Mercurial > repos > iuc > cnvkit_segment

comparison segment.xml @ 1:c4a22d0fdba5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:45:41 +0000
parents 9d9a8f230a2f
children
comparison
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0:9d9a8f230a2f 1:c4a22d0fdba5
2 <description>Infer copy number segments from the given coverage table</description> 2 <description>Infer copy number segments from the given coverage table</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro="creators"/>
7 <expand macro="requirements"/> 8 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$filename' ./tumor.cnr && 10 ln -s '$filename' ./tumor.cnr &&
10 #if $additional_SNP_allelic_process.vcf 11 #if $additional_SNP_allelic_process.vcf
11 ln -s '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf && 12 ln -s '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
47 #if str($additional_SNP_allelic_process.zygosity_freq) 48 #if str($additional_SNP_allelic_process.zygosity_freq)
48 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq 49 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq
49 #end if 50 #end if
50 ]]></command> 51 ]]></command>
51 <inputs> 52 <inputs>
52 <param name="filename" type="data" format="tabular" label="Input CNR file" help="" /> 53 <param name="filename" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="Use the output of the CNVkit fix" />
53 <section name="additional_SNP_allelic_process" title="additional process for SNP b_allele frequencies" expanded="false"> 54 <section name="additional_SNP_allelic_process" title="additional process for SNP b_allele frequencies" expanded="false">
54 <expand macro="additionally_SNP_process" /> 55 <expand macro="additionally_SNP_process" />
55 </section> 56 </section>
56 <section name="advanced_settings" title="Advanced settings" expanded="false"> 57 <section name="advanced_settings" title="Advanced settings" expanded="false">
57 <expand macro="segment_optional" /> 58 <expand macro="segment_optional" />