diff muse_call.xml @ 0:c4f5e1994690 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muse_call.xml	Mon Jul 02 10:40:32 2018 -0400
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+<tool id="muse_call" name="muse call" version="1.0.rc">
+  <description>First 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="1.7">samtools</requirement>
+  </requirements>
+  <command> <![CDATA[
+    ##creation of the bam indexes and execution of the MuSE call command with all the advanced options
+    samtools index $input2 && samtools index $input3 && MuSE call -O variant_call -f $input1 $input2 $input3
+    #if $region
+      -r $region
+    #end if
+    #if $positions
+      -l $positions
+    #end if]]>
+  </command>
+  <inputs>
+    <param format="fasta" name="input1" type="data" label="reference" help="fasta"/>
+    <param format="bam" name="input2" type="data" label="tumor bam" help="tumor sample bamfile"/>
+    <param format="bam" name="input3" type="data" label="normal bam" help="normal sample bamfile"/>
+    <param name="region" type="text" optional="true" label="region" help="(chr:pos-pos)"/>
+    <param format="txt,bed" name="positions" type="data" optional="true" label="list of regions" help="file txt or BED (chr:pos-pos or BED),with one region per line" />
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" from_work_dir="variant_call.MuSE.txt" label="${tool.name} on ${on_string}"/>
+  </outputs>
+  <tests>
+      <test>
+	<param name="input1" value="test_fasta.fa" ftype="fasta"/>
+        <param name="input2" value="Muse_test_tumoral.bam"/>
+        <param name="input3" value="Muse_test_normal.bam"/>
+        <output name="output" file="results.txt" lines_diff="8"/>
+      </test>
+  </tests>
+  <help>
+     **MuSE call**, takes as input the indexed reference genome FASTA file  and the BAM file from normal and tumoral sample.
+     The BAM files require aligning all the sequence reads against the reference genome using the Burrows-Wheeler alignment tool (BWA),
+     with either the backtrack or the maximal exact matches (MEM) algorithm. In addition,
+     the BAM files need to be processed by following the Genome Analysis Toolkit (GATK) Best Practices that include:
+     Marking duplicates,realigning the paired tumor-normal BAMs jointly recalibrating base quality scores.
+     More information at MuSE: http://bioinformatics.mdanderson.org/main/MuSE
+
+         Galaxy wrapper for MuSE call implements all options available through the command line. Supported options are described below.
+
+                Usage:   MuSE call [options] tumor.bam matched_normal.bam
+                        Options:
+                             -f FILE    faidx indexed reference sequence file
+                             -r STR     single region (chr:pos-pos) where somatic
+                                        mutations are called
+                             -l FILE    list of regions (chr:pos-pos or BED), one
+                                        region per line
+                             -O STR     output file name (suffix '.MuSE.txt' is
+                                        automatically added)
+  </help>
+  <citations>
+    <citation type="doi">10.1186/s13059-016-1029-6</citation>
+  </citations>
+</tool>