Mercurial > repos > p.lucas > varscan_readcount

changeset 5:0f875edd8d91 draft

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Uploaded v2
author p.lucas
date Thu, 10 Feb 2022 09:55:55 +0000
parents 97f22e5a417d
children 9001935fe8c0
files varscan_readcount.xml
diffstat 1 files changed, 25 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/varscan_readcount.xml	Thu Feb 10 08:19:19 2022 +0000
+++ b/varscan_readcount.xml	Thu Feb 10 09:55:55 2022 +0000
@@ -1,31 +1,26 @@
-<tool id="varscan" name="VarScan Readcount" version="1">
-    <description>To use varscan readcount tool</description>
-    <requirements>
-        <requirement type="package" version="2.4.4">varscan</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        varscan readcounts ${input} --min-coverage ${min_cov} --min-base-qual ${min_base_qual} --output-file ${output}
-    ]]></command>
-    <inputs>
-        <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/>
-        <param name="min_cov" type="integer" value="1" min="1" max="2000" label="Minimum read depth" help="Minimum depth at a position to make a call [1]"/>
-        <param name="min_base_qual" type="integer" value="20" min="1" max="500" label="Minimum base quality" label="Minimum base quality at a position to count a read [20]"/>
-    </inputs>
-    <outputs>
-        <data name="output" format="vcf"/>
-    </outputs>
-    <help>
-      command: varscan readcounts --help
-
-      Min coverage:   1
-      Min base qual:  20
-      USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS
-      OPTIONS:
-        --variants-file A list of variants at which to report readcounts
-        --output-file   Output file to contain the readcounts
-        --min-coverage  Minimum read depth at a position to make a call (1)
-        --min-base-qual Minimum base quality at a position to count a read (20)
-    </help>
+<tool id="varscan" name="VarScan Readcount" version="2">
+  <description>To use varscan readcount tool</description>
+  <requirements>
+    <requirement type="package" version="2.4.4">varscan</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+    varscan readcounts ${input} --min-coverage ${min_cov} --min-base-qual ${min_base_qual} --output-file ${output}
+  ]]></command>
+  <inputs>
+    <param name="input" format="pileup" type="data" label="Pileup dataset"/>
+    <param name="min_cov" type="integer" value="1" min="1" max="2000" label="Minimum read depth" help="Minimum depth at a position to make a call [1]"/>
+    <param name="min_base_qual" type="integer" value="20" min="1" max="500" label="Minimum base quality" label="Minimum base quality at a position to count a read [20]"/>
+  </inputs>
+  <outputs>
+    <data name="output" format="vcf"/>
+  </outputs>
+  <help>
+    COMMAND: varscan readcounts --help
+    USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS
+    OPTIONS:
+      --variants-file A list of variants at which to report readcounts
+      --output-file   Output file to contain the readcounts
+      --min-coverage  Minimum read depth at a position to make a call (default: 1)
+      --min-base-qual Minimum base quality at a position to count a read (default: 20)
+  </help>
 </tool>
-
-