Mercurial > repos > iuc > cnvkit_heatmap
comparison heatmap.xml @ 0:ff6b3f5a7ffb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
| author | iuc |
|---|---|
| date | Sun, 14 May 2023 20:11:11 +0000 |
| parents | |
| children | d8c45afa221c |
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| -1:000000000000 | 0:ff6b3f5a7ffb |
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| 1 <tool id="cnvkit_heatmap" name="CNVkit Heatmap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |
| 2 <description>Plot copy number for multiple samples as a heatmap</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 #import re | |
| 10 #set $names = [] | |
| 11 #set $x=1 | |
| 12 #for $x, $file in enumerate($filenames): | |
| 13 #set $name_base = re.sub('[^\w\-_\.]', '_', $file.element_identifier) | |
| 14 #set $name = $name_base + '_' + str(x) | |
| 15 #silent $names.append( $name ) | |
| 16 ln -s '$file' ${name}.cns && | |
| 17 #end for | |
| 18 cnvkit.py heatmap | |
| 19 #for $name in $names: | |
| 20 ${name}.cns | |
| 21 #end for | |
| 22 --output sample-heatmap.png | |
| 23 $advanced_settings.by_bin | |
| 24 #if $advanced_settings.chromosome | |
| 25 --chromosome '$advanced_settings.chromosome' | |
| 26 #end if | |
| 27 $advanced_settings.desaturate | |
| 28 $advanced_settings.male_reference | |
| 29 #if str($advanced_settings.Sample_sex.sex) == "yes": | |
| 30 #if '$advanced_settings.Sample_sex.sample_sex' == "Male" | |
| 31 #set $sample_sex_val = "Male" | |
| 32 --sample-sex '$segment_method_val' | |
| 33 #else | |
| 34 --sample-sex '$advanced_settings.Sample_sex.sample_sex' | |
| 35 #end if | |
| 36 #end if | |
| 37 $advanced_settings.no_shift_xy | |
| 38 $advanced_settings.vertical | |
| 39 $advanced_settings.delimit_samples | |
| 40 #if $advanced_settings.title | |
| 41 --title '$advanced_settings.title' | |
| 42 #end if | |
| 43 ]]></command> | |
| 44 <inputs> | |
| 45 <param name="filenames" multiple="true" type="data" format="cns" label="cns sample file" help="Sample coverages as raw probes cnr or segments cns)" /> | |
| 46 <section name="advanced_settings" title="Advanced settings" expanded="false"> | |
| 47 <expand macro="heatmap_optional" /> | |
| 48 <expand macro="sample_sex_condition" /> | |
| 49 </section> | |
| 50 </inputs> | |
| 51 <outputs> | |
| 52 <data name="out_heatmap_png" format="png" label="${tool.name} on ${on_string}: Heatmap png file" from_work_dir="sample-heatmap.png" /> | |
| 53 </outputs> | |
| 54 <tests> | |
| 55 <test expect_num_outputs="1"> | |
| 56 <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" /> | |
| 57 <param name="by_bin" value="1" /> | |
| 58 <param name="desaturate" value="1" /> | |
| 59 <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" > | |
| 60 <assert_contents><has_size value="9000" delta="5000" /></assert_contents> | |
| 61 </output> | |
| 62 </test> | |
| 63 <test expect_num_outputs="1"> | |
| 64 <conditional name="Sample_sex"> | |
| 65 <param name="sex" value="yes" /> | |
| 66 </conditional> | |
| 67 <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" /> | |
| 68 <param name="by_bin" value="1" /> | |
| 69 <param name="desaturate" value="1" /> | |
| 70 <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" > | |
| 71 <assert_contents><has_size value="9000" delta="5000" /></assert_contents> | |
| 72 </output> | |
| 73 </test> | |
| 74 </tests> | |
| 75 <help><![CDATA[ | |
| 76 Draw copy number (either bins (.cnn, .cnr) or segments (.cns)) for multiple samples as a heatmap | |
| 77 ]]></help> | |
| 78 <expand macro="citations" /> | |
| 79 </tool> |