|
17
|
1 <tool id="cg_junctiondiff" name="junctiondiff(beta) 1.5" version="1.0.0">
|
|
|
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 -->
|
|
|
6
|
|
|
7 <description>reports difference between junction calls</description> <!--adds description in toolbar-->
|
|
|
8
|
|
|
9 <requirements>
|
|
|
10 <requirement type="binary">cgatools</requirement>
|
|
|
11 </requirements>
|
|
|
12
|
|
|
13 <command> <!--run executable-->
|
|
|
14 cgatools | head -1;
|
|
|
15 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 $stat
|
|
|
24 --output-prefix cg_
|
|
|
25 ;
|
|
|
26 mv cg_diff-*tsv cg_diff.tsv
|
|
|
27 </command>
|
|
|
28
|
|
|
29 <outputs>
|
|
|
30 <data format="tabular" name="output1" from_work_dir="cg_diff.tsv" label="${tool.name} on ${on_string}: diff"/>
|
|
|
31 <data format="tabular" name="output2" from_work_dir="cg_report.tsv" label="${tool.name} on ${on_string}: report">
|
|
|
32 <filter>(stat == '--statout')</filter>
|
|
|
33 </data>
|
|
|
34 </outputs>
|
|
|
35
|
|
|
36 <inputs>
|
|
|
37 <!--form field to select crr file-->
|
|
|
38 <param name="crr" type="select" label="Reference genome (.crr file)">
|
|
|
39 <options from_data_table="cg_crr_files" />
|
|
|
40 </param>
|
|
|
41
|
|
|
42 <!--conditional to select variant file input-->
|
|
|
43 <conditional name="data_sources">
|
|
|
44 <param name="data_source" type="select" label="Where are the input junction files?">
|
|
|
45 <option value="in" selected="true">imported into Galaxy</option>
|
|
|
46 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
|
|
|
47 </param>
|
|
|
48 <when value="in">
|
|
|
49 <!--form field to select variant files-->
|
|
|
50 <param name="inputA" type="data" format="tabluar" label="Junction file A">
|
|
|
51 <validator type="unspecified_build" />
|
|
|
52 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
|
|
|
53 metadata_name="dbkey" metadata_column="1"
|
|
|
54 message="cgatools is not currently available for this build."/>
|
|
|
55 </param>
|
|
|
56 <param name="inputB" type="data" format="tabluar" label="Junction file B">
|
|
|
57 <validator type="unspecified_build" />
|
|
|
58 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
|
|
|
59 metadata_name="dbkey" metadata_column="1"
|
|
|
60 message="cgatools is not currently available for this build."/>
|
|
|
61 </param>
|
|
|
62 </when>
|
|
|
63 <when value="out">
|
|
|
64 <!--form field to enter external input files-->
|
|
|
65 <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"/>
|
|
|
66 <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"/>
|
|
|
67 </when>
|
|
|
68 </conditional>
|
|
|
69
|
|
|
70 <!--form field to select stats output-->
|
|
|
71 <param name="stat" type="select" label="Print input file stats">
|
|
|
72 <option value="">no</option>
|
|
|
73 <option value="--statout">yes</option>
|
|
|
74 </param>
|
|
|
75
|
|
|
76 <param name="scoreA" type="integer" label="Score threshold value for input file A (default 10)" value="10"/>
|
|
|
77 <param name="scoreB" type="integer" label="Score threshold value for input file B (default 0)" value="0"/>
|
|
|
78 <param name="distance" type="integer" label="Max distance between coordinates of potentially compatible junctions (default 200)" value="200"/>
|
|
|
79 <param name="minlength" type="integer" label="Minimum deletion junction length to be included into the difference file (default 500)" value="500"/>
|
|
|
80 </inputs>
|
|
|
81
|
|
|
82
|
|
|
83 <help>
|
|
|
84
|
|
|
85 **What it does**
|
|
|
86
|
|
|
87 This tool reports difference between junction calls of Complete Genomics junctions files
|
|
|
88
|
|
|
89 **cgatools 1.5.0 Documentation**
|
|
|
90
|
|
|
91 Userguide: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-user-guide.pdf
|
|
|
92
|
|
|
93 Release notes: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-release-notes.pdf
|
|
|
94
|
|
|
95 **Command line reference**::
|
|
|
96
|
|
|
97 COMMAND NAME
|
|
|
98 junctiondiff - Reports difference between junction calls of Complete Genomics junctions files.
|
|
|
99
|
|
|
100 DESCRIPTION
|
|
|
101 junctiondiff takes two junction files A and B as input and produces the
|
|
|
102 following output:
|
|
|
103 - "diff-inputFileName" - the junctions from an input file A that are not
|
|
|
104 present in input file B.
|
|
|
105 - "report.txt" - a brief summary report (if --statout is used)
|
|
|
106
|
|
|
107 Two junctions are considered equivalent if:
|
|
|
108 - they come from different files
|
|
|
109 - left and right positions of one junction are not more than "--distance"
|
|
|
110 bases apart from the corresponding positions of another junction
|
|
|
111 - the junction scores are equal or above the scoreThreshold
|
|
|
112 - they are on the same strands
|
|
|
113
|
|
|
114 OPTIONS
|
|
|
115 -h [ --help ]
|
|
|
116 Print this help message.
|
|
|
117
|
|
|
118 --beta
|
|
|
119 This is a beta command. To run this command, you must pass the --beta
|
|
|
120 flag.
|
|
|
121
|
|
|
122 -s [ --reference ] arg
|
|
|
123 Reference file.
|
|
|
124
|
|
|
125 -a [ --junctionsA ] arg
|
|
|
126 input junction file A.
|
|
|
127
|
|
|
128 -b [ --junctionsB ] arg
|
|
|
129 input junction file B.
|
|
|
130
|
|
|
131 -A [ --scoreThresholdA ] arg (=10)
|
|
|
132 score threshold value for the input file A.
|
|
|
133
|
|
|
134 -B [ --scoreThresholdB ] arg (=0)
|
|
|
135 score threshold value for the input file B.
|
|
|
136
|
|
|
137 -d [ --distance ] arg (=200)
|
|
|
138 Max distance between coordinates of potentially compatible junctions.
|
|
|
139
|
|
|
140 -l [ --minlength ] arg (=500)
|
|
|
141 Minimum deletion junction length to be included into the difference
|
|
|
142 file.
|
|
|
143
|
|
|
144 -o [ --output-prefix ] arg
|
|
|
145 The path prefix for all the output reports.
|
|
|
146
|
|
|
147 -S [ --statout ]
|
|
|
148 (Debug) Report various input file statistics. Experimental feature.
|
|
|
149
|
|
|
150 SUPPORTED FORMAT_VERSION
|
|
|
151 1.5 or later
|
|
|
152 </help>
|
|
|
153 </tool>
|
