Mercurial > repos > iuc > cnvkit_heatmap

diff heatmap.xml @ 4:7b9178a6bffc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 11:57:15 +0000
parents 10ff342adcbe
children
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--- a/heatmap.xml	Mon Jan 20 16:26:08 2025 +0000
+++ b/heatmap.xml	Sat Mar 01 11:57:15 2025 +0000
@@ -43,7 +43,7 @@
             #end if
     ]]></command>
     <inputs>
-        <param name="filenames" multiple="true" type="data" format="tabular" label="CN segmentation calls cns file/s" help="Sample coverages as raw probes cnr or segments cns" />
+        <param name="filenames" multiple="true" type="data" format="cns" label="CN segmentation calls cns file/s" 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" />
@@ -54,7 +54,7 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" />
+            <param name="filenames" ftype="cns" value="tumor.cns,sample.cns" />
             <section name="advanced_settings">
                 <param name="desaturate" value="1" />
             </section>
@@ -63,7 +63,7 @@
             </output> 
         </test>
         <test expect_num_outputs="1">
-            <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" />
+            <param name="filenames" ftype="cns" value="tumor.cns,sample.cns" />
             <section name="advanced_settings">
                 <param name="desaturate" value="1" />
                 <conditional name="Sample_sex">
@@ -77,6 +77,24 @@
     </tests>
     <help><![CDATA[
         Draw copy number (either bins (.cnn, .cnr) or segments (.cns)) for multiple samples as a heatmap
+    
+-----
+
+**Segmented log2 ratios (.cns)**
+
+Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
+
+.. csv-table::
+   :header-rows: 0
+
+    "chromosome","start, end: Genomic coordinates of the segment"
+    "gene","Gene(s) overlapping the segment."
+    "log2","Mean log2 ratio of the segment."
+    "probes","Mean log2 ratio of the segment."
+    "depth","Average read depth."
+    "weight","Reliability weight."
+    "p_value","Statistical confidence (lower = more significant)."
+
     ]]></help>
     <expand macro="citations" />
 </tool>