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1 <!--Sequenza - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
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2 Copyright (C) 2015 Institut Curie
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3
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4 This program is free software: you can redistribute it and/or modify
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5 it under the terms of the GNU General Public License as published by
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6 the Free Software Foundation, either version 3 of the License, or
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7 (at your option) any later version.
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8
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9 This program is distributed in the hope that it will be useful,
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10 but WITHOUT ANY WARRANTY; without even the implied warranty of
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11 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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12 GNU General Public License for more details.
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13
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14 You should have received a copy of the GNU General Public License
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15 along with this program. If not, see <http://www.gnu.org/licenses/>.-->
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16 <tool id="sequenza_tool" name="Sequenza" version="1.2">
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17 <description>allele-specific copy number and mutation profiles</description>
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18 <requirements>
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19 <requirement type="package" version="2.7">python</requirement>
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20 <requirement type="package" version="2.1.1">sequenza</requirement>
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21 </requirements>
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22 <command interpreter="python">
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23 sequenza_wrapper.py -name $sampleName -outGalaxy $HTMLFile -format $fileFormat.format -estimation $usePersonalEstimation.estimation -gcContent $gc_content_file
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24 #if $fileFormat.format == "BAM":
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25 #if $fileFormat.reference_source.reference_source_selector=="cached":
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26 -selector $fileFormat.reference_source.reference_source_selector
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27 -normal $fileFormat.reference_source.normal_file
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28 -tumor $fileFormat.reference_source.tumor_file
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29 -ref_file $fileFormat.reference_source.ref_file.fields.path
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30 -samtools_options '
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31 $fileFormat.skip_anomalous_read_pairs
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32 $fileFormat.disable_probabilistic_realignment
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33 -d "$fileFormat.max_reads_per_bam"
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34 -q "$fileFormat.minimum_mapping_quality"
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35 -Q "$fileFormat.minimum_base_quality"
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36 '
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37 #else:
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38 -selector $fileFormat.reference_source.reference_source_selector
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39 -normal $fileFormat.reference_source.normal_file
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40 -tumor $fileFormat.reference_source.tumor_file
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41 -ref_file $fileFormat.reference_source.ref_file
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42 #end if
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43 #else:
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44 -normal $fileFormat.normal_file
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45 -tumor $fileFormat.tumor_file
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46 #end if
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47 #if $usePersonalEstimation.estimation == "yes":
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48 -cellularity $usePersonalEstimation.cellularity
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49 -ploidy $usePersonalEstimation.ploidy
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50 #end if
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51 </command>
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52 <inputs>
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53 <param name="sampleName" type="text" value="sample" size="30" label="Sample name">
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54 <sanitizer invalid_char="">
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55 <valid initial="string.letters,string.digits"><add value="_"/></valid>
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56 </sanitizer>
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57 </param>
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58 <conditional name="fileFormat">
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59 <param name="format" type="select" label="File format" >
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60 <option value="BAM" selected="true">BAM</option>
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61 <option value="pileup" >Pileup</option>
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62 <option value="pileup_gz" >Pileup.gz</option>
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63 </param>
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64 <when value="BAM">
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65 <conditional name="reference_source">
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66 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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67 <option value="cached">Locally cached</option>
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68 <option value="history">History</option>
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69 </param>
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70 <when value="cached">
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71 <param name="normal_file" type="data" format="bam" label="Normal BAM file" >
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72 <validator type="unspecified_build" />
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73 <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." />
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74 </param>
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75 <param name="tumor_file" type="data" format="bam" label="Tumor BAM file" >
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76 <validator type="unspecified_build" />
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77 <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." />
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78 </param>
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79 <param name="ref_file" type="select" label="Using reference genome">
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80 <options from_data_table="sam_fa_indexes">
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81 </options>
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82 </param>
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83 </when>
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84 <when value="history">
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85 <param name="normal_file" type="data" format="bam" label="Normal BAM file" >
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86 <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."/>
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87 </param>
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88 <param name="tumor_file" type="data" format="bam" label="Tumor BAM file" >
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89 <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."/>
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90 </param>
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91 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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92 </when>
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93 </conditional>
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94 <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" />
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95 <param name="disable_probabilistic_realignment" type="boolean" truevalue="-B" falsevalue="" checked="False" label="Disable probabilistic realignment for the computation of base alignment quality (BAQ)" />
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96 <param name="max_reads_per_bam" type="integer" value="100000" label="Max reads per BAM" />
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97 <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for an alignment to be used" />
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98 <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" />
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99 </when>
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100 <when value="pileup">
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101 <param name="normal_file" type="data" format="pileup" label="Normal pileup file" />
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102 <param name="tumor_file" type="data" format="pileup" label="Tumor pileup file" />
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103 </when>
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104 <when value="pileup_gz">
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105 <param name="normal_file" type="data" format="pileup.gz" label="Normal pileup.gz file" />
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106 <param name="tumor_file" type="data" format="pileup.gz" label="Tumor pileup.gz file" />
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107 </when>
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108 </conditional >
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109 <param name="gc_content_file" type="data" format="txt" label="GC content file" />
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110 <conditional name="usePersonalEstimation">
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111 <param name="estimation" type="select" label="Do you want to use personal cellularity and ploidy? Otherwise Sequenza estimates cellularity and ploidy" >
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112 <option value="no" selected="true">No</option>
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113 <option value="yes" >Yes</option>
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114 </param>
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115 <when value="no" />
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116 <when value="yes">
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117 <param name="cellularity" type="integer" value="30" min="0" max="100" label="Cellularity used (%)" />
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118 <param name="ploidy" type="integer" value="2" label="Ploidy used" />
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119 </when>
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120 </conditional >
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121 </inputs>
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122 <outputs>
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123 <data format="html" name="HTMLFile" label="HTML output - Sequenza results" />
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124 </outputs>
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125 <tests>
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126 <test>
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127 <param name="sampleName" value="test_curie"/>
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128 <param name="fileFormat" value="pileup"/>
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129 <param name="normal_file" value="constit_2.pileup"/>
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130 <param name="tumor_file" value="tumor_2.pileup"/>
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131 <param name="gc_content_file" value="hg19_chro1.gc50Base.txt"/>
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132 <param name="estimation" value="yes"/>
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133 <param name="cellularity" value="30"/>
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134 <param name="ploidy" value="2"/>
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135 <output name="HTMLFile" file="test_sequenza_1.dat" ftype="html"/>
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136 </test>
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137 </tests>
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138 <help>
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139
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140 **What it does**
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141
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142 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.
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143
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144 </help>
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145 <citations>
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146 <citation type="bibtex">@article{Favero01012015,
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147 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.},
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148 title = {Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data},
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149 volume = {26},
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150 number = {1},
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151 pages = {64-70},
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152 year = {2015},
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153 doi = {10.1093/annonc/mdu479},
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154 URL = {http://annonc.oxfordjournals.org/content/26/1/64.abstract},
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155 eprint = {http://annonc.oxfordjournals.org/content/26/1/64.full.pdf+html},
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156 journal = {Annals of Oncology}
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157 }</citation>
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158 </citations>
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159 </tool>
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