Mercurial > repos > iuc > cnvkit_call
diff call.xml @ 0:2120d778cfde draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
| author | iuc |
|---|---|
| date | Sun, 14 May 2023 20:08:32 +0000 |
| parents | |
| children | cc56d01a0b36 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/call.xml Sun May 14 20:08:32 2023 +0000 @@ -0,0 +1,128 @@ +<tool id="cnvkit_call" name="CNVkit Call" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> + <description>Call copy number variants from segmented log2 ratios</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="xrefs"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input_sample_file' ./tumor.cns && + #if $additional_SNP_allelic_process.vcf + ln -s '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf && + #end if + cnvkit.py call + ./tumor.cns + #if $advanced_settings.method == "threshold" + #set $method_val = "threshold" + --method '$method_val' + #else + --method '$advanced_settings.method' + #end if + #if $advanced_settings.center == "median" + #set $center_val = "median" + --center '$center_val' + #else + --center '$advanced_settings.center' + #end if + #if str($advanced_settings.thresholds) + --thresholds'$advanced_settings.thresholds' + #end if + #if str($advanced_settings.center_at) + --center-at '$advanced_settings.center_at' + #end if + #if str($advanced_settings.add_filter.Filter) == "yes": + #if '$advanced_settings.add_filter.filter' == "ampdel" + #set $filter_val = "ampdel" + --filter '$filter_val' + #else + --filter '$advanced_settings.add_filter.filter' + #end if + #end if + #if str($advanced_settings.ploidy) + --ploidy $advanced_settings.ploidy + #end if + #if str($advanced_settings.purity) + --purity $advanced_settings.purity + #end if + $advanced_settings.drop_low_coverage + #if str($advanced_settings.Sample_sex.sex) == "yes": + #if '$advanced_settings.Sample_sex.sample_sex' == "Male" + #set $sample_sex_val = "Male" + --sample-sex '$segment_method_val' + #else + --sample-sex '$advanced_settings.Sample_sex.sample_sex' + #end if + #end if + $advanced_settings.male_reference + #if $additional_SNP_allelic_process.vcf + --vcf ./vcf_file.vcf + #end if + #if $additional_SNP_allelic_process.sample_id + --sample-id '$additional_SNP_allelic_process.sample_id' + #end if + #if $additional_SNP_allelic_process.normal_id + --normal-id '$additional_SNP_allelic_process.normal_id' + #end if + #if str($additional_SNP_allelic_process.min_variant_depth) + --min-variant-depth $additional_SNP_allelic_process.min_variant_depth + #end if + #if str($additional_SNP_allelic_process.zygosity_freq) + --zygosity-freq $additional_SNP_allelic_process.zygosity_freq + #end if + ]]></command> + <inputs> + <param name="input_sample_file" type="data" format="tabular" label="CNS file" help="" /> + <section name="additional_SNP_allelic_process" title="additional SNP b_allele frequencies process" expanded="false"> + <expand macro="additionally_SNP_process" /> + </section> + <section name="advanced_settings" title="Advanced settings" expanded="false"> + <expand macro="call_optional" /> + <expand macro="sample_sex_condition" /> + <conditional name="add_filter"> + <param name="Filter" type="select" label="Add filters" help=""> + <option value="yes">Add filters</option> + <option value="no">don't add filters</option> + </param> + <when value="yes"> + <expand macro="filter" /> + </when> + <when value="no"> + </when> + </conditional> + </section> + </inputs> + <outputs> + <data name="out_sample_Bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest " from_work_dir="tumor.call.cns" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_sample_file" ftype="tabular" value="tumor.cns" /> + <param name="zygosity_freq" value="0.25" /> + <param name="min_variant_depth" value="40" /> + <param name="purity" value="1" /> + <output name="out_sample_Bintest"> + <assert_contents><has_text_matching expression="chrM"/></assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="Sample_sex"> + <param name="sex" value="yes" /> + </conditional> + <param name="input_sample_file" ftype="tabular" value="tumor.cns" /> + <param name="min_variant_depth" value="40" /> + <param name="purity" value="1" /> + <output name="out_sample_Bintest"> + <assert_contents><has_text_matching expression="chrM"/></assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number using either: + A list of threshold log2 values for each copy number state (-m threshold), or rescaling - for a given known + tumor cell fraction and normal ploidy, then simple rounding to the nearest integer copy number (-m clonal). + + The output is Segmented log2 ratios (.cns) file with those columns + chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes) + ]]></help> + <expand macro="citations" /> +</tool>