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comparison scatter.xml @ 0:ec9731970f8b 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 20:10:25 +0000
parents
children 3323a7867128
comparison
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-1:000000000000 0:ec9731970f8b
1 <tool id="cnvkit_scatter" name="CNVkit Scatter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Plot bin-level log2 coverages and segmentation calls together</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_cnr_file' ./tumor.cnr &&
10 #if $advanced_settings.segment
11 ln -s '$advanced_settings.segment' ./segment.cns &&
12 #end if
13 #if $advanced_settings.range_list
14 ln -s '$advanced_settings.range_list' ./list.bed &&
15 #end if
16 #if $advanced_settings.additional_SNP_allelic_process.vcf
17 ln -s '$advanced_settings.additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
18 #end if
19 cnvkit.py scatter
20 ./tumor.cnr
21 --output sample-scatter.png
22 #if $advanced_settings.segment
23 --segment ./segment.cns
24 #end if
25 #if $advanced_settings.chromosome
26 --chromosome '$advanced_settings.chromosome'
27 #end if
28 #if $advanced_settings.gene
29 --gene '$advanced_settings.gene'
30 #end if
31 #if $advanced_settings.range_list
32 --range-list ./list.bed
33 #end if
34 #if str($advanced_settings.width)
35 --width $advanced_settings.width
36 #end if
37 #if $advanced_settings.plot_aesthetics.antitarget_marker
38 --antitarget-marker '$advanced_settings.plot_aesthetics.antitarget_marker'
39 #end if
40 $advanced_settings.plot_aesthetics.by_bin
41 #if $advanced_settings.plot_aesthetics.segment_color
42 --segment-color '$advanced_settings.plot_aesthetics.segment_color'
43 #end if
44 #if $advanced_settings.plot_aesthetics.title
45 --title '$advanced_settings.plot_aesthetics.title'
46 #end if
47 $advanced_settings.plot_aesthetics.trend
48 #if str($advanced_settings.plot_aesthetics.y_max)
49 --y-max $advanced_settings.plot_aesthetics.y_max
50 #end if
51 #if str($advanced_settings.plot_aesthetics.y_min)
52 --y-min $advanced_settings.plot_aesthetics.y_min
53 #end if
54 #if str($advanced_settings.plot_aesthetics.fig_size)
55 --fig-size $advanced_settings.plot_aesthetics.fig_size
56 #end if
57 #if $advanced_settings.additional_SNP_allelic_process.vcf
58 --vcf ./vcf_file.vcf
59 #end if
60 #if $advanced_settings.additional_SNP_allelic_process.sample_id
61 --sample-id '$advanced_settings.additional_SNP_allelic_process.sample_id'
62 #end if
63 #if $advanced_settings.additional_SNP_allelic_process.normal_id
64 --normal-id '$advanced_settings.additional_SNP_allelic_process.normal_id'
65 #end if
66 #if str($advanced_settings.additional_SNP_allelic_process.min_variant_depth)
67 --min-variant-depth $advanced_settings.additional_SNP_allelic_process.min_variant_depth
68 #end if
69 #if str($advanced_settings.additional_SNP_allelic_process.zygosity_freq)
70 --zygosity-freq $advanced_settings.additional_SNP_allelic_process.zygosity_freq
71 #end if
72 ]]></command>
73 <inputs>
74 <param name="input_cnr_file" type="data" format="tabular" label="cnn file" help="" />
75 <section name="advanced_settings" title="Advanced settings" expanded="false">
76 <expand macro="scatter_optional" />
77 <section name="plot_aesthetics" title="Plot aesthetics" expanded="false">
78 <expand macro="scatter_plot" />
79 </section>
80 <section name="additional_SNP_allelic_process" title="Plot aesthetics" expanded="false">
81 <expand macro="additionally_SNP_process" />
82 </section>
83 </section>
84 </inputs>
85 <outputs>
86 <data name="out_scatter_file" format="png" label="${tool.name} on ${on_string}: diagram pdf file" from_work_dir="sample-scatter.png" />
87 </outputs>
88 <tests>
89 <test expect_num_outputs="1">
90 <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
91 <param name="zygosity_freq" value="0.25" />
92 <param name="by_bin" value="1" />
93 <output name="out_scatter_file" file="sample-scatter.png" ftype="png" compare="sim_size">
94 <assert_contents><has_size value="12000" delta="5000" /></assert_contents>
95 </output>
96 </test>
97 </tests>
98 <help><![CDATA[
99 Plot bin-level log2 coverages and segmentation calls together. Without any further arguments,
100 this plots the genome-wide copy number in a form familiar to those who have used array CGH.
101 ]]></help>
102 <expand macro="citations" />
103 </tool>