diff vcf.xml @ 1:974b39eb89b6 draft default tip

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

--- a/vcf.xml	Mon Jan 20 16:31:16 2025 +0000
+++ b/vcf.xml	Sat Mar 01 11:55:26 2025 +0000
@@ -30,14 +30,14 @@
             #end if
     ]]></command>
      <inputs>
-        <param name="input_segmented_file" type="data" format="tabular" label="Segmented Copy Ratio Data File (cns file)" help="" />
+        <param name="input_segmented_file" type="data" format="cns" label="Segmented Copy Ratio Data File (cns file)" help="" />
         <section name="advanced_settings" title="Advanced settings" expanded="false">
-            <param argument="--cnr" optional="true" type="data" format="tabular" label="Bin-level copy ratios (cnr)" help="" />
-            <param argument="--sample-id" optional="true" type="text" label="Sample ID" value="" help="Sample name to write in the genotype field of the output VCF file" />
+            <param argument="--cnr" optional="true" type="data" format="cnr" label="Bin-level copy ratios (cnr)" help="" />
+            <param argument="--sample-id" type="text" label="Sample ID" help="Sample name to write in the genotype field of the output VCF file" />
             <param argument="--ploidy" optional="true" type="integer" label="Ploidy" min="1" value="2" help="Ploidy of the sample cells. [Default: 2]" />
             <expand macro="sample_sex"/>
             <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" />
-            <param argument="--diploid-parx-genome" optional="true" type="text" label="Diploid Parx Genome" value="" help="Considers the given human genome's PAR of chromosome X as autosomal. Example: 'grch38'" />
+            <param argument="--diploid-parx-genome" type="text" label="Diploid Parx Genome" help="Considers the given human genome's PAR of chromosome X as autosomal. Example: 'grch38'" />
         </section>  
         </inputs>
     <outputs>
@@ -45,16 +45,52 @@
     </outputs>
        <tests>
         <test expect_num_outputs="1">
-            <param name="input_segmented_file" ftype="tabular" value="sample.cns" />
+            <param name="input_segmented_file" ftype="cns" value="sample.cns" />
             <param name="sample_id" value="SampleID" />
             <param name="sample_sex" value="Female" />
             <output name="CNVs_VCF" file="sample.cnv.vcf" ftype="vcf" lines_diff="2" />
         </test>
     </tests>
     <help><![CDATA[
-        Export the segmented copy number data (from a .cns file) to the standard VCF 4.2 format. 
-        The resulting VCF file describes copy number gains and losses across each segment and contains 
-        INFO fields for breakpoints (CIPOS, CIEND) if bin-level data (.cnr) is provided.
+Export the segmented copy number data (from a .cns file) to the standard VCF 4.2 format. 
+The resulting VCF file describes copy number gains and losses across each segment and contains 
+INFO fields for breakpoints (CIPOS, CIEND) if bin-level data (.cnr) is provided.
+
+-----
+
+**Bin-level log2 ratios (.cnr)**
+
+Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
+
+.. csv-table::
+   :header-rows: 0
+
+    "chromosome","Genomic chromosome (e.g., chr1, chrX)"
+    "start","Start position of the bin."
+    "end","End position of the bin."
+    "gene","Gene name(s) overlapping the bin (if applicable)."
+    "log2","Normalized log2 ratio (sample coverage / reference coverage)."
+    "depth","Average read depth in the bin."
+    "weight","Reliability weight of the bin (higher = more reliable)."
+
+-----
+
+**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>