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date Thu, 27 Sep 2012 13:37:59 -0400
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1 <tool id="cg_evidence2sam" name="evidence2sam(beta) 1.6" version="1.0.0">
2 <!--
3 This tool creates a GUI for the evidence2sam function of cgatools from Complete Genomics, Inc.
4 written 8-31-2012 by bcrain@completegenomics.com
5 -->
6
7 <description>converts evidence mappings to SAM format</description>
8
9 <command>
10 <!-- print version of cgatools to STDOUT-->
11 cgatools | head -1;
12
13 <!-- print command lines to STDOUT-->
14 echo "cgatools evidence2sam --beta
15 --reference $crr.fields.path
16 --output $output
17 --evidence-dnbs $data_sources.input
18 --consistent-mapping-range $range
19 #if $region.selectregion == "yes"
20 --extract-genomic-region $region.coordinates
21 #end if
22 $duplicates
23 $mates
24 $intervals
25 $skip
26 $svcandidates
27 $unmapped
28 $primary
29 ";
30
31 <!-- execute cgatools-->
32 cgatools evidence2sam --beta
33 --reference $crr.fields.path
34 --evidence-dnbs $data_sources.input
35 #if $region.selectregion == "yes"
36 --extract-genomic-region $region.coordinates
37 #end if
38 $duplicates
39 $mates
40 $intervals
41 $skip
42 $svcandidates
43 $unmapped
44 $primary
45 --consistent-mapping-range $range
46 --output $output
47 </command>
48
49 <outputs>
50 <data format="tabular" name="output" label="${tool.name} output"/>
51 </outputs>
52
53 <inputs>
54 <!--form field to select crr file-->
55 <param name="crr" type="select" label="Reference genome (.crr file)">
56 <options from_data_table="cg_crr_files" />
57 </param>
58
59 <!--conditional to select input file-->
60 <conditional name="data_sources">
61 <param name="data_source" type="select" label="Where is the input evidence file?">
62 <option value="in">imported into Galaxy</option>
63 <option value="out" selected="true">located outside Galaxy (data on server or mounted drive)</option>
64 </param>
65
66 <!--form field to select evidence files-->
67 <when value="in">
68 <param name="input" type="data" format="tabluar" label="EvidenceDnbs file">
69 <validator type="dataset_ok_validator" />
70 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
71 metadata_name="dbkey" metadata_column="1"
72 message="cgatools is not currently available for this build."/>
73 </param>
74 </when>
75
76 <!--form field to enter external input file-->
77 <when value="out">
78 <param name="input" type="text" label="EvidenceDnbs file (/path/file)" size="40" help="e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/EVIDENCE/evidenceDnbs-chr21-GS00000YYYY-ASM.tsv.bz2">
79 <validator type="empty_field" message="You must supply an evidenceDnbs file"/>
80 </param>
81 </when>
82 </conditional>
83
84 <!--form field to select chromosomal region-->
85 <conditional name="region">
86 <param name="selectregion" type="select" label="Do you what to extract specific genomic region?">
87 <option value="no" selected="true">no</option>
88 <option value="yes">yes</option>
89 </param>
90
91 <when value="yes">
92 <param name="coordinates" type="text" label="Enter genomic coordinates to avoid converting the entire file (chr,from,to)" size="40" help="Specify the region as a half-open interval chr,from,to (e.g. chrX,15203639,15412498)"/>
93 </when>
94 </conditional>
95
96 <!--form field to select duplicate handling-->
97 <param name="duplicates" type="select" label="Keep local duplicates of DNB mappings (default no)" help="All the output SAM records will be marked as 'not primary' if this option is used.">
98 <option value="" selected="true">no</option>
99 <option value="--keep-duplicates">yes</option>
100 </param>
101
102 <!--form field to generate mate sequence-->
103 <param name="mates" type="select" label="Generate mate sequence (R2) and score (Q2) tags (default no)">
104 <option value="" selected="true">no</option>
105 <option value="--add-mate-sequence">yes</option>
106 </param>
107
108 <!--form field to generate interval ids-->
109 <param name="intervals" type="select" label="Generate interval id (ZI:I) and allele id (ZA:I) tags (default no)">
110 <option value="" selected="true">no</option>
111 <option value="--add-allele-id">yes</option>
