# HG changeset patch
# User jbrayet
# Date 1440150345 14400
# Node ID cf16a057e271ff4338a584dfcf44486d16fb9f78
# Parent  8687649c8ec3fc5608fba098b2940b6d8dc1d1ac
Deleted selected files

diff -r 8687649c8ec3 -r cf16a057e271 sequenza_wrapper.py
--- a/sequenza_wrapper.py	Thu Aug 20 05:44:55 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,279 +0,0 @@
-#! /usr/bin/python
-# -*- coding: utf8 -*-
-"""#Sequenza Galaxy - 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/>.
-#
-###########################################################'
-#
-#usage: sequenza_wrapper.py [-h] -normal <NORMAL_FILE> -tumor <TUMOR_FILE>
-#                           -name <SAMPLE_NAME> -gcContent <GC_FILE> -format
-#                           <FILE_FORMAT> -estimation <ESTIMATION>
-#                           [-ref_file <REF_FILE>] [-cellularity <CELLULARITY>]
-#                           [-ploidy <PLOIDY>] [-selector_index <SELECTOR>]
-#                           [-samtools_options <SAMTOOLS_OPTIONS>] -outGalaxy
-#                           <OUT_GALAXY>
-#
-#Run Sequenza with Galaxy.
-#
-#optional arguments:
-#  -h, --help            show this help message and exit
-#  -normal <NORMAL_FILE>, --normalFile <NORMAL_FILE>
-#                        Normal input file (BAM, pileup, pileup.gz).
-#  -tumor <TUMOR_FILE>, --tumorFile <TUMOR_FILE>
-#                        Tumor input file (BAM, pileup, pileup.gz).
-#  -name <SAMPLE_NAME>, --sampleName <SAMPLE_NAME>
-#                        Sample Name.
-#  -gcContent <GC_FILE>, --GCfile <GC_FILE>
-#                        GC content file (txt).
-#  -format <FILE_FORMAT>, --fileFormat <FILE_FORMAT>
-#                        Files format.
-#  -estimation <ESTIMATION>, --usePersonalEstimation <ESTIMATION>
-#                        To use sequenza estimation or not.
-#  -ref_file <REF_FILE>, --refFile <REF_FILE>
-#                        Index file to samtools mpileup.
-#  -cellularity <CELLULARITY>, --cellularityToUsed <CELLULARITY>
-#                        If estimation = no, cellularity used.
-#  -ploidy <PLOIDY>, --ploidyToUsed <PLOIDY>
-#                        If estimation = no, plody used.
-#  -selector_index <SELECTOR>, --selector <SELECTOR>
-#                        Source for the reference list.
-#  -samtools_options <SAMTOOLS_OPTIONS>, --samtoolsOptions <SAMTOOLS_OPTIONS>
-#                        Samtools options (-A, -B, -d, -q and -Q).
-#  -outGalaxy <OUT_GALAXY>, --outGalaxy <OUT_GALAXY>
-#
-#Version 1.2 - 05/08/2015 - Adapted from Jocelyn Brayet, France Genomique team
-#
-###########################################################"""
-__author__ =  'Jocelyn Brayet'
-
-###########################################################'
-## Import
-
-import argparse
-import glob
-import os
-import signal
-import subprocess
-
-## Tested with python 2.6.6
-sequenzaVersion = '1.2 - 05/08/2015'
-
-################################ functions ############################################################
-## Define a function to test arguments
-
-def testNone(argument):
-	"""
-	Test if argument is None or not.
-		argument -> argument gived by user (XML file)
-	"""
-
-	if not argument is None:
-		variable = argument[0]
-	else:
-		variable = ""
-	return variable
-
-def subprocess_setup():
-	""" 
-	Python installs a SIGPIPE handler by default. This is usually not what non-Python subprocesses expect.
-	"""
-
-	signal.signal(signal.SIGPIPE, signal.SIG_DFL)
-
-def createHTML(resultFile,resultPath,sample):
-	"""
-	Building a result HTML displayed in Galaxy.
