diff varscan_copynumber.xml @ 0:a584f046e4a7 draft

planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan_copynumber.xml	Tue Jul 10 13:36:24 2018 -0400
@@ -0,0 +1,86 @@
+<tool id="varscan_copynumber" name="VarScan copynumber" version="@VERSION@.0">
+    <description>Determine relative tumor copy number from tumor-normal pileups</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command><![CDATA[
+
+        varscan copynumber
+            '${normal_pileup}'
+            '${tumor_pileup}'
+            galaxy_out
+            --min-coverage ${min_coverage}
+            --min-base-qual ${min_base_qual}
+            --min-map-qual ${min_map_qual}
+
+            --min-segment-size ${min_segment_size}
+            --max-segment-size ${max_segment_size}
+            --p-value ${p_value}
+            --data-ratio ${data_ratio}
+
+    ]]></command>
+
+    <inputs>
+        <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
+        <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
+
+        <param argument="--min-coverage" name="min_coverage" type="integer" value="20" min="1" max="200"
+            label="Minimum read depth" help="Minimum coverage threshold for copynumber segments"/>
+
+        <param argument="--min-base-qual" name="min_base_qual" type="integer" value="20" min="1" max="200"
+            label="Minimum base quality to count for coverage"/>
+        <param argument="--min-map-qual" name="min_map_qual" type="integer" value="20" min="1" max="200"
+            label="Minimum read mapping quality to count for coverage"/>
+
+        <param argument="--min-segment-size" name="min_segment_size" type="integer" value="10" min="1" max="200"
+            label="Minimum number of consecutive bases to report a segment" help="" />
+        <param argument="--max-segment-size" name="max_segment_size" type="integer" value="100" min="1" max="200"
+            label="Max size before a new segment is made" help="" />
+
+        <expand macro="p_value" label="P-value threshold for significant copynumber change-point" value="0.01" />
+
+        <param argument="--data-ratio" name="data_ratio" type="float" value="1.0" min="0.0" max="1.0"
+            label="The normal/tumor input data ratio for copynumber adjustment"/>
+
+        <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
+
+    </inputs>
+    <outputs>
+        <data name="output" from_work_dir="galaxy_out.copynumber" format="interval"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" />
+            <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" />
+            <output name="output" file="varscan_copynumber_result1.interval" lines_diff="0" />
+        </test>
+    </tests>
+
+    <help>
+**VarScan Overview**
+
+VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data.
+It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_.
+
+This tool estimates the relative tumor copy number from tumor-normal pileups.
+
+.. _VarScan: http://dkoboldt.github.io/varscan/
+.. _online: http://dkoboldt.github.io/varscan/using-varscan.html
+
+**Input**
+
+::
+
+  mpileup file - The SAMtools mpileup files for the normal and tumor tissue
+ 
+
+**Output**
+
+VarScan produces a VCF 4.1 dataset as output.
+
+
+    </help>
+    <expand macro="citations" />
+</tool>