112 </param>
113
114 <!--form field to skip not mapped reads-->
115 <param name="skip" type="select" label="Skip not mapped records (default no)">
116 <option value="" selected="true">no</option>
117 <option value="--skip-not-mapped">yes</option>
118 </param>
119
120 <!--form field to skip not mapped reads-->
121 <param name="svcandidates" type="select" label="Mate unique single arm mappings in SAM including those on different stands and chromosomes (default no)">
122 <option value="" selected="true">no</option>
123 <option value="--mate-sv-candidates">yes</option>
124 </param>
125
126 <!--form field to skip not mapped reads-->
127 <param name="unmapped" type="select" label="Generate mate sequence and score tags for inconsistent mappings only (default no)">
128 <option value="" selected="true">no</option>
129 <option value="--add-unmapped-mate-info">yes</option>
130 </param>
131
132 <!--form field to skip not mapped reads-->
133 <param name="primary" type="select" label="Use primary mappings only (default no)" help="Report only the best mappings">
134 <option value="" selected="true">no</option>
135 <option value="--primary-mappings-only">yes</option>
136 </param>
137
138 <param name="range" type="integer" value="1300" label="Maximum distance between consistent mates (default 1300)">
139 <validator type="empty_field" message="You must enter a value, the default is 1300" />
140 </param>
141 </inputs>
142
143 <stdio>
144 <regex match="failed" source="stderr" level="fatal"/>
145 <regex match="error" source="stderr" level="fatal"/>
146 <regex match="Export the sequence:" source="stderr" level="warning" description="Finished:" />
147 </stdio>
148
149 <help>
150
151 **What it does**
152
153 This tool uses cgatools evidence2sam to convert Complete Genomics evidence mappings to SAM format
154
155 **cgatools 1.6.0 Documentation**
156
157 Userguide: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-user-guide.pdf
158
159 Release notes: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-release-notes.pdf
160
161 **Command line reference**::
162
163 COMMAND NAME
164 evidence2sam - Converts CGI variant evidence data into SAM format.
165
166 DESCRIPTION
167 The evidence2sam converter takes as input evidence mapping files
168 (evidenceDnbs-*) and generates one SAM file as an output. The output is
169 sent into stdout by default. By default, all the evidence mapping records
170 from the input are converted into a pair of corresponding SAM records - one
171 record for each HalfDNB. The negative gaps in CGI mappings are represented
172 using GS/GQ/GC tags.
173
174 OPTIONS
175 -h [ --help ]
176 Print this help message.
177
178 --beta
179 This is a beta command. To run this command, you must pass the --beta
180 flag.
181
182 -e [ --evidence-dnbs ] arg
183 Input evidence dnbs file.
184
185 -s [ --reference ] arg
186 Reference file.
187
188 -o [ --output ] arg (=STDOUT)
189 The output SAM file (may be omitted for stdout).
190
191 -r [ --extract-genomic-region ] arg
192 defines a region as a half-open interval 'chr,from,to'.
193
194 --keep-duplicates
195 Keep local duplicates of DNB mappings.All the output SAM records will
196 be marked as not primary if this option is used.
197
198 --add-allele-id
199 Generate interval id and allele id tags.
200
201 --skip-not-mapped
202 Skip not mapped records
203
204 --add-mate-sequence
205 Generate mate sequence and score tags.
206
207 --mate-sv-candidates
208 Inconsistent mappings are normally converted as single arm mappings
209 with no mate information provided. If the option is used map2sam will
210 mate unique single arm mappings in SAM including those on different
211 stands and chromosomes. To distinguish these "artificially" mated
212 records a tag "XS:i:1" is used. The MAPQ provided for these records is
213 a single arm mapping weight.
214
215 --add-unmapped-mate-info
216 works like add-mate-sequence, but is applied to inconsistent mappings
217 only
218
219 --primary-mappings-only
220 report only the best mappings
221
222 --consistent-mapping-range arg (=1300)
223 limit the maximum distance between consistent mates
224
225
226 SUPPORTED FORMAT_VERSION
227 0.3 or later
228 </help>
229 </tool>