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comparison segment.xml @ 0:4b66caf52375 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 20:03:26 +0000
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children dce9f84abf16
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-1:000000000000 0:4b66caf52375
1 <tool id="cnvkit_segment" name="CNVkit Segment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Infer copy number segments from the given coverage table</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 '$filename' ./tumor.cnr &&
10 #if $additional_SNP_allelic_process.vcf
11 ln -s '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
12 #end if
13 #import os
14 cnvkit.py segment
15 ./tumor.cnr
16 --output sample.cns
17 --processes \${GALAXY_SLOTS:-4}
18 #if $advanced_settings.dataframe
19 --dataframe '$advanced_settings.dataframe'
20 #end if
21 #if $advanced_settings.method == "cbs"
22 #set $method_val = "cbs"
23 --method '$method_val'
24 #else
25 --method '$advanced_settings.method'
26 #end if
27 #if str($advanced_settings.threshold)
28 --threshold $advanced_settings.threshold
29 #end if
30 $advanced_settings.drop_low_coverage
31 #if str($advanced_settings.drop_outliers)
32 --drop-outliers $advanced_settings.drop_outliers
33 #end if
34 $advanced_settings.smooth_cbs
35 #if $additional_SNP_allelic_process.vcf
36 --vcf ./vcf_file.vcf
37 #end if
38 #if $additional_SNP_allelic_process.sample_id
39 --sample-id '$additional_SNP_allelic_process.sample_id'
40 #end if
41 #if $additional_SNP_allelic_process.normal_id
42 --normal-id '$additional_SNP_allelic_process.normal_id'
43 #end if
44 #if str($additional_SNP_allelic_process.min_variant_depth)
45 --min-variant-depth $additional_SNP_allelic_process.min_variant_depth
46 #end if
47 #if str($additional_SNP_allelic_process.zygosity_freq)
48 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq
49 #end if
50 ]]></command>
51 <inputs>
52 <param name="filename" type="data" format="tabular" label="Input CNR file" help="" />
53 <section name="additional_SNP_allelic_process" title="additional process for SNP b_allele frequencies" expanded="false">
54 <expand macro="additionally_SNP_process" />
55 </section>
56 <section name="advanced_settings" title="Advanced settings" expanded="false">
57 <expand macro="segment_optional" />
58 </section>
59 </inputs>
60 <outputs>
61 <data name="out_sample_segment" format="tabular" label="${tool.name} on ${on_string}: Sample segment" from_work_dir="sample.cns" />
62 </outputs>
63 <tests>
64 <test expect_num_outputs="1">
65 <param name="filename" ftype="tabular" value="tumor.cnr" />
66 <param name="method" value="hmm" />
67 <param name="threshold" value="2" />
68 <param name="drop_outliers" value="2" />
69 <param name="drop_low_coverage" value="1" />
70 <output name="out_sample_segment">
71 <assert_contents><has_text text="chromosome"/></assert_contents>
72 </output>
73 </test>
74 </tests>
75 <help><![CDATA[
76 Infer copy number segments from the given coverage table. Segmentation runs independently on
77 each chromosome arm, and can be parallelized with the processes option (except for the HMM methods), similar to batch
78
79 Segmented log2 ratios (.cns) output file contains those columns
80 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
81 ]]></help>
82 <expand macro="citations" />
83 </tool>