diff call.xml @ 6:79b2add55e02 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb

--- a/call.xml	Mon Jan 20 16:44:31 2025 +0000
+++ b/call.xml	Sat Mar 01 12:03:36 2025 +0000
@@ -72,7 +72,7 @@
             #end if
     ]]></command>
     <inputs>
-        <param name="input_sample_file" type="data" format="tabular" label="CN segmentation calls cns file" help="" />
+        <param name="input_sample_file" type="data" format="cns" label="CN segmentation calls cns file" help="" />
         <section name="additional_SNP_allelic_process" title="additional SNP b_allele frequencies process" expanded="false">
             <expand macro="additionally_SNP_process" />
         </section>
@@ -93,11 +93,11 @@
         </section>
     </inputs>
     <outputs>
-        <data name="out_sample_Bintest" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
+        <data name="out_sample_Bintest" format="cns" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="input_sample_file" ftype="tabular" value="tumor.cns" />
+            <param name="input_sample_file" ftype="cns" value="tumor.cns" />
             <section name="additional_SNP_allelic_process">
                 <param name="zygosity_freq" value="0.25" />
                 <param name="min_variant_depth" value="40" />
@@ -116,7 +116,7 @@
                 </conditional>
                 <param name="purity" value="1" />
             </section>
-            <param name="input_sample_file" ftype="tabular" value="tumor.cns" />
+            <param name="input_sample_file" ftype="cns" value="tumor.cns" />
             <section name="additional_SNP_allelic_process">
                 <param name="min_variant_depth" value="40" />
             </section>
@@ -132,6 +132,23 @@
         
         The output is Segmented log2 ratios (.cns) file with those columns
         chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
+
+-----
+
+**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>