_settings.Sample_sex.sample_sex'
54 #end if
55 #end if
56 $advanced_settings.male_reference
57 #if $additional_SNP_allelic_process.vcf
58 --vcf ./vcf_file.vcf
59 #end if
60 #if $additional_SNP_allelic_process.sample_id
61 --sample-id '$additional_SNP_allelic_process.sample_id'
62 #end if
63 #if $additional_SNP_allelic_process.normal_id
64 --normal-id '$additional_SNP_allelic_process.normal_id'
65 #end if
66 #if str($additional_SNP_allelic_process.min_variant_depth)
67 --min-variant-depth $additional_SNP_allelic_process.min_variant_depth
68 #end if
69 #if str($additional_SNP_allelic_process.zygosity_freq)
70 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq
71 #end if
72 ]]></command>
73 <inputs>
74 <param name="input_sample_file" type="data" format="tabular" label="CNS file" help="" />
75 <section name="additional_SNP_allelic_process" title="additional SNP b_allele frequencies process" expanded="false">
76 <expand macro="additionally_SNP_process" />
77 </section>
78 <section name="advanced_settings" title="Advanced settings" expanded="false">
79 <expand macro="call_optional" />
80 <expand macro="sample_sex_condition" />
81 <conditional name="add_filter">
82 <param name="Filter" type="select" label="Add filters" help="">
83 <option value="yes">Add filters</option>
84 <option value="no">don't add filters</option>
85 </param>
86 <when value="yes">
87 <expand macro="filter" />
88 </when>
89 <when value="no">
90 </when>
91 </conditional>
92 </section>
93 </inputs>
94 <outputs>
95 <data name="out_sample_Bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest " from_work_dir="tumor.call.cns" />
96 </outputs>
97 <tests>
98 <test expect_num_outputs="1">
99 <param name="input_sample_file" ftype="tabular" value="tumor.cns" />
100 <param name="zygosity_freq" value="0.25" />
101 <param name="min_variant_depth" value="40" />
102 <param name="purity" value="1" />
103 <output name="out_sample_Bintest">
104 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
105 </output>
106 </test>
107 <test expect_num_outputs="1">
108 <conditional name="Sample_sex">
109 <param name="sex" value="yes" />
110 </conditional>
111 <param name="input_sample_file" ftype="tabular" value="tumor.cns" />
112 <param name="min_variant_depth" value="40" />
113 <param name="purity" value="1" />
114 <output name="out_sample_Bintest">
115 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
116 </output>
117 </test>
118 </tests>
119 <help><![CDATA[
120 Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number using either:
121 A list of threshold log2 values for each copy number state (-m threshold), or rescaling - for a given known
122 tumor cell fraction and normal ploidy, then simple rounding to the nearest integer copy number (-m clonal).
123
124 The output is Segmented log2 ratios (.cns) file with those columns
125 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
126 ]]></help>
127 <expand macro="citations" />
128 </tool>