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1 <tool id="multigps" name="MultiGPS" version="0.5.0.0">
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2 <description>analyzes collections of multi-condition ChIP-seq data</description>
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3 <requirements>
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4 <requirement type="package" version="4.11.0">meme</requirement>
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5 <requirement type="package" version="3.11.0">edger</requirement>
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6 <requirement type="package" version="2.14">biocbasics</requirement>
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7 </requirements>
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8 <command>
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9 <![CDATA[
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10 ## when I don't run on my mac...
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11 ## java -Xmx20G -jar $__tool_directory__/multigps_v0.5.jar
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12 mkdir multigps_out &&
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13 java -jar $__tool_directory__/multigps_v0.5.jar
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14 --threads="\${GALAXY_SLOTS:-4}"
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15 --verbose
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16 --geninfo ${chromInfo}
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17 #if str($use_motif_cond.use_motif) == "yes":
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18 #set seq_dir = python "$get_seq_dir"
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19 --seq "${seq_dir}"
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20 --mememinw $use_motif_cond.min_motif_width
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21 --mememaxw $use_motif_cond.max_motif_width
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22 --design $design_file
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23 #if str($gauss_model_smoothing_cond.gauss_model_smoothing) == "yes":
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24 --gaussmodelsmoothing
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25 --gausssmoothparam $gauss_model_smoothing_cond.gauss_model_smoothing.gauss_smooth
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26 #end if
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27 --out multigps_out
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28 ]]>
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29 </command>
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30 <configfiles>
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31 <configfile name="design_file">
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32 <![CDATA[
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33 #for input in $input_files:
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34 #set filename = "{$input['input'].filename}"
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35 #set signal_control = $input['signal_control']
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36 #set format = $input['input'].ext
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37 #set condition_name = $input['condition_name']
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38 #set replicate_name = $input['replicate_name']
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39 #set line = '\t'.join($filename, $signal_control, $format, $condition_name, $replicate_name])
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40 ${line}
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41 #end for
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42 ]]>
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43 </configfile>
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44 <configfile name="get_seq_dir">
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45 <![CDATA[
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46 #!/usr/bin/env python
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47 import os
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48 import tempfile
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49
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50 # All inputs must have the same dbkey, and MultiGPS requires a directory, not the reference file.
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51 if $use_motif_cond.reference_genome_cond.reference_genome_source == "cached":
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52 return os.path.split($use_motif_cond.reference_genome_cond.reference_genome.fields.path)[0]
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53 else:
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54 seq_dir = tempfile.mkdtemp(prefix="tmp-multigps-")
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55 # Populate the directory with the history dataset
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56 tmp_filename = "%s.fa" % $use_motif_cond.reference_genome_cond.reference_genome.dbkey
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57 ln -f -s $use_motif_cond.reference_genome_cond.reference_genome.filename os.path.join(seq_dir, tmp_filename)
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58 return seq_dir
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59 ]]>
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60 </configfile>
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61 </configfiles>
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62 <inputs>
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63 <repeat name="input_files" title="Input Files" min="1">
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64 <param name="input" type="data" format="bam,bed,scidx" label="Add file">
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65 <validator type="unspecified_build" />
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66 </param>
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67 <param name="signal_control" type="select" label="Signal or control" display="checkboxes" >
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68 <option value="signal" selected="True">Signal</option>
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69 <option value="control">Control</option>
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70 </param>
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71 <param label="Condition name" name="condition_name" type="text" />
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72 <param label="Replicate name" name="replicate_name" type="text" />
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73
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74 <conditional name="use_motif_cond">
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75 <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?">
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76 <option value="yes" selected="True">Yes</option>
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77 <option value="no">No</option>
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78 </param>
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79 <when value="yes">
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80 <conditional name="reference_genome_cond">
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81 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
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82 <option value="cached">Locally Cached</option>
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83 <option value="history">From History</option>
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84 </param>
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85 <when value="cached">
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86 <param name="reference_genome" type="select" label="Using reference genome">
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87 <options from_data_table="fasta_indexes"/>
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88 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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89 </param>
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90 </when>
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91 <when value="history">
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92 <param name="reference_genome" type="data" format="fasta" label="Using reference genome"/>
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93 </when>
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94 </conditional>
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95 <param name="min_motif_width" type="integer" min="0" value="6" label="Minimum motif width for MEME">
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96 <param name="max_motif_width" type="integer" min="0" value="16" label="Maximum motif width for MEME">
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97 </when>
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98 <when value="no">
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99 </conditional>
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100
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101
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102 </repeat>
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103
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104 <param name="genome_info_file" type="data" format="tabular" label="Genome information dataset" help="What's this? See the help section below."/>
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105 <conditional name="gauss_model_smoothing_cond">
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106 <param name="gauss_model_smoothing" type="select" label="Turn on Gaussian model smoothing?" help="Smoothing is done with a cubic spline.">
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107 <option value="yes" selected="True">Yes</option>
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108 <option value="no">No</option>
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109 </param>
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110 <when value="yes">
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111 <param name="gauss_smooth" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." />
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112 </when>
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113 <when value="no" />
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114 </conditional>
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115 </inputs>
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116 <outputs>
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117 <data name="output_report" format="txt" label="MultiGPS-Report"/>
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118 <data name="output_gff" format="gff" label="MultiGPS-GFF" />
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119 <data name="output_gz" format="gz" label="MultiGPS-GZ" />
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120 </outputs>
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121 <help>
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122
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123 **What it does**
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124
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125 MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing
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126 differential binding events between conditions. MultiGPS encourages consistency in the reported binding
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127 event locations across conditions and provides accurate estimation of ChIP enrichment levels at each event.
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128 MultiGPS loads all data to memory, so you will need a lot of available memory if you are running analysis
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129 over many conditions or large datasets.
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130
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131 -----
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132
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133 **Options**
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134
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135 * **Input Files**
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136
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137 </help>
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138 <citations>
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139 <citation type="doi">10.1371/journal.pcbi.1003501</citation>
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140 </citations>
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141 </tool>
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