|
0
|
1 <tool id="bwa_0_7_5" name="Map with BWA (Version 0.7.5)" version="0.7.5">
|
|
|
2 <requirements>
|
|
|
3 <requirement type="package" version="0.7.5">bwa</requirement>
|
|
|
4 </requirements>
|
|
|
5 <description>This new version BWA (0.7.5) use 'mem' algorithm for mapping, dosen't need 'aln', 'samse', 'sampe' and picard AddOrReplace anymore.</description>
|
|
|
6 <parallelism method="basic"></parallelism>
|
|
|
7 <command interpreter="python">
|
|
|
8 bwa_0_7_5.py
|
|
|
9 --threads="1"
|
|
|
10 --fileSource="${genomeSource.refGenomeSource}"
|
|
|
11 #if $genomeSource.refGenomeSource == "history":
|
|
|
12 ##build index on the fly
|
|
|
13 --ref="${genomeSource.ownFile}"
|
|
|
14 --dbkey="${dbkey}"
|
|
|
15 #else:
|
|
|
16 ##use precomputed indexes
|
|
|
17 --ref="${genomeSource.indices.fields.path}"
|
|
|
18 #end if
|
|
|
19
|
|
|
20 ## input file(s)
|
|
|
21 --fastq="${paired.fastq}"
|
|
|
22 #if $paired.sPaired == "paired":
|
|
|
23 --rfastq="${paired.rfastq}"
|
|
|
24 #end if
|
|
|
25
|
|
|
26 ## output file
|
|
|
27 --output="${output}"
|
|
|
28
|
|
|
29 ## run parameters
|
|
|
30 --genAlignType="${paired.sPaired}"
|
|
|
31 --params="${params.source_select}"
|
|
|
32 #if $params.source_select != "pre_set":
|
|
|
33 --minEditDistSeed="${params.minEditDistSeed}"
|
|
|
34 --bandWidth="${params.bandWidth}"
|
|
|
35 --offDiagonal="${params.offDiagonal}"
|
|
|
36 --internalSeeds="${params.internalSeeds}"
|
|
|
37 --seedsOccurrence="${params.seedsOccurrence}"
|
|
|
38 --mateRescue="${params.mateRescue}"
|
|
|
39 --skipPairing="${params.skipPairing}"
|
|
|
40 --seqMatch="${params.seqMatch}"
|
|
|
41 --mismatch="${params.mismatch}"
|
|
|
42 --gapOpen="${params.gapOpen}"
|
|
|
43 --gapExtension="${params.gapExtension}"
|
|
|
44 --clipping="${params.clipping}"
|
|
|
45 --unpairedReadpair="${params.unpairedReadpair}"
|
|
|
46 --interPairEnd="${params.interPairEnd}"
|
|
|
47 --minScore="${params.minScore}"
|
|
|
48 --mark="${params.mark}"
|
|
|
49
|
|
|
50 #if $params.readGroup.specReadGroup == "yes"
|
|
|
51 --rgid="${params.readGroup.rgid}"
|
|
|
52 --rgsm="${params.readGroup.rgsm}"
|
|
|
53 --rgpl="${params.readGroup.rgpl}"
|
|
|
54 --rglb="${params.readGroup.rglb}"
|
|
|
55 --rgpu="${params.readGroup.rgpu}"
|
|
|
56 --rgcn="${params.readGroup.rgcn}"
|
|
|
57 --rgds="${params.readGroup.rgds}"
|
|
|
58 --rgdt="${params.readGroup.rgdt}"
|
|
|
59 --rgfo="${params.readGroup.rgfo}"
|
|
|
60 --rgks="${params.readGroup.rgks}"
|
|
|
61 --rgpg="${params.readGroup.rgpg}"
|
|
|
62 --rgpi="${params.readGroup.rgpi}"
|
|
|
63 #end if
|
|
|
64 #end if
|
|
|
65 </command>
|
|
|
66
|
|
|
67 <inputs>
|
|
|
68 <conditional name="genomeSource">
|
|
|
69 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
|
|
|
70 <option value="indexed">Use a built-in index</option>
|
|
|
71 <option value="history">Use one from the history</option>
|
|
|
72 </param>
|
|
|
73 <when value="indexed">
|
|
|
74 <param name="indices" type="select" label="Select a reference genome">
|
|
|
75 <options from_data_table="bwa_indexes">
|
|
|
76 <filter type="sort_by" column="2" />
|
|
|
77 <validator type="no_options" message="No indexes are available" />
|
|
|
78 </options>
|
|
|
79 </param>
|
|
|
80 </when>
|
|
|
81 <when value="history">
|
|
|
82 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
|
|
|
83 </when>
|
|
|
84 </conditional>
|
|
|
85 <conditional name="paired">
|
|
|
86 <param name="sPaired" type="select" label="Is this library mate-paired?">
|
|
|
87 <option value="single">Single-end</option>
|
|
|
88 <option value="paired">Paired-end</option>
|
|
|
89 </param>
|
|
|
90 <when value="single">
|
|
|
91 <param name="fastq" type="data" format="fastqsanger,fastqillumina" label="FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
|
|
|
92 </when>
|
|
|
93 <when value="paired">
|
|
|
94 <param name="fastq" type="data" format="fastqsanger,fastqillumina" label="Forward FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
|
|
|
95 <param name="rfastq" type="data" format="fastqsanger,fastqillumina" label="Reverse FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
|
|
|
96 </when>
|
|
|
97 </conditional>
|
|
|
98 <conditional name="params">
|
|
|
99 <param name="source_select" type="select" label="BWA settings to use" help="For most mapping needs use Commonly Used settings. If you want full control use Full Parameter List">
|
|
|
100 <option value="pre_set">Commonly Used</option>
|
|
|
101 <option value="full">Full Parameter List</option>
|
|
|
102 </param>
|
|
|
103 <when value="pre_set" />
|
|
|
104 <when value="full">
|
|
|
105 <param name="minEditDistSeed" type="integer" value="19" label="Minimum seed length" />
|
|
|
