Mercurial > repos > iuc > cnvkit_diagram
comparison diagram.xml @ 0:9d18753f47b4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
author | iuc |
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date | Sun, 14 May 2023 20:10:02 +0000 |
parents | |
children | 697c61206f5f |
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1 <tool id="cnvkit_diagram" name="CNVkit Diagram" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |
2 <description>Draw copy number on chromosomes as a diagram</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 cnvkit.py diagram | |
14 ./tumor.cnr | |
15 --output sample-diagram.pdf | |
16 #if $advanced_settings.segment | |
17 --segment ./segment.cns | |
18 #end if | |
19 #if str($advanced_settings.threshold) | |
20 --threshold $advanced_settings.threshold | |
21 #end if | |
22 #if str($advanced_settings.min_probes) | |
23 --min-probes $advanced_settings.min_probes | |
24 #end if | |
25 $advanced_settings.male_reference | |
26 #if str($advanced_settings.Sample_sex.sex) == "yes": | |
27 #if '$advanced_settings.Sample_sex.sample_sex' == "Male" | |
28 #set $sample_sex_val = "Male" | |
29 --sample-sex '$segment_method_val' | |
30 #else | |
31 --sample-sex '$advanced_settings.Sample_sex.sample_sex' | |
32 #end if | |
33 #end if | |
34 $advanced_settings.no_shift_xy | |
35 #if $plot_aesthetics.title | |
36 --title '$plot_aesthetics.title' | |
37 #end if | |
38 #if $advanced_settings.chromosome | |
39 --chromosome '$advanced_settings.chromosome' | |
40 #end if | |
41 $plot_aesthetics.no_gene_labels | |
42 ]]></command> | |
43 <inputs> | |
44 <param name="input_cnr_file" type="data" format="tabular" label="cnn file" help="" /> | |
45 <section name="advanced_settings" title="Advanced settings" expanded="false"> | |
46 <expand macro="diagram_optional" /> | |
47 <expand macro="sample_sex_condition" /> | |
48 </section> | |
49 <section name="plot_aesthetics" title="Plot aesthetics" expanded="false"> | |
50 <expand macro="diagram_plot" /> | |
51 </section> | |
52 </inputs> | |
53 <outputs> | |
54 <data name="out_diagram_file" format="pdf" label="${tool.name} on ${on_string}: diagram pdf file" from_work_dir="sample-diagram.pdf" /> | |
55 </outputs> | |
56 <tests> | |
57 <test expect_num_outputs="1"> | |
58 <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" /> | |
59 <param name="segment" ftype="tabular" value="sample.cns" /> | |
60 <param name="threshold" value="10" /> | |
61 <param name="male_reference" value="1" /> | |
62 <output name="out_diagram_file" file="sample-diagram.pdf" ftype="pdf" compare="sim_size" > | |
63 <assert_contents><has_size value="6000" delta="2000" /></assert_contents> | |
64 </output> | |
65 </test> | |
66 <test expect_num_outputs="1"> | |
67 <conditional name="Sample_sex"> | |
68 <param name="sex" value="yes" /> | |
69 </conditional> | |
70 <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" /> | |
71 <param name="segment" ftype="tabular" value="sample.cns" /> | |
72 <param name="threshold" value="10" /> | |
73 <param name="male_reference" value="1" /> | |
74 <output name="out_diagram_file" file="sample-diagram.pdf" ftype="pdf" compare="sim_size" > | |
75 <assert_contents><has_size value="6000" delta="2000" /></assert_contents> | |
76 </output> | |
77 </test> | |
78 </tests> | |
79 <help><![CDATA[ | |
80 Draw copy number (log2 coverages, segments) on chromosomes as a diagram. If both the raw probes and | |
81 segments are given, show them side-by-side on each chromosome (segments on the left side, probes on the | |
82 right side). | |
83 ]]></help> | |
84 <expand macro="citations" /> | |
85 </tool> |