# HG changeset patch
# User greg
# Date 1676921999 0
# Node ID 48d49a58161c8e97a53116f01fdc92520130ca73

Uploaded

diff -r 000000000000 -r 48d49a58161c .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Mon Feb 20 19:39:59 2023 +0000
@@ -0,0 +1,10 @@
+categories:
+  - Variant Analysis
+description: VarScan is a variant caller for high-throughput sequencing data
+long_description: |
+  VarScan is a variant caller for high-throughput sequencing data.
+name: varscan_pileup
+owner: greg
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/pima/varscan_pileup
+homepage_url: https://github.com/gregvonkuster/galaxy_tools
+type: unrestricted
diff -r 000000000000 -r 48d49a58161c macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Feb 20 19:39:59 2023 +0000
@@ -0,0 +1,17 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.4.4</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">varscan</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/gr.129684.111</citation>
+            <citation type="doi">10.1002/0471250953.bi1504s44</citation>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 48d49a58161c varscan_pileup.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan_pileup.xml	Mon Feb 20 19:39:59 2023 +0000
@@ -0,0 +1,65 @@
+<tool id="varscan_pileup" name="VarScan pileup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>for variant detection</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+varscan ${cmd} '${input}'
+--min-coverage ${min_coverage} 
+--min-reads2 ${min_reads2} 
+--min-avg-qual ${min_avg_qual}
+--min-var-freq ${min_var_freq}
+--min-freq-for-hom ${min_freq_for_hom}
+--p-value ${p_value}
+--output-vcf 1 > '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" format="pileup" type="data" label="Samtools pileup file"/>
+        <param name="cmd" type="select" label="Analysis type">
+          <option value="pileup2snp" selected="True">Identify SNPs from a pileup file</option>
+          <option value="pileup2indel">Identify indels a pileup file</option>
+          <option value="pileup2cns">Call consensus and variants from a pileup file</option>
+        </param>
+        <param argument="--min-coverage" type="integer" value="8" min="1" max="200" label="Minimum coverage"/>
+        <param argument="--min-reads2" type="integer" value="2" min="1" max="200" label="Minimum supporting reads"/>
+        <param argument="--min-avg-qual" type="integer" value="15" min="1" max="50" label="Minimum base quality" help="The minimum base quality at the variant position required to use a read for calling"/>
+        <param argument="--min-var-freq" type="float" value="0.01" min="0" max="1" label="Minimum variant allele frequency" help="Minimum variant allele frequency required for calling a variant"/>
+        <param argument="--min-freq-for-hom" type="float" value="0.75" min="0" max="1" label="Minimum homozygous variant allele frequency" help="Minimum variant allele frequency (default: 0.75) required for calling a homozygous genotype"/>
+        <param argument="--p-value" type="float" value="0.01" min="0" max="1" label="Default p-value threshold for calling variants"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="vcf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input1.pileup"/>
+            <param name="cmd" value="pileup2snp"/>
+            <param name="min_coverage" value="15"/>
+            <param name="min_avg_qual" value="15"/>
+            <param name="min_var_freq" value="0.8"/>
+            <param name="p_value" value="0.01"/>
+            <output name="output" file="output1.vcf" ftype="vcf"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**VarScan Overview**
+
+VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. Full documentation of the command line package is available here_.
+
+.. _VarScan: http://dkoboldt.github.io/varscan/
+.. _here: http://dkoboldt.github.io/varscan/using-varscan.html
+
+**Input**
+
+::
+
+  pileup file - The SAMtools pileup file
+ 
+**Output**
+
+VarScan produces a VCF dataset as output.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>