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comparison tools/cgatools17/junctions2events_v17.xml @ 1:3a2e0f376f26 draft

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Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
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0:751b62d30ae1 1:3a2e0f376f26
1 <tool id="junctions2events" name="Junctions2Events" version="1.7.1">
2 <description> Groups related junctions and annotates each group with information about the structural rearrangement (event) that these junctions represent </description>
3
4 <requirements>
5 <requirement type="package" version="1">cgatools17</requirement>
6 </requirements>
7
8 <command>
9 cgatools | head -1;
10 cgatools junctions2events --beta
11 --reference ${refs.fields.crr_path}
12 --junctions $junctions
13 #if $alljunctions
14 --all-junctions $alljunctions
15 #end if
16 --repmask-data ${refs.fields.repmask_path}
17 --gene-data ${refs.fields.genedata_path}
18 #if $more_options.options_type_selector == "more"
19 --regulatory-region-length $regreglen
20 --contained-genes-max-range $contgenmax
21 --max-related-junction-distance $maxreljdist
22 --max-pairing-distance $maxpairdist
23 --max-copy-target-length $maxcopylen
24 --max-simple-event-distance $maxsed
25 #if $more_options.mobelname
26 --mobile-element-names $mobelname
27 #end if
28 --max-distance-to-m-e $maxdisttome
29 #end if
30 </command>
31
32 <inputs>
33 <!-- select reference -->
34 <param name="refs" type="select" label="Reference Build">
35 <options from_data_table="cg_anno_files" />
36 </param>
37
38 <!-- select junction files -->
39 <param name="junctions" type="data" format="tabular" label="Junctions file (allJunctions of highConfidenceJunction)"/>
40 <param name="alljunctions" type="data" format="tabular" optional="true" label="Optional: allJunctions file"/>
41
42 <!-- advanced settings -->
43 <conditional name="more_options">
44 <param name="options_type_selector" type="select" label="Advanced Options">
45 <option value="hide" selected="True">Less options</option>
46 <option value="show">More options</option>
47 </param>
48 <when value="less">
49 <!-- no options -->
50 </when>
51 <when value="show">
52 <param name="regreglen" type="integer" value="7500" min="0" label="regulatory region length" help="Length of the region upstream of the gene that may contain regulatory sequence for the gene" />
53 <param name="contgenmax" type="integer" value="-1" min="0" label="contained genes max range" help="Maximum length of a copy or deletion event to annotate with all genes that overlap the copied or deleted segment. (Negative value causes all events to be annotated regardless of the length)" />
54 <param name="maxreljdist" type="integer" value="700" min="0" label="max related junctions distance" help="Junctions occurring within this distance are presumed to be related" />
55 <param name="maxpairdist" type="integer" value="10000000" min="0" label="max pairing distance" help="Maximum allowed distance between junction sides wshen searching for paired junctions caused by the same event." />
56 <param name="maxcopylen" type="integer" value="1000" min="0" label="max copy target length" help="Pairs of junctions will be classified as a copy event only if the length of the implied copy target region is below this threshold." />
57 <param name="maxsed" type="integer" value="10000000" min="0" label="max simple event distance" help="When given a choice of identifying an event as a mobile element copy or as a simple deletion/duplication, prefer the latter explanation if the length of the affected sequence is below this threshold" />
58 <param name="mobelname" type="select" multiple="true" display="checkboxes" label="mobile element names" help="Names of mobile elements that are known to be active and sometimes copy flanking 3' sequence" >
59 <option value="L1HS"> L1HS </option>
60 <option value="AluY"> AluY </option>
61 <option value="SVA"> SVA </option>
62 </param>
63 <param name="maxdisttome" type="integer" value="2000" min="0" label="max distance to ME" help="Maximum allowed distance from the junction side to the element when searching for a mobile element related to a junction" />
64 </when>
65 </conditional>
66
67 <!-- prefix for output file so you dont have to manually rename history items -->
68 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
69 </inputs>
70
71 <outputs>
72 <data format="tabular" name="annotatedjunctions" from_work_dir="AnnotatedJunctions.tsv" label="$fname AnnotatedJunctions file of ${tool.name} on ${on_string}"/>
73 <data format="tabular" name="events" from_work_dir="Events.tsv" label="$fname Events file of ${tool.name} on ${on_string}"/>
74 </outputs>
75
76 <help>
77
78 **What it does**
79
80 This tool searches for groups of related junctions and for every group
81 attempts to determine the event that caused the junctions.
82
83 **cgatools 1.7.1 Documentation**
84
85 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
86
87 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
88
89 **Command line reference**::
90
91 COMMAND NAME
92 junctions2events - Groups and annotates junction calls by event type.
93
94
95 OPTIONS
96 -h [ --help ]
97 Print this help message.
98
99 --beta
100 This is a beta command. To run this command, you must pass the --beta
101 flag.
102
103 --reference arg
104 Reference file.
105
106 --output-prefix arg
107 The path prefix for all output reports.
108
109 --junctions arg
110 Primary input junction file.
111
112 --all-junctions arg
113 Superset of the input junction file to use when searching for the
114 related junctions. The default is to use only the junctions in the
115 primary junction file.
116
117 --repmask-data arg
118 The file that contains repeat masker data.
119
120 --gene-data arg
121 The file that contains gene location data.
122
123 --regulatory-region-length arg (=7500)
124 Length of the region upstream of the gene that may contain regulatory
125 sequence for the gene. Junctions that connect this region to another
126 gene will be annotated as a special kind of gene fusion.
127
128 --contained-genes-max-range arg (=-1)
129 Maximum length of a copy or deletion event to annotate with all genes
130 that overlap the copied or deleted segment. Negative value causes all
131 events to be annotated regardless of the length.
132
133 --max-related-junction-distance arg (=700)
134 Junctions occurring within this distance are presumed to be related.
135
136 --max-pairing-distance arg (=10000000)
137 When searching for paired junctions caused by the same event, maximum
138 allowed distance between junction sides.
139
140 --max-copy-target-length arg (=1000)
141 Pairs of junctions will be classified as a copy event only if the
142 length of the implied copy target region is below this threshold.
143
144 --max-simple-event-distance arg (=10000000)
145 When given a choice of explaining an event as a mobile element copy or
146 as a simple deletion/duplication, prefer the latter explanation if the
147 length of the affected sequence if below this threshold.
148
149 --mobile-element-names arg (=L1HS,SVA)
150 Comma-separated list of the names of the mobile elements that are known
151 to be active and sometimes copy flanking 3' sequence.
152
153 --max-distance-to-m-e arg (=2000)
154 When searching for a mobile element related to a junction, maximum
155 allowed distance from the junction side to the element.
156
157 --max-related-junction-output arg (=100)
158 Maximum number of related junctions included into annotation field
159
160
161 SUPPORTED FORMAT_VERSION
162 1.5 or later
163
164 </help>
165 </tool>
166
167