diff heatmap.xml @ 0:ff6b3f5a7ffb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/heatmap.xml	Sun May 14 20:11:11 2023 +0000
@@ -0,0 +1,79 @@
+<tool id="cnvkit_heatmap" name="CNVkit Heatmap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Plot copy number for multiple samples as a heatmap</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        #import re
+        #set $names = []
+        #set $x=1
+        #for $x, $file in enumerate($filenames):
+            #set $name_base = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
+            #set $name = $name_base + '_' + str(x)
+            #silent $names.append( $name )
+            ln -s '$file' ${name}.cns  &&
+        #end for
+        cnvkit.py heatmap
+            #for $name in $names:
+                ${name}.cns
+            #end for
+            --output sample-heatmap.png
+            $advanced_settings.by_bin
+            #if $advanced_settings.chromosome
+                --chromosome '$advanced_settings.chromosome'
+            #end if
+            $advanced_settings.desaturate
+            $advanced_settings.male_reference
+            #if str($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
+            $advanced_settings.vertical
+            $advanced_settings.delimit_samples
+            #if $advanced_settings.title
+                --title '$advanced_settings.title'
+            #end if
+    ]]></command>
+    <inputs>
+        <param name="filenames" multiple="true" type="data" format="cns" label="cns sample file" help="Sample coverages as raw probes cnr or segments cns)" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <expand macro="heatmap_optional" />
+            <expand macro="sample_sex_condition" />
+        </section>  
+    </inputs>
+    <outputs>
+        <data name="out_heatmap_png" format="png" label="${tool.name} on ${on_string}: Heatmap png file" from_work_dir="sample-heatmap.png" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" />
+            <param name="by_bin" value="1" />
+            <param name="desaturate" value="1" />
+            <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" >
+                <assert_contents><has_size value="9000" delta="5000" /></assert_contents>
+            </output> 
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="Sample_sex">
+                <param name="sex" value="yes" />
+            </conditional>
+            <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" />
+            <param name="by_bin" value="1" />
+            <param name="desaturate" value="1" />
+            <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" >
+                <assert_contents><has_size value="9000" delta="5000" /></assert_contents>
+            </output> 
+        </test>
+    </tests>
+    <help><![CDATA[
+        Draw copy number (either bins (.cnn, .cnr) or segments (.cns)) for multiple samples as a heatmap
+    ]]></help>
+    <expand macro="citations" />
+</tool>