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1 <tool id="hmcan" name="HMCan" version="1.11">
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2 <description>Histone Modification detection in Cancer samples</description>
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3 <requirements>
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4 <container type="docker">institutcuriengsintegration/hmcan:1.0</container>
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5 </requirements>
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6 <command interpreter="python">hmcan_wrapper.py '${input_chip_file}' '${input_control_file}' '${hmcan_config_file}' '${gccount_config_file}' '${project_name}' '${output_peaks_file}' '${output_regions_file}' '${output_density_file}' '${output_posterior_proba_file}' '${hmcan_log_report}' '$genome['chr_len_file']' '${file_format}' '${genome.genome_selector}' '${__root_dir__}' 2> '${hmcan_log_report}'</command>
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7
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8
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9 <!--
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10 ###NoteToSelf:
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11 in this version, you still need to :
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12 -Get the correct paths to mappability.GEM
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13 - go to hmcan_wrapper.py
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14 - set the correct paths to binary files (HMCAN, GCCOUNT)
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15 -->
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16
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17 <!-- INPUT DESCRIPTION -->
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18 <inputs>
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19 <!-- project name-->
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20 <param name="project_name" type="text" size="20" label="Project name" help="NOTE: spaces are not allowed.">
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21 <validator type="empty_field" message="You must specify a file name."/>
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22 </param>
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23
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24 <!-- input files NB: format= only if attribute type is data, formats (bed,sam..) are contained in datatypes_conf.xml.sample f-->
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25 <param name="input_chip_file" type="data" format="bed,sam,bam" label="ChIP seq alignment file"/>
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26 <param name="input_control_file" type="data" format="bed,sam,bam" label="Control alignment file"/>
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27 <!-- format-->
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28 <param name="file_format" type="select" label="Select alignment format">
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29 <option value="bed" selected="true">BED</option>
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30 <option value="bam">BAM</option>
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31 <option value="sam">SAM</option>
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32 </param>
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33 <!-- lengths-->
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34 <param name="min_len" type="integer" value="145" label="Minumum fragment length used in the ChIP-seq experiment"/>
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35 <param name="med_len" type="integer" value="150" label="Median fragment length used in the ChIP-seq experiment"/>
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36 <param name="max_len" type="integer" value="155" label="Maximum fragment length used in the ChIP-seq experiment"/>
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37 <param name="bin_size" type="integer" value="50" label="Bin size"/>
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38 <param name="merge_dist" type="integer" value="2000" label="Merge distance" help=" Maximum distance to merge single peaks into a region.This parameter should be set with respect to the nature of the mark; narrow marks (e.g H3K4me1, H3K4me3) can cover 200bp-2Kb, wide marks (e.g. H3K36me3, H3K27me3) can cover 10Kb-100Kb."/>
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39
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40 <param name="p_value" type="float" value="0.01" label="P Value"/>
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41 <param name="input_blacklist_file" type="data" format="bed" label=".BED file with blacklist regions" help="An example of such a bed file for hg19 can be found here: http://xfer.curie.fr/get/GaQHuEopJTw/hg19-blacklist.bed"/>
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42 <!-- SELECT GENOME UNDER STUDY (hg19, hg18, hg38,mm9, mm10)-->
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43 <!-- Each genome is associated with :
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44 ** Mappability Track
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45 ** chr_length file: -->
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46 <conditional name="genome">
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47 <param name="genome_selector" type="select" label="Select the version of the genome under study">
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48 <option value="hg19" selected="true">hg19</option>
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49 <option value="hg18">hg18</option>
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50 <option value="mm10">mm10</option>
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51 <option value="mm9">mm9</option>
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52 </param>
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53 <!-- set the correct genome_path / mappability / chr_len for all genomes! -->
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54 <when value="hg18">
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55 <param name="genome_path" type="hidden" value="/galaxy/annotations"/>
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56 <param name="mappability" type="hidden" value="/galaxy/annotations"/>
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57 <param name="chr_len_file" type="hidden" value="/galaxy/annotations"/>
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58 </when>
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59 <when value="hg19">
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60 <param name="genome_path" type="hidden" value="/galaxy/annotations"/>
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61 <param name="mappability" type="hidden" value="/galaxy/annotations"/>
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62 <param name="chr_len_file" type="hidden" value="/galaxy/annotations"/>
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63 </when>
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64 <when value="mm9">
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65 <param name="genome_path" type="hidden" value="/galaxy/annotations"/>
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66 <param name="mappability" type="hidden" value="/galaxy/annotations"/>
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67 <param name="chr_len_file" type="hidden" value="/galaxy/annotations"/>
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68 </when>
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69 <when value="mm10">
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70 <param name="genome_path" type="hidden" value="/galaxy/annotations"/>
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71 <param name="mappability" type="hidden" value="/galaxy/annotations"/>
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72 <param name="chr_len_file" type="hidden" value="/galaxy/annotations"/>
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73 </when>
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74
