diff diagram.xml @ 0:9d18753f47b4 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/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