Mercurial > repos > iuc > cnvkit_call
comparison call.xml @ 2:0a5e2fc51dfb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
| author | iuc |
|---|---|
| date | Fri, 29 Sep 2023 15:40:43 +0000 |
| parents | cc56d01a0b36 |
| children |
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| 1:cc56d01a0b36 | 2:0a5e2fc51dfb |
|---|---|
| 2 <description>Call copy number variants from segmented log2 ratios</description> | 2 <description>Call copy number variants from segmented log2 ratios</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 '$input_sample_file' ./tumor.cns && | 10 ln -s '$input_sample_file' ./tumor.cns && |
| 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 '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf && |
| 69 #if str($additional_SNP_allelic_process.zygosity_freq) | 70 #if str($additional_SNP_allelic_process.zygosity_freq) |
| 70 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq | 71 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq |
| 71 #end if | 72 #end if |
| 72 ]]></command> | 73 ]]></command> |
| 73 <inputs> | 74 <inputs> |
| 74 <param name="input_sample_file" type="data" format="tabular" label="CNS file" help="" /> | 75 <param name="input_sample_file" type="data" format="tabular" label="CN segmentation calls cns file" help="" /> |
| 75 <section name="additional_SNP_allelic_process" title="additional SNP b_allele frequencies process" expanded="false"> | 76 <section name="additional_SNP_allelic_process" title="additional SNP b_allele frequencies process" expanded="false"> |
| 76 <expand macro="additionally_SNP_process" /> | 77 <expand macro="additionally_SNP_process" /> |
| 77 </section> | 78 </section> |
| 78 <section name="advanced_settings" title="Advanced settings" expanded="false"> | 79 <section name="advanced_settings" title="Advanced settings" expanded="false"> |
| 79 <expand macro="call_optional" /> | 80 <expand macro="call_optional" /> |
| 90 </when> | 91 </when> |
| 91 </conditional> | 92 </conditional> |
| 92 </section> | 93 </section> |
| 93 </inputs> | 94 </inputs> |
| 94 <outputs> | 95 <outputs> |
| 95 <data name="out_sample_Bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest " from_work_dir="tumor.call.cns" /> | 96 <data name="out_sample_Bintest" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" /> |
| 96 </outputs> | 97 </outputs> |
| 97 <tests> | 98 <tests> |
| 98 <test expect_num_outputs="1"> | 99 <test expect_num_outputs="1"> |
| 99 <param name="input_sample_file" ftype="tabular" value="tumor.cns" /> | 100 <param name="input_sample_file" ftype="tabular" value="tumor.cns" /> |
| 100 <param name="zygosity_freq" value="0.25" /> | 101 <param name="zygosity_freq" value="0.25" /> |