-		resultFile -> HTML file
-		resultPath -> Galaxy result path
-		sample -> sample name
-	"""
-
-	resultHTML=open(resultFile,"w")
-
-	cmdLine="cd "+resultPath.replace(os.path.basename(resultPath),"")+"; tar czf all_files.tar.gz "+os.path.basename(resultPath)
-	os.system(cmdLine)
-	os.system("mv "+resultPath.replace(os.path.basename(resultPath),"")+"all_files.tar.gz "+resultPath)
-
-	resultHTML.write("<html>\n<head>\n</head>\n<body>\n")
-	resultHTML.write("<h1><a target='_top' href='http://cran.r-project.org/web/packages/sequenza/index.html'>Sequenza</a> - results</h1>\n")
-	resultHTML.write("<p align='center'>\n<table width=70% border=1>\n<font size='30pt'><tr>\n<th colspan=3>Additional files</th>\n</tr>\n")
-	resultHTML.write("<tr>\n<td><a href='out.seqz.gz'>Out Sequenza</a><br><a href='out.small.seqz.gz'>Out small Sequenza</a></td>\n<td><a href='"+sample+"_sequenza_cp_table.RData'>Cellularity and ploidy matrix (RData)</a><br><a href='"+sample+"_sequenza_extract.RData'>Sequenza extract (RData)</a></td><td><a href='logFile.txt'>Log file</a><br><a href='all_files.tar.gz'>All files</a></td>\n</tr>\n")
-	resultHTML.write("</font>\n</table>\n</p>\n")
-	resultHTML.write("<h2>Genome-wide view of the allele and copy number state</h2>\n")
-	resultHTML.write("<p align='center'><embed src='"+sample+"_analyse.pdf' width='800px' height='590px'></p>\n")
-	resultHTML.write("<p align='center'>Genome-wide allele-specific copy number profile obtained from exome sequencing (top), genome-wide absolute copy number profile obtained from exome sequencing (middle) and depth ratio (bottom).</p>\n")
-
-	fileList=glob.glob(resultPath+"/segments_*.txt")
-	alternativeSolutionsList=""
-
-	for segmentsFile in fileList:
-		if not "segments_1.txt" in segmentsFile:
-			alternativeSolutionsList = alternativeSolutionsList+" "+segmentsFile
-
-	os.system("mkdir "+resultPath+"/segments")
-	os.system("mv "+alternativeSolutionsList+" "+resultPath+"/segments")
-	cmdLine="cd "+resultPath+"; tar czf "+sample+"_segments.tar.gz segments"
-	os.system(cmdLine)
-
-	resultHTML.write("<p align='center'>File (best solution or user solution): <a href='"+sample+"_segments.txt'>Segments</a></p>\n")
-	resultHTML.write("<p align='center'>File (alternative solutions): <a href='"+sample+"_segments.tar.gz'>Segments</a></p>\n")
-	resultHTML.write("<p align='center'>File : <a href='"+sample+"_mutations.txt'>Mutations</a></p>\n")
-	resultHTML.write("<h2>Confidence intervals, confidence region and point estimate</h2>\n")
-	resultHTML.write("<p align='center'><embed src='"+sample+"_CP_contours.pdf' width='580px' height='580px'></p>\n")
-	resultHTML.write("<p align='center'>Result from the inference over the defined range of cellularity and ploidy. Color intensity indicates the log posterior probability of corresponding cellularity/ploidy values.</p>\n")
-	resultHTML.write("<p align='center'><embed src='"+sample+"_CN_bars.pdf' width='580px' height='580px'></p>\n")
-	resultHTML.write("<p align='center'><embed src='"+sample+"_model_fit.pdf' width='580px' height='580px'></p>\n")
-	resultHTML.write("<p align='center'>Observed depth ratio and BAF values for each genomic segment (black circles and dots) along with the representative joint LPP density (colors). The representative joint LPP density is calculated for the best cellularity and ploidy.</p>\n")
-	resultHTML.write("<p align='center'>File : <a href='"+sample+"_cellularity_ploidy.txt'>Cellularity and ploidy</a></p>\n")
-	resultHTML.write("<p align='center'><embed src='"+sample+"_alternative_fit.pdf' width='580px' height='580px'></p>\n")
-	resultHTML.write("<p align='center'>Observed depth ratio and BAF values for each genomic segment (black circles and dots) along with the representative joint LPP density (colors). The representative joint LPP density is calculated for the alternative cellularity and ploidy (scroll).</p>\n")        
