diff muse_sump.xml @ 0:c4f5e1994690 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muse_sump.xml	Mon Jul 02 10:40:32 2018 -0400
@@ -0,0 +1,48 @@
+<tool id="muse" name="muse_sump" version="1.0.rc">
+  <description>Second step of somatic point mutation caller for tumor-normal paired samples in next-generation sequencing data. </description>
+  <requirements>
+        <requirement type="package" version="1.0.rc" >muse</requirement>
+	<requirement type="package" version="0.2.5" >tabix</requirement>
+  </requirements>
+  <command> <![CDATA[bgzip -c $input2 > dbsnp.vcf.gz && tabix -p vcf -f dbsnp.vcf.gz && MuSE sump -O prova $selection -I $input1 -D dbsnp.vcf.gz]]></command>
+  <inputs>
+    <param format="txt" name="input1" type="data" label="MuSE call output" help="txt file from MuSE call"/>
+    <param format="vcf" name="input2" type="data" label="dbSNP vcf file" help="dbSNP vcf file"/>
+    <param name="selection" type="select" label="List Selection">
+        <option value="-E" selected="true">input generated from whole exome sequencing</option>
+        <option value="-G"                >input generated from whole genome sequencing</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="output" from_work_dir="prova" label="${tool.name} on ${on_string}"/>
+  </outputs>
+  <tests>
+      <test>
+	<param name="input1" value="results.txt"/>
+        <param name="input2" value="dbsnp.vcf"/>
+        <output name="output" file="sump_results.vcf" lines_diff="10"/>
+      </test>
+  </tests>
+  <help>
+    **MuSE sump**, takes as input the output file from ‘MuSE call’ and the dbSNP file.
+    More information at MuSE: http://bioinformatics.mdanderson.org/main/MuSE
+
+        Galaxy wrapper for MuSE sump implements all options available through the command line.Supported options are described below.
+
+                 Usage:   MuSE sump [options]
+                          Options:
+                                -I FILE    single input file generated by 'MuSE call'
+                                -G         input generated from whole genome sequencing data
+                                -E         input generated from whole exome sequencing data
+                                -O STR     output file name (VCF format)
+                                -D FILE    dbSNP vcf file that should be bgzip compressed,
+                                           tabix indexed and based on the same reference
+                                           genome used in 'MuSE call'.
+	**IMPORTANT** the wrapper will automatically compress the vcf and create the tabix index
+
+					   
+    </help>
+    <citations>
+      <citation type="doi">10.1186/s13059-016-1029-6</citation>
+    </citations>
+</tool>