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comparison tools/cgatools17/mkvcf_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="cg_mkvcf" name="Make VCF" version="1.7.1">
2
3 <description>Converts masterVar and/or junction files to VCF.</description>
4
5 <requirements>
6 <requirement type="package" version="1">cgatools17</requirement>
7 </requirements>
8
9 <command> <!--run executable-->
10 cgatools | head -1;
11 cgatools mkvcf --beta
12 --reference ${crr.fields.crr_path}
13 --output $output
14 $nc
15 --calibration-root ${crr.fields.calibration_root}
16 #if $varfiles
17 #if $junctionfiles <!-- masterVar and SV -->
18 --source-names masterVar,SV
19 #for $v in $varfiles
20 --master-var ${v.input}
21 #end for
22 #for $j in $junctionfiles
23 --junction-file ${j.input}
24 #end for
25
26 #else <!-- masterVar only -->
27 --source-names masterVar
28 #for $v in $varfiles
29 --master-var ${v.input}
30 #end for
31 #end if
32 #else
33 #if $junctionfiles <!-- SV only -->
34 --source-names SV
35 #for $j in $junctionfiles
36 --junction-file ${j.input}
37 #end for
38 #end if
39 #end if
40 #if $more_options.options_type_selector == "more"
41 --junction-score-threshold $jst
42 --junction-side-length-threshold $jslt
43 --junction-distance-tolerance $jdt
44 --junction-length-threshold $jlt
45 $jnp
46 $jthc
47 #end if
48 </command>
49
50 <inputs>
51 <!-- reference crr -->
52 <param name="crr" type="select" label="Reference Build">
53 <options from_data_table="cg_anno_files" />
54 </param>
55
56 <!--form field to select masterVar files-->
57 <repeat name="varfiles" title="MasterVar files">
58 <param name="input" type="data" format="tabular" label="Dataset"/>
59 </repeat>
60
61 <!--form field to select junction files-->
62 <repeat name="junctionfiles" title="Junctions files">
63 <param name="input" type="data" format="tabular" label="Dataset"/>
64 </repeat>
65
66 <param name="nc" type="boolean" truevalue="--include-no-calls" falsevalue="" selected="False" label="Include no-calls?" help="Include small variants VCF records for loci that are no-called across all input genomes"/>
67
68 <!-- advanced settings -->
69 <conditional name="more_options">
70 <param name="options_type_selector" type="select" label="Advanced Options">
71 <option value="hide" selected="True">Hide</option>
72 <option value="show">Show</option>
73 </param>
74 <when value="hide">
75 <!-- no options -->
76 </when>
77 <when value="show">
78 <param name="jst" type="text" value="10" label="Junction Score Threshold" help="Minimum number of discordant mate pairs for a junction that is required to be labeled as PASS in the FT record"/>
79 <param name="jslt" type="text" value="70" label="Junction Side Length Threshold" help="Minumum junction side length for a reported junction that is required to be labeled as PASS in the FT record"/>
80 <param name="jdt" type="text" value="200" label="Junction Distance Tolerance" help="Maximum allowed distance between junctions considered to match (i.e. potentially reflect the same evolutionary event)"/>
81 <param name="jlt" type="text" value="500" label="Junction Length Threshold" help="Maxumum length between breakpoints terquired to call an intrachromosomal junction"/>
82 <param name="jnp" type="boolean" truevalue="--junction-normal-priority" falsevalue="" selected="false" label="Junction Normal Priority" help="Normal junction priority for VCF output. Should be used only when comparing two genomes, a tumour and its matched normal"/>
83 <param name="jthc" type="boolean" truevalue="--junction-tumor-hc" falsevalue="" selected="false" label="Junction Tumour High Confidence" help="Output only high confidence junctions from the second of two genomes. Useful as a means of identifying a set of high-confidence somatic junctions."/>
84
85 </when>
86 </conditional>
87
88 <!-- prefix for output file so you dont have to manually rename history items -->
89 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
90 </inputs>
91 <outputs>
92 <data format="vcf" name="output" label="$fname ${tool.name} on ${on_string}"/>
93 </outputs>
94
95
96 <help>
97 **What it does**
98
99 This tool joins two tab-delimited files based on equal fields or overlapping regions.
100
101 **cgatools 1.7.1 Documentation**
102
103 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
104
105 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
106
107 **Command line reference**::
108
109 COMMAND NAME
110 mkvcf - Converts var file(s) or masterVar file(s) to VCF.