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75 </conditional>
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76 <!-- Booleans + LOGING-->
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77 <param name="print_wig" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Print density profil in WIG file" />
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78 <param name="print_posterior_proba" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Print bins posterior probabilites in WIG format" />
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79 <param name="print_logging" type="boolean" truevalue= "True" falsevalue="False" checked="true" label="Print HMCan log"/>
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80 <!-- HMM advanced-->
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81 <conditional name="option_type">
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82 <param name="option_type_selector" type="select" label="Advanced options">
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83 <option value="basic" selected="true">Hide advanced options</option>
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84 <option value="advanced">Show advanced options</option>
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85 </param>
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86 <!-- WHENS-->
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87 <when value="basic"/>
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88 <when value="advanced"> <!-- if advanced create HHM parameters form-->
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89 <param name="max_iter" type="integer" value="20" label="Maximun interation for HMCan algorithm"/>
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90 <param name="iteration_score_threshold" type="integer" value="2" label="Iteration score threshold" help="minimum score to accept a peak into the next iteration"/>
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91 <param name="final_score_threshold" type="integer" value="0" label="Score threshold" help="score threshold to report peak or regions"/>
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92 </when>
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93
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94 </conditional>
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95 </inputs>
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96
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97 <!-- OUTPUT DESCRIPTION -->
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98 <outputs>
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99 <data name="output_peaks_file" format="bed" label="${project_name} histone peaks (bed)"/>
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100 <data name="output_regions_file" format="bed" label="${project_name} histone regions (bed)"/>
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101
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102 <!-- <filter>if this is true, data will be created as normal</filter> -->
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103 <data name="output_density_file" format="wig" label="${project_name} density profile (wig)">
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104 <filter>print_wig==True</filter>
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105 </data>
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106
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107 <data name="output_posterior_proba_file" format="wig" label="${project_name} peaks prosterior probability (wig)">
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108 <filter>print_posterior_proba==True</filter>
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109 </data>
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110
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111 <data name="hmcan_log_report" format="txt" label="${tool.name} log report (txt)">
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112 <filter> print_logging==True</filter>
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113 </data>
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114 </outputs>
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115
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116 <configfiles>
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117 <configfile name="hmcan_config_file">format ${file_format}
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118 GCIndex
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119 genomePath $genome['genome_path'] <!-- /data/tmp/amira/example_seq-->
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120 minLength ${min_len}
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121 medLength ${med_len}
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122 maxLength ${max_len}
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123 smallBinLength ${bin_size}
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124 largeBinLength
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125 pvalueThreshold ${p_value}
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126 mergeDistance ${merge_dist}
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127 blackListFile ${input_blacklist_file}
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128 #if str($option_type ['option_type_selector'])=="advanced":
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129 iterationThreshold ${option_type['iteration_score_threshold']}
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130 finalThreshold ${option_type['final_score_threshold']}
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131 maxIter ${option_type['max_iter']}
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132 #else:
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133 iterationThreshold 5
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134 finalThreshold 10
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135 maxIter 20
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136 #end if
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137 PrintWig ${print_wig}
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138 PrintPosterior ${print_posterior_proba}
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139 </configfile>
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140 <configfile name="gccount_config_file">[general]
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141
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142 window =
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143 step =
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144 outputDir = .
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145 chrFiles = $genome['genome_path']
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146 chrLenFile = $genome['chr_len_file']
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147 gemMappabilityFile = $genome['mappability']
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148 </configfile>
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149 </configfiles>
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150
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151 <help>
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152 **What it does**
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153
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154 HMCan detects histone modifications in cancer samples.
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155
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156 **Cite HMCan**
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157
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158 If you use this tool, please cite : HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.Haitham Ashoor; Aurelie Herault; Aurelie Kamoun; Francois Radvanyi; Vladimir B. Bajic; Emmanuel Barillot; Valentina Boeva.Bioinformatics 2013; doi: 10.1093/bioinformatics/btt524
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159
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160 </help>
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161 </tool>
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162
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