106 <param name="bandWidth" type="integer" value="100" label="Band width for banded alignment" />
|
|
|
107 <param name="offDiagonal" type="integer" value="100" label="off-diagonal X-dropoff" />
|
|
|
108 <param name="internalSeeds" type="float" value="1.5" label="look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]" />
|
|
|
109 <param name="seedsOccurrence" type="integer" value="10000" label="skip seeds with more than INT occurrences" />
|
|
|
110 <param name="mateRescue" type="boolean" truevalue="True" falsevalue="False" checked="False" label="skip seeds with more than INT occurrences" />
|
|
|
111 <param name="skipPairing" type="boolean" truevalue="True" falsevalue="False" checked="False" label="skpe pairing, mate rescue performed unless -S also in use" />
|
|
|
112 <param name="seqMatch" type="integer" value="1" label="score of a sequence match" />
|
|
|
113 <param name="mismatch" type="integer" value="4" label="penalty for a mismatch" />
|
|
|
114 <param name="gapOpen" type="integer" value="6" label="gap open penalty" />
|
|
|
115 <param name="gapExtension" type="text" value="None" label="gap extension penalty; a gap of size k cost {-O} + {-E}*k [1]" />
|
|
|
116 <param name="clipping" type="integer" value="5" label="penalty for clipping" />
|
|
|
117 <param name="unpairedReadpair" type="integer" value="17" label="penalty for an unpaired read pair" />
|
|
|
118 <param name="interPairEnd" type="boolean" truevalue="True" falsevalue="False" checked="False" label="first query file consists of interleaved paired-end sequences" />
|
|
|
119 <param name="minScore" type="integer" value="30" label="minimum score to output" />
|
|
|
120 <param name="mark" type="boolean" truevalue="True" falsevalue="False" checked="False" label="mark shorter split hits as secondary (for Picard/GATK compatibility)" />
|
|
|
121
|
|
|
122 <conditional name="readGroup">
|
|
|
123 <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)">
|
|
|
124 <option value="yes">Yes</option>
|
|
|
125 <option value="no" selected="True">No</option>
|
|
|
126 </param>
|
|
|
127 <when value="yes">
|
|
|
128 <param name="rgid" type="text" size="25" label="[Essential]Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG
|
|
|
129 tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group
|
|
|
130 IDs may be modified when merging SAM files in order to handle collisions." />
|
|
|
131 <param name="rgpl" type="text" size="25" label="[Essential]Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA,
|
|
|
132 SOLID, HELICOS, IONTORRENT and PACBIO" />
|
|
|
133 <param name="rglb" type="text" size="25" label="[Essential]Library name (LB)" help="Required if RG specified" />
|
|
|
134 <param name="rgsm" type="text" size="25" label="[Essential]Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
|
|
|
135 <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
|
|
|
136 <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" />
|
|
|
137 <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" />
|
|
|
138 <param name="rgdt" type="text" size="25" label="Date that run was produced (DT)" help="Optional. ISO8601 format date or date/time, like YYYY-MM-DD" />
|
|
|
139 <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each
|
|
|
140 flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by
|
|
|
141 various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" />
|
|
|
142 <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" help="Optional" />
|
|
|
143 <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" />
|
|
|
144 <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" />
|
|
|
145 </when>
|
|
|
146 <when value="no" />
|
|
|
147 </conditional>
|
|
|
148 </when>
|
|
|
149 </conditional>
|
|
|
150 </inputs>
|
|
|
151
|
|
|
152 <outputs>
|
|
|
153 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
|
|
|
154 <actions>
|
|
|
155 <conditional name="genomeSource.refGenomeSource">
|
|
|
156 <when value="indexed">
|
|
|
157 <action type="metadata" name="dbkey">
|
|
|
158 <option type="from_data_table" name="bwa_indexes" column="1">
|
|
|
159 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
|
|
|
160 <filter type="param_value" ref="genomeSource.indices" column="0"/>
|
|
|
161 </option>
|
|
|
162 </action>
|
|
|
163 </when>
|
|
|
164 <when value="history">
|
|
|
165 <action type="metadata" name="dbkey">
|
|
|
166 <option type="from_param" name="genomeSource.ownFile" param_attribute="dbkey" />
|
|
|
167 </action>
|
|
|
168 </when>
|
|
|
169 </conditional>
|
|
|
170 </actions>
|
|
|
171 </data>
|
|
|
172 </outputs>
|
|
|
173
|
|
|
174 <tests>
|
|
|
175 <test>
|
|
|
176 </test>
|
|
|
177 <test>
|
|
|
178 </test>
|
|
|
179 <test>
|
|
|
180 </test>
|
|
|
181 </tests>
|
|
|
182
|
|
|
183
|
|
|
184 </tool>
|
|
|
185
|
|
|
186
|