-	resultHTML.write("<p align='center'>File : <a href='"+sample+"_alternative_solutions.txt'>Alternative solutions</a></p>\n")
-	resultHTML.write("<h2>Normalization of depth ratio</h2>\n")
-	resultHTML.write("<p align='center'><a href='"+sample+"_gc_stat.png'><img border='1' width='680px' height='300px' src='"+sample+"_gc_stat.png'></a></p>\n")
-	resultHTML.write("<p align='center'>Visualization of depth.ratio bias in relation of GC content (left), and resulting normalization effect (right)</p>\n")
-	resultHTML.write("<h2>Plot chromosome view with mutations, BAF, depth ratio and segments (best solution or user solution)</h2>\n")
-	resultHTML.write("<p align='center'><embed src='"+sample+"_chromosome_view.pdf' width='680px' height='680px'></p>\n")
-	resultHTML.write("<p align='center'>Plots of mutant allele frequency (top), B allele frequency (middle) and depth ratio (bottom) vs. chromosome position (scroll).</p>\n")
-	resultHTML.write("</body>\n</html>")
-	resultHTML.close()
-
-if __name__ == '__main__':
-
-	########### sequenza arguments ####################
-	parser = argparse.ArgumentParser(description='Run Sequenza with Galaxy.', epilog='Version '+sequenzaVersion)
-	
-	parser.add_argument('-normal', '--normalFile', metavar='<NORMAL_FILE>', type=str, nargs=1, help='Normal input file (BAM, pileup, pileup.gz).', required=True)
-	parser.add_argument('-tumor', '--tumorFile', metavar='<TUMOR_FILE>', type=str, nargs=1, help='Tumor input file (BAM, pileup, pileup.gz).', required=True)
-	parser.add_argument('-name', '--sampleName', metavar='<SAMPLE_NAME>', type=str, nargs=1, help='Sample Name.', required=True)
-	parser.add_argument('-gcContent', '--GCfile', metavar='<GC_FILE>', type=str, nargs=1, help='GC content file (txt).', required=True)
-	parser.add_argument('-format', '--fileFormat', metavar='<FILE_FORMAT>', type=str, nargs=1, help='Files format.', required=True)
-	parser.add_argument('-estimation', '--usePersonalEstimation', metavar='<ESTIMATION>', type=str, nargs=1, help='To use sequenza estimation or not.', required=True)
-	parser.add_argument('-ref_file', '--refFile', metavar='<REF_FILE>', type=str, nargs=1, help='Index file to samtools mpileup.', required=False)
-	parser.add_argument('-cellularity', '--cellularityToUsed', metavar='<CELLULARITY>', type=int, nargs=1, help='If estimation = no, cellularity used.', required=False)
-	parser.add_argument('-ploidy', '--ploidyToUsed', metavar='<PLOIDY>', type=int, nargs=1, help='If estimation = no, plody used.', required=False)
-	parser.add_argument('-selector_index', '--selector', metavar='<SELECTOR>', type=str, nargs=1, help='Source for the reference list.', required=False)
-	parser.add_argument('-samtools_options', '--samtoolsOptions', metavar='<SAMTOOLS_OPTIONS>', type=str, nargs=1, help='Samtools options (-A, -B, -d, -q and -Q).', required=False)
-
-	################################ galaxy arguments ############################################################
-	parser.add_argument('-outGalaxy', '--outGalaxy', metavar='<OUT_GALAXY>', type=str, nargs=1, required=True)
-	###########################################################'
-
-	args = parser.parse_args()
-
-	normalFile = testNone(args.normalFile)
-	tumorFile = testNone(args.tumorFile)
-	sampleName = testNone(args.sampleName)
-	gcContent = testNone(args.GCfile)
-	fileFormat = testNone(args.fileFormat)
-	usePersonalEstimation = testNone(args.usePersonalEstimation)
-	refFile = testNone(args.refFile)
-	cellularityToUsed = testNone(args.cellularityToUsed)
-	ploidyToUsed = testNone(args.ploidyToUsed)
-	selector = testNone(args.selector)
-	samtoolsOptions = testNone(args.samtoolsOptions)
-	outGalaxyValue = testNone(args.outGalaxy)
-
-	################Rscrip PATH#################
