diff varscan_somatic.xml @ 0:72b8ce355fae 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_somatic.xml	Tue Jul 10 13:35:40 2018 -0400
@@ -0,0 +1,101 @@
+<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.0">
+    <description>Call germline/somatic variants from tumor-normal pileups</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command><![CDATA[
+        varscan somatic
+            '${normal_pileup}'
+            '${tumor_pileup}'
+            galaxy_out
+            --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}
+            --normal-purity ${normal_purity}
+            --tumor-purity ${tumor_purity}
+            --tumor-purity ${tumor_purity}
+            --min-coverage-normal ${min_coverage_normal}
+            --somatic-p-value ${somatic_p_value}
+            --p-value ${p_value}
+            #if str($strand_filter) == 'yes':
+              --strand-filter 1
+            #end if
+
+            --output-vcf 1
+    ]]></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=""/>
+
+        <expand macro="min_coverage" />
+        <param argument="--min-coverage-normal" name="min_coverage_normal" type="integer" value="8" min="1" max="200"
+            label="Minimum read depth from the normal sample" help="Minimum depth at a position to make a call" />
+        <param argument="--min-coverage-tumor" name="min_coverage_tumor" type="integer" value="6" min="1" max="200"
+            label="Minimum read depth from the tumor sample" help="Minimum depth at a position to make a call" />
+        <expand macro="min_reads2" />
+        <expand macro="min_avg_qual" />
+        <expand macro="min_var_freq" value="0.10" />
+        <expand macro="min_freq_for_hom" />
+        <param argument="--normal-purity" name="normal_purity" type="float" value="1.00" min="0" max="1.00"
+            label="Estimated purity (non-tumor content) of normal sample"/>
+        <param argument="--tumor-purity" name="tumor_purity" type="float" value="1.00" min="0" max="1.00"
+            label="Estimated purity (tumor content) of tumor sample"/>
+        <expand macro="p_value" label="P-value threshold to call a heterozygote" value="0.99"/>
+        <param argument="--somatic-p-value" name="somatic_p_value" type="float" value="0.05" min="0" max="1"
+            label="p-value threshold for calling somatic sites"/>
+        <expand macro="strand_filter" />
+    </inputs>
+    <outputs>
+        <data name="output_indel" from_work_dir="galaxy_out.indel.vcf" format="vcf"/>
+        <data name="output_snp" from_work_dir="galaxy_out.snp.vcf" format="vcf"/>
+    </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" />
+            <param name="min_coverage" value="2" />
+            <param name="min_coverage_normal" value="2" />
+            <param name="min_coverage_tumor" value="2" />
+            <param name="min_reads2" value="1" />
+            <param name="min_avg_qual" value="5" />
+            <param name="min_var_freq" value="0.01" />
+            <param name="min_freq_for_hom" value="0.75" />
+            <param name="normal_purity" value="0.6" />
+            <param name="tumor_purity" value="0.6" />
+            <param name="p_value" value="0.99" />
+            <output name="output_indel" file="varscan_somatic_indel_result1.vcf" lines_diff="0" />
+            <output name="output_snp" file="varscan_somatic_snp_result1.vcf" 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 calls germline/somatic variants 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>