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date Thu, 27 Sep 2012 13:37:59 -0400
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1 <tool id="cg_junctiondiff" name="junctiondiff(beta) 1.6" version="1.0.1">
2 <!--
3 This tool creates a GUI for the junctiondiff function of cgatools from Complete Genomics, Inc.
4 written 6-18-2012 by bcrain@completegenomics.com
5 updated 8-14-2012 by bcrain@completegenomics.com
6 -->
7
8 <description>reports difference between junction calls</description>
9
10 <command>
11 <!-- print version of cgatools to STDOUT-->
12 cgatools | head -1;
13
14 <!-- print command lines to STDOUT-->
15 echo "cgatools junctiondiff --beta
16 --reference $crr.fields.path
17 --junctionsA $data_sources.inputA
18 --junctionsB $data_sources.inputB
19 --scoreThresholdA $scoreA
20 --scoreThresholdB $scoreB
21 --distance $distance
22 --minlength $minlength
23 --output-prefix cg_
24 $stat
25 ";
26
27 <!-- execute cgatools-->
28 cgatools junctiondiff --beta
29 --reference $crr.fields.path
30 --junctionsA $data_sources.inputA
31 --junctionsB $data_sources.inputB
32 --scoreThresholdA $scoreA
33 --scoreThresholdB $scoreB
34 --distance $distance
35 --minlength $minlength
36 --output-prefix cg_
37 $stat
38 ;
39 mv cg_diff-*tsv cg_diff.tsv
40 </command>
41
42 <outputs>
43 <data format="tabular" name="output1" from_work_dir="cg_diff.tsv" label="${tool.name} diff"/>
44 <data format="tabular" name="output2" from_work_dir="cg_report.tsv" label="${tool.name} report">
45 <filter>(stat == '--statout')</filter>
46 </data>
47 </outputs>
48
49 <inputs>
50 <!--form field to select crr file-->
51 <param name="crr" type="select" label="Reference genome (.crr file)">
52 <options from_data_table="cg_crr_files" />
53 </param>
54
55 <!--conditional to select variant file input-->
56 <conditional name="data_sources">
57 <param name="data_source" type="select" label="Where are the input junction files?">
58 <option value="in" selected="true">imported into Galaxy</option>
59 <option value="out">located outside Galaxy (data on server or mounted drive)</option>
60 </param>
61
62 <!--form field to select junction files-->
63 <when value="in">
64 <param name="inputA" type="data" format="tabluar" label="Junction file A">
65 <validator type="dataset_ok_validator" />
66 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
67 metadata_name="dbkey" metadata_column="1"
68 message="cgatools is not currently available for this build."/>
69 </param>
70 <param name="inputB" type="data" format="tabluar" label="Junction file B">
71 <validator type="dataset_ok_validator" />
72 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
73 metadata_name="dbkey" metadata_column="1"
74 message="cgatools is not currently available for this build."/>
75 </param>
76 </when>
77
78 <!--form field to enter external input files-->
79 <when value="out">
80 <param name="inputA" type="text" label="Junction file A (/path/junction_file)" size="40" help="e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/SV/allJunctionsBeta-GS00000YYYY-ASM.tsv">
81 <validator type="empty_field" message="You must supply a junction file"/>
82 </param>
83 <param name="inputB" type="text" label="Junction file B (/path/junction_file)" size="40" help="e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/SV/allJunctionsBeta-GS00000YYYY-ASM.tsv">
84 <validator type="empty_field" message="You must supply a junction file"/>
85 </param>
86 </when>
87 </conditional>
88
89 <!--form field to select stats output-->
90 <param name="stat" type="select" label="Print input file stats">
91 <option value="">no</option>
92 <option value="--statout">yes</option>
93 </param>
94
95 <!--other parameters-->
96 <param name="scoreA" type="integer" label="Score threshold value for input file A (default 10)" value="10">
97 <validator type="empty_field" message="You must enter a value, the default is 10" />
98 </param>
99 <param name="scoreB" type="integer" label="Score threshold value for input file B (default 0)" value="0">
100 <validator type="empty_field" message="You must enter a value, the default is 0" />
101 </param>
102 <param name="distance" type="integer" label="Max distance between coordinates of potentially compatible junctions (default 200)" value="200">
103 <validator type="empty_field" message="You must enter a value, the default is 200" />
104 </param>
105 <param name="minlength" type="integer" label="Minimum deletion junction length to be included into the difference file (default 500)" value="500">
106 <validator type="empty_field" message="You must enter a value, the default is 500" />
107 </param>
108 </inputs>
109
110
111 <help>
112
113 **What it does**
114
115 This tool uses cgatools junctiondiff to report difference between junction calls of two Complete Genomics junctions files
116
117 **cgatools 1.6.0 Documentation**
118
119 Userguide: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-user-guide.pdf
120
121 Release notes: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-release-notes.pdf
122
123 **Command line reference**::
124
125 COMMAND NAME
126 junctiondiff - Reports difference between junction calls of Complete Genomics junctions files.
127
128 DESCRIPTION
129 junctiondiff takes two junction files A and B as input and produces the
130 following output:
131 - "diff-inputFileName" - the junctions from an input file A that are not
132 present in input file B.
133 - "report.txt" - a brief summary report (if --statout is used)
134
135 Two junctions are considered equivalent if:
136 - they come from different files
137 - left and right positions of one junction are not more than "--distance"
138 bases apart from the corresponding positions of another junction
139 - the junction scores are equal or above the scoreThreshold
140 - they are on the same strands
141
142 OPTIONS
143 -h [ --help ]
144 Print this help message.
145
146 --beta
147 This is a beta command. To run this command, you must pass the --beta
148 flag.
149
150 -s [ --reference ] arg
151 Reference file.
152
153 -a [ --junctionsA ] arg
154 input junction file A.
155
156 -b [ --junctionsB ] arg
157 input junction file B.
158
159 -A [ --scoreThresholdA ] arg (=10)
160 score threshold value for the input file A.
161
162 -B [ --scoreThresholdB ] arg (=0)
163 score threshold value for the input file B.
164
165 -d [ --distance ] arg (=200)
166 Max distance between coordinates of potentially compatible junctions.
167
168 -l [ --minlength ] arg (=500)
169 Minimum deletion junction length to be included into the difference
170 file.
171
172 -o [ --output-prefix ] arg
173 The path prefix for all the output reports.
174
175 -S [ --statout ]
176 (Debug) Report various input file statistics. Experimental feature.
177
178 SUPPORTED FORMAT_VERSION
179 1.5 or later
180 </help>
181 </tool>