Mercurial > repos > yufei-luo > bwa_0_7_5
comparison bwa_0_7_5/bwa_0_7_5.xml @ 0:839e36b39c3f draft
Uploaded
author | yufei-luo |
---|---|
date | Mon, 12 Aug 2013 08:44:05 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:839e36b39c3f |
---|---|
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 |