Mercurial > repos > iuc > cnvkit_diagram
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/diagram.xml Sun May 14 20:10:02 2023 +0000 @@ -0,0 +1,85 @@ +<tool id="cnvkit_diagram" name="CNVkit Diagram" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> + <description>Draw copy number on chromosomes as a diagram</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="xrefs"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input_cnr_file' ./tumor.cnr && + #if $advanced_settings.segment + ln -s '$advanced_settings.segment' ./segment.cns && + #end if + cnvkit.py diagram + ./tumor.cnr + --output sample-diagram.pdf + #if $advanced_settings.segment + --segment ./segment.cns + #end if + #if str($advanced_settings.threshold) + --threshold $advanced_settings.threshold + #end if + #if str($advanced_settings.min_probes) + --min-probes $advanced_settings.min_probes + #end if + $advanced_settings.male_reference + #if str($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.no_shift_xy + #if $plot_aesthetics.title + --title '$plot_aesthetics.title' + #end if + #if $advanced_settings.chromosome + --chromosome '$advanced_settings.chromosome' + #end if + $plot_aesthetics.no_gene_labels + ]]></command> + <inputs> + <param name="input_cnr_file" type="data" format="tabular" label="cnn file" help="" /> + <section name="advanced_settings" title="Advanced settings" expanded="false"> + <expand macro="diagram_optional" /> + <expand macro="sample_sex_condition" /> + </section> + <section name="plot_aesthetics" title="Plot aesthetics" expanded="false"> + <expand macro="diagram_plot" /> + </section> + </inputs> + <outputs> + <data name="out_diagram_file" format="pdf" label="${tool.name} on ${on_string}: diagram pdf file" from_work_dir="sample-diagram.pdf" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" /> + <param name="segment" ftype="tabular" value="sample.cns" /> + <param name="threshold" value="10" /> + <param name="male_reference" value="1" /> + <output name="out_diagram_file" file="sample-diagram.pdf" ftype="pdf" compare="sim_size" > + <assert_contents><has_size value="6000" delta="2000" /></assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="Sample_sex"> + <param name="sex" value="yes" /> + </conditional> + <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" /> + <param name="segment" ftype="tabular" value="sample.cns" /> + <param name="threshold" value="10" /> + <param name="male_reference" value="1" /> + <output name="out_diagram_file" file="sample-diagram.pdf" ftype="pdf" compare="sim_size" > + <assert_contents><has_size value="6000" delta="2000" /></assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Draw copy number (log2 coverages, segments) on chromosomes as a diagram. If both the raw probes and + segments are given, show them side-by-side on each chromosome (segments on the left side, probes on the + right side). + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file