-	RscriptPath = "Rscript --vanilla "
-	############################################
-
-	pathFile = os.path.dirname(os.path.realpath(__file__))
-	samtoolsPath = pathFile.replace("copy_number","samtools/")
-        outGalaxyValueDir = outGalaxyValue.replace(".dat","_files")
-	os.popen("mkdir "+outGalaxyValueDir)
-	os.popen("chmod 777 -R "+outGalaxyValueDir)
-
-	log = open(outGalaxyValueDir+"/logFile.txt", "w")
-
-	log.write(samtoolsOptions)
-
-	if fileFormat=="BAM" :
-		if selector=="cached":
-			
-			cmd=samtoolsPath+"samtools_wrapper.py -p 'samtools mpileup' -p \'-f \""+refFile+"\"\' -d \" \" \""+normalFile+"\" \"bam\" \"bam_normal\" -p\' "+samtoolsOptions+" > \""+normalFile+".tmp\" \'"
-			proc = subprocess.Popen( args=cmd, shell=True)
-        		proc.wait()
-			os.system("gzip -f -c "+normalFile+".tmp > "+normalFile+".gz")
-			os.system("rm -f "+normalFile+".tmp")
-
-			cmd=samtoolsPath+"samtools_wrapper.py -p 'samtools mpileup' -p \'-f \""+refFile+"\"\' -d \" \" \""+tumorFile+"\" \"bam\" \"bam_normal\" -p\' "+samtoolsOptions+" > \""+tumorFile+".tmp\" \'"
-			proc = subprocess.Popen( args=cmd, shell=True)
-        		proc.wait()
-			os.system("gzip -f -c "+tumorFile+".tmp > "+tumorFile+".gz")
-			os.system("rm -f "+tumorFile+".tmp")
-
-		else:
-
-			cmd=samtoolsPath+"samtools_wrapper.py -p 'samtools mpileup' -d \'-f \""+refFile+"\"\' \"fa\" \"reference_input\" -d \" \" \""+normalFile+"\" \"bam\" \"bam_normal\" -p\' "+samtoolsOptions+" > \""+normalFile+".tmp\" \'"
-			proc = subprocess.Popen( args=cmd, shell=True)
-        		proc.wait()
-			os.system("gzip -f -c "+normalFile+".tmp > "+normalFile+".gz")
-			os.system("rm -f "+normalFile+".tmp")
-
-			cmd=samtoolsPath+"samtools_wrapper.py -p 'samtools mpileup' -d \'-f \""+refFile+"\"\' \"fa\" \"reference_input\" -d \" \" \""+tumorFile+"\" \"bam\" \"bam_normal\" -p\' "+samtoolsOptions+" > \""+tumorFile+".tmp\" \'"
-			proc = subprocess.Popen( args=cmd, shell=True)
-        		proc.wait()
-			os.system("gzip -f -c "+tumorFile+".tmp > "+tumorFile+".gz")
-			os.system("rm -f "+tumorFile+".tmp")
-
-	if fileFormat=="pileup" :
-		os.system("gzip -f -c "+normalFile+" > "+ normalFile+".gz")
-		os.system("gzip -f -c "+tumorFile+" > "+tumorFile+".gz")
-
-	if fileFormat=="pileup_gz" :
-		os.system("cp -f "+normalFile+" "+normalFile+".gz")
-		os.system("cp -f "+tumorFile+" "+tumorFile+".gz")
-
-	
-
-
-	#############################################################
-
-	if usePersonalEstimation=="yes":
-
-		cellularityToUsed = float(cellularityToUsed)/100
-		command = RscriptPath+pathFile+"/Sequenza_analysis.R -normal "+normalFile+".gz"+" -tumor "+tumorFile+".gz"+" -out "+outGalaxyValueDir+" -gcContent "+gcContent+" -name "+sampleName+ " -cellularity "+str(cellularityToUsed)+" -ploidy "+str(ploidyToUsed)
-		log.write(str(command))
-
-		Rscrpit = subprocess.Popen(command, preexec_fn=subprocess_setup, stdout=log, stderr=log, shell=True)
-		Rscrpit.wait()
-
-	else :
-
-		command = RscriptPath+pathFile+"/Sequenza_analysis.R -normal "+normalFile+".gz"+" -tumor "+tumorFile+".gz"+" -out "+outGalaxyValueDir+" -gcContent "+gcContent+" -name "+sampleName+ " -cellularity 0 -ploidy 0"
-		log.write(str(command))
-
-		Rscrpit = subprocess.Popen(command, preexec_fn=subprocess_setup, stdout=log, stderr=log, shell=True)
-		Rscrpit.wait()
-
-	#############################################################
-
-	createHTML(outGalaxyValue,outGalaxyValueDir,sampleName)
-
-
-	log.close()
-
-	
-
-
-
-
-
-
-
-
-
-
diff -r 8687649c8ec3 -r cf16a057e271 sequenza_wrapper.xml
--- a/sequenza_wrapper.xml	Thu Aug 20 05:44:55 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,160 +0,0 @@
-<!--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="2.11.1">fontconfig</requirement>
-    <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>