# HG changeset patch
# User jbrayet
# Date 1439903133 14400
# Node ID 3b7cb5a0ebf82e7da7f5f1ec8a6777495974e879
# Parent  55981156b1b3f82604cc20536683e37c2347a245
Uploaded

diff -r 55981156b1b3 -r 3b7cb5a0ebf8 sequenza_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sequenza_wrapper.xml	Tue Aug 18 09:05:33 2015 -0400
@@ -0,0 +1,159 @@
+<!--Sequenza - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
+Copyright (C) 2015  Institut Curie
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.-->
+<tool id="sequenza_tool" name="Sequenza" version="1.2">
+  <description>allele-specific copy number and mutation profiles</description>
+  <requirements>
+    <requirement type="package" version="2.7">python</requirement>
+    <requirement type="package" version="2.1.1">sequenza</requirement>
+  </requirements>
+  <command interpreter="python">
+    sequenza_wrapper.py -name $sampleName -outGalaxy $HTMLFile -format $fileFormat.format -estimation $usePersonalEstimation.estimation -gcContent $gc_content_file
+    #if $fileFormat.format == "BAM":
+      #if $fileFormat.reference_source.reference_source_selector=="cached":
+        -selector $fileFormat.reference_source.reference_source_selector
+        -normal $fileFormat.reference_source.normal_file
+        -tumor $fileFormat.reference_source.tumor_file
+        -ref_file $fileFormat.reference_source.ref_file.fields.path
+	-samtools_options '
+	$fileFormat.skip_anomalous_read_pairs
+        $fileFormat.disable_probabilistic_realignment
+	-d "$fileFormat.max_reads_per_bam"
+        -q "$fileFormat.minimum_mapping_quality"
+        -Q "$fileFormat.minimum_base_quality"
+	'
+      #else:
+        -selector $fileFormat.reference_source.reference_source_selector
+        -normal $fileFormat.reference_source.normal_file
+        -tumor $fileFormat.reference_source.tumor_file
+        -ref_file $fileFormat.reference_source.ref_file
+      #end if
+    #else:
+      -normal $fileFormat.normal_file
+      -tumor $fileFormat.tumor_file
+    #end if
+    #if $usePersonalEstimation.estimation == "yes":
+      -cellularity $usePersonalEstimation.cellularity
+      -ploidy $usePersonalEstimation.ploidy
+    #end if
+  </command>
+  <inputs>
+    <param name="sampleName" type="text" value="sample" size="30" label="Sample name">
+      <sanitizer invalid_char="">
+        <valid initial="string.letters,string.digits"><add value="_"/></valid>
+      </sanitizer>
+    </param>
+    <conditional name="fileFormat">
+      <param name="format" type="select" label="File format" >
+        <option value="BAM" selected="true">BAM</option>
+        <option value="pileup" >Pileup</option>
+        <option value="pileup_gz" >Pileup.gz</option>
+      </param>
+      <when value="BAM">
+        <conditional name="reference_source">
+      	  <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
+            <option value="cached">Locally cached</option>
+            <option value="history">History</option>
+          </param>
+        <when value="cached">
+          <param name="normal_file" type="data" format="bam" label="Normal BAM file" >
+	    <validator type="unspecified_build" />
+            <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> 
+          </param>
+          <param name="tumor_file" type="data" format="bam" label="Tumor BAM file" >
+	    <validator type="unspecified_build" />
+            <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> 
+          </param>
+          <param name="ref_file" type="select" label="Using reference genome">
+            <options from_data_table="sam_fa_indexes">
+          </options>
+          </param>
+        </when>
+        <when value="history">
+          <param name="normal_file" type="data" format="bam" label="Normal BAM file" >
+            <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+          </param>
+          <param name="tumor_file" type="data" format="bam" label="Tumor BAM file" >
+            <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+          </param>
+          <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+        </when>
+        </conditional>
+	<param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" />
+        <param name="disable_probabilistic_realignment" type="boolean" truevalue="-B" falsevalue="" checked="False" label="Disable probabilistic realignment for the computation of base alignment quality (BAQ)" />
+        <param name="max_reads_per_bam" type="integer" value="100000" label="Max reads per BAM" />
+        <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for an alignment to be used" />
+        <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" />
+      </when>
+      <when value="pileup">
+        <param name="normal_file" type="data" format="pileup" label="Normal pileup file" />
+        <param name="tumor_file" type="data" format="pileup" label="Tumor pileup file" />
+      </when>
+      <when value="pileup_gz">
+        <param name="normal_file" type="data" format="pileup.gz" label="Normal pileup.gz file" />
+        <param name="tumor_file" type="data" format="pileup.gz" label="Tumor pileup.gz file" />
+      </when>
+    </conditional >
+    <param name="gc_content_file" type="data" format="txt" label="GC content file" />
+    <conditional name="usePersonalEstimation">
+      <param name="estimation" type="select" label="Do you want to use personal cellularity and ploidy? Otherwise Sequenza estimates cellularity and ploidy" >
+        <option value="no" selected="true">No</option>
+        <option value="yes" >Yes</option>
+      </param>
+      <when value="no" />
+      <when value="yes">
+        <param name="cellularity" type="integer" value="30" min="0" max="100" label="Cellularity used (%)" />
+        <param name="ploidy" type="integer" value="2" label="Ploidy used" />
+      </when>
+    </conditional >
+  </inputs>
+  <outputs>
+    <data format="html" name="HTMLFile" label="HTML output - Sequenza results" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="sampleName" value="test_curie"/>
+      <param name="fileFormat" value="pileup"/>
+      <param name="normal_file" value="constit_2.pileup"/>
+      <param name="tumor_file" value="tumor_2.pileup"/>
+      <param name="gc_content_file" value="hg19_chro1.gc50Base.txt"/>
+      <param name="estimation" value="yes"/>
+      <param name="cellularity" value="30"/>
+      <param name="ploidy" value="2"/>
+      <output name="HTMLFile" file="test_sequenza_1.dat" ftype="html"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
+
+  </help>
+  <citations>
+    <citation type="bibtex">@article{Favero01012015,
+      author = {Favero, F. and Joshi, T. and Marquard, A. M. and Birkbak, N. J. and Krzystanek, M. and Li, Q. and Szallasi, Z. and Eklund, A. C.}, 
+      title = {Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data},
+      volume = {26}, 
+      number = {1}, 
+      pages = {64-70}, 
+      year = {2015}, 
+      doi = {10.1093/annonc/mdu479}, 
+      URL = {http://annonc.oxfordjournals.org/content/26/1/64.abstract}, 
+      eprint = {http://annonc.oxfordjournals.org/content/26/1/64.full.pdf+html}, 
+      journal = {Annals of Oncology} 
+      }</citation>
+    </citations>
+</tool>