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author greg
date Wed, 23 Dec 2015 10:08:24 -0500
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1 <tool id="multigps" name="MultiGPS" version="0.5.0.0">
2 <description>analyzes collections of multi-condition ChIP-seq data</description>
3 <requirements>
4 <requirement type="package" version="4.11.0">meme</requirement>
5 <requirement type="package" version="3.11.0">edger</requirement>
6 <requirement type="package" version="2.14">biocbasics</requirement>
7 </requirements>
8 <command>
9 <![CDATA[
10 ## when I don't run on my mac...
11 ## java -Xmx20G -jar $__tool_directory__/multigps_v0.5.jar
12 mkdir multigps_out &&
13 java -jar $__tool_directory__/multigps_v0.5.jar
14 --threads="\${GALAXY_SLOTS:-4}"
15 --verbose
16 --geninfo ${chromInfo}
17 #if str($use_motif_cond.use_motif) == "yes":
18 #set seq_dir = python "$get_seq_dir"
19 --seq "${seq_dir}"
20 --mememinw $use_motif_cond.min_motif_width
21 --mememaxw $use_motif_cond.max_motif_width
22 --design $design_file
23 #if str($gauss_model_smoothing_cond.gauss_model_smoothing) == "yes":
24 --gaussmodelsmoothing
25 --gausssmoothparam $gauss_model_smoothing_cond.gauss_model_smoothing.gauss_smooth
26 #end if
27 --out multigps_out
28 ]]>
29 </command>
30 <configfiles>
31 <configfile name="design_file">
32 <![CDATA[
33 #for input in $input_files:
34 #set filename = "{$input['input'].filename}"
35 #set signal_control = $input['signal_control']
36 #set format = $input['input'].ext
37 #set condition_name = $input['condition_name']
38 #set replicate_name = $input['replicate_name']
39 #set line = '\t'.join($filename, $signal_control, $format, $condition_name, $replicate_name])
40 ${line}
41 #end for
42 ]]>
43 </configfile>
44 <configfile name="get_seq_dir">
45 <![CDATA[
46 #!/usr/bin/env python
47 import os
48 import tempfile
49
50 # All inputs must have the same dbkey, and MultiGPS requires a directory, not the reference file.
51 if $use_motif_cond.reference_genome_cond.reference_genome_source == "cached":
52 return os.path.split($use_motif_cond.reference_genome_cond.reference_genome.fields.path)[0]
53 else:
54 seq_dir = tempfile.mkdtemp(prefix="tmp-multigps-")
55 # Populate the directory with the history dataset
56 tmp_filename = "%s.fa" % $use_motif_cond.reference_genome_cond.reference_genome.dbkey
57 ln -f -s $use_motif_cond.reference_genome_cond.reference_genome.filename os.path.join(seq_dir, tmp_filename)
58 return seq_dir
59 ]]>
60 </configfile>
61 </configfiles>
62 <inputs>
63 <repeat name="input_files" title="Input Files" min="1">
64 <param name="input" type="data" format="bam,bed,scidx" label="Add file">
65 <validator type="unspecified_build" />
66 </param>
67 <param name="signal_control" type="select" label="Signal or control" display="checkboxes" >
68 <option value="signal" selected="True">Signal</option>
69 <option value="control">Control</option>
70 </param>
71 <param label="Condition name" name="condition_name" type="text" />
72 <param label="Replicate name" name="replicate_name" type="text" />
73
74 <conditional name="use_motif_cond">
75 <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?">
76 <option value="yes" selected="True">Yes</option>
77 <option value="no">No</option>
78 </param>
79 <when value="yes">
80 <conditional name="reference_genome_cond">
81 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
82 <option value="cached">Locally Cached</option>
83 <option value="history">From History</option>
84 </param>
85 <when value="cached">
86 <param name="reference_genome" type="select" label="Using reference genome">
87 <options from_data_table="fasta_indexes"/>
88 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
89 </param>
90 </when>
91 <when value="history">
92 <param name="reference_genome" type="data" format="fasta" label="Using reference genome"/>
93 </when>
94 </conditional>
95 <param name="min_motif_width" type="integer" min="0" value="6" label="Minimum motif width for MEME">
96 <param name="max_motif_width" type="integer" min="0" value="16" label="Maximum motif width for MEME">
97 </when>
98 <when value="no">
99 </conditional>
100
101
102 </repeat>
103
104 <param name="genome_info_file" type="data" format="tabular" label="Genome information dataset" help="What's this? See the help section below."/>
105 <conditional name="gauss_model_smoothing_cond">
106 <param name="gauss_model_smoothing" type="select" label="Turn on Gaussian model smoothing?" help="Smoothing is done with a cubic spline.">
107 <option value="yes" selected="True">Yes</option>
108 <option value="no">No</option>
109 </param>
110 <when value="yes">
111 <param name="gauss_smooth" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." />
112 </when>
113 <when value="no" />
114 </conditional>
115 </inputs>
116 <outputs>
117 <data name="output_report" format="txt" label="MultiGPS-Report"/>
118 <data name="output_gff" format="gff" label="MultiGPS-GFF" />
119 <data name="output_gz" format="gz" label="MultiGPS-GZ" />
120 </outputs>
121 <help>
122
123 **What it does**
124
125 MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing
126 differential binding events between conditions. MultiGPS encourages consistency in the reported binding
127 event locations across conditions and provides accurate estimation of ChIP enrichment levels at each event.
128 MultiGPS loads all data to memory, so you will need a lot of available memory if you are running analysis
129 over many conditions or large datasets.
130
131 -----
132
133 **Options**
134
135 * **Input Files**
136
137 </help>
138 <citations>
139 <citation type="doi">10.1371/journal.pcbi.1003501</citation>
140 </citations>
141 </tool>