111
112 DESCRIPTION
113 Converts var file(s) or masterVar file(s) to VCF.
114
115 OPTIONS
116 -h [ --help ]
117 Print this help message.
118
119 --beta
120 This is a beta command. To run this command, you must pass the --beta
121 flag.
122
123 --reference arg
124 The reference crr file.
125
126 --output arg (=STDOUT)
127 The output file (may be omitted for stdout).
128
129 --field-names arg (=GT,PS,NS,AN,AC,SS,FT,CGA_XR,CGA_FI,GQ,HQ,EHQ,CGA_CEHQ,GL,
130 CGA_CEGL,DP,AD,CGA_RDP,CGA_ODP,CGA_OAD,CGA_ORDP,CGA_PFAM,
131 CGA_MIRB,CGA_RPT,CGA_SDO,CGA_SOMC,CGA_SOMR,CGA_SOMS,GT,CGA_GP,
132 CGA_NP,CGA_CP,CGA_PS,CGA_CT,CGA_TS,CGA_CL,CGA_LS,CGA_SCL,CGA_SLS,
133 CGA_LAF,CGA_LLAF,CGA_ULAF,GT,FT,CGA_IS,CGA_IDC,CGA_IDCL,CGA_IDCR,
134 CGA_RDC,CGA_NBET,CGA_ETS,CGA_KES,GT,FT,CGA_BF,CGA_MEDEL,MATEID,
135 SVTYPE,CGA_BNDG,CGA_BNDGO,CGA_BNDMPC,CGA_BNDPOS,CGA_BNDDEF,CGA_BNDP)
136 Comma-separated list of field names. By default, all fields are
137 included, but you may override this option to ensure only a subset of
138 the fields is included in the VCF output. For a description of each
139 field, see the cgatools user guide.
140
141 --source-names arg (=masterVar,CNV,SV,MEI)
142 Comma-separated list of source names. The following source names are
143 available:
144 masterVar - Includes records extracted from the masterVar file.
145 CNV - Includes CNV-related records.
146 SV - Includes records derived from junctions files.
147 MEI - Includes records describing mobile element insertions.
148 Some of these source types are only available for more recent pipeline
149 versions, and some of these source types do not support multi-genome
150 VCFs. For more information about which source types are available for
151 which versions of the Complete Genomics pipeline software, see the
152 cgatools user guide.
153
154 --genome-root arg
155 For each genome to include in the VCF, the genome root directory, for
156 example /data/GS00118-DNA_A01; this directory is expected to contain
157 the ASM and LIB subdirectories, for example. You must supply this
158 option for each genome in the VCF, unless you are using
159 --source-names=masterVar and you have specified the --master-var option
160 for each genome in the VCF.
161
162 --master-var arg
163 For each genome to include in the VCF, the masterVar file. If
164 genome-roots parameter is given, this parameter defaults to the
165 masterVar in the given genome-root.
166
167 --include-no-calls
168 Small variants VCF records include loci that have no
169 reference-inconsistent calls.
170
171
172 --calibration-root arg
173 The directory containing calibration data. For example, there should
174 exist a file calibration-root/0.0.0/metrics.tsv. This option is only
175 required if CGA_CEHQ or CGA_CEGL are included in the --field-names
176 parameter.
177
178 --junction-file arg
179 For each genome to include in the VCF, the junctions file. If
180 genome-roots parameter is given, this parameter defaults to the
181 respective junctions file in the export directory.
182
183 --junction-score-threshold arg (=10)
184 Junction score thresholds (discordant mate pair count).
185
186 --junction-side-length-threshold arg (=70)
187 Junction side length threshold.
188
189 --junction-distance-tolerance arg (=200)
190 Distance tolerance for junction compatibility.
191
192 --junction-length-threshold arg (=500)
193 Length threshold for compatible junctions.
194
195 --junction-normal-priority
196 Normal junction priority for vcf output.
197
198 --junction-tumor-hc
199 use high confidence junctions for tumors.
200
201
202 SUPPORTED FORMAT_VERSION
203 0.3 or later
204 </help>
205 </tool>