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comparison pilon.cwl @ 0:eaf4a7ae3a8f draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
author sanbi-uwc
date Thu, 11 Aug 2016 06:56:35 -0400
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children ee888e5fe28f
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-1:000000000000 0:eaf4a7ae3a8f
1 #!/usr/bin/env cwl-runner
2
3 cwlVersion: v1.0
4 class: CommandLineTool
5 stdout: output.txt
6
7 requirements:
8 - class: EnvVarRequirement
9 envDef:
10 - envName: CLASSPATH
11 envValue: /home/pvh/Documents/code/SANBI/pilon/pilon-1.18.jar
12 # - class: InlineJavascriptRequirement
13
14 inputs:
15 java_opts:
16 type: string?
17 doc: "JVM arguments should a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")"
18 inputBinding:
19 position: 1
20 genome:
21 type: File
22 doc: |
23 The input genome we are trying to improve, which must be the reference used
24 for the bam alignments. At least one of --frags or --jumps must also be given.
25 inputBinding:
26 position: 5
27 prefix: "--genome"
28 frags:
29 type:
30 - 'null'
31 - type: array
32 items: File
33 inputBinding:
34 prefix: --frags
35 position: 6
36 doc: |
37 A bam file consisting of fragment paired-end alignments, aligned to the --genome
38 argument using bwa or bowtie2. This argument may be specifed more than once.
39 secondaryFiles:
40 - ".bai"
41 jumps:
42 type:
43 - 'null'
44 - type: array
45 items: File
46 inputBinding:
47 prefix: --jumps
48 position: 6
49 doc: |
50 A bam file consisting of fragment paired-end alignments, aligned to the --genome
51 argument using bwa or bowtie2. This argument may be specifed more than once.
52 secondaryFiles:
53 - ".bai"
54 unpaired:
55 type:
56 - 'null'
57 - type: array
58 items: File
59 inputBinding:
60 prefix: --unpaired
61 position: 6
62 doc: |
63 A bam file consisting of unpaired alignments, aligned to the --genome argument
64 using bwa or bowtie2. This argument may be specifed more than once.
65 secondaryFiles:
66 - ".bai"
67 bam:
68 type:
69 - 'null'
70 - type: array
71 items: File
72 inputBinding:
73 prefix: "--bam"
74 position: 6
75 secondaryFiles:
76 - ".bai"
77 doc: |
78 A bam file of unknown type; Pilon will scan it and attempt to classify it as one
79 of the above bam types.
80 vcf_output:
81 type: boolean
82 default: false
83 inputBinding:
84 position: 7
85 prefix: "--vcf"
86 output_prefix:
87 type: string
88 default: pilon
89 inputBinding:
90 prefix: "--output"
91 position: 7
92 variant_output:
93 type: boolean
94 default: false
95 doc: Sets up heuristics for variant calling, as opposed to assembly improvement, equivalent to "--vcf --fix all,breaks"
96 inputBinding:
97 prefix: --variant
98 position: 7
99 changes:
100 type: boolean
101 default: false
102 doc: Output file describing changes in FASTA output
103 inputBinding:
104 prefix: --changes
105 position: 7
106 tracks:
107 type: boolean
108 default: false
109 doc: Write many track files (*.bed, *.wig) suitable for viewing in a genome browser.
110 inputBinding:
111 prefix: --tracks
112 position: 7
113 vcfqe:
114 type: boolean
115 default: false
116 doc: Add a QE (quality-weighted evidence) field rather than the default QP (quality-weighted percentage of evidence) field.
117 inputBinding:
118 prefix: --vcfqe
119 position: 7
120 chunksize:
121 type: int?
122 doc: Input FASTA elements larger than this will be processed in smaller pieces not to exceed this size (default 10000000).
123 inputBinding:
124 prefix: --chunksize
125 position: 8
126 vcf:
127 type: boolean
128 default: false
129 doc: Generate a VCF file describing variants
130 inputBinding:
131 prefix: --vcf
132 position: 8
133 diploid:
134 type: boolean
135 default: false
136 doc: Sample is from diploid organism; will eventually affect calling of heterozygous SNPs
137 inputBinding:
138 prefix: --diploid
139 position: 8
140 fix:
141 type: string?
142 doc: |
143 A comma-separated list of categories of issues to try to fix:
144 "bases": try to fix individual bases and small indels;
145 "gaps": try to fill gaps;
146 "local": try to detect and fix local misassemblies;
147 "all": all of the above (default);
148 "none": none of the above; new fasta file will not be written.
149 The following are experimental fix types:
150 "amb": fix ambiguous bases in fasta output (to most likely alternative).
151 "breaks": allow local reassembly to open new gaps (with "local").
152 "novel": assemble novel sequence from unaligned non-jump reads.
153 inputBinding:
154 prefix: --fix
155 position: 8
156 dumpreads:
157 type: boolean
158 default: false
159 doc: Dump reads for local re-assemblies.
160 inputBinding:
161 prefix: --dumpreads
162 position: 8
163 duplicates:
164 type: boolean
165 default: false
166 doc: Use reads marked as duplicates in the input BAMs (ignored by default).
167 inputBinding:
168 prefix: --duplicates
169 position: 8
170 iupac:
171 type: boolean
172 default: false
173 doc: Output IUPAC ambiguous base codes in the output FASTA file when appropriate.
174 inputBinding:
175 prefix: --iupac
176 position: 8
177 nonpf:
178 type: boolean
179 default: false
180 doc: Use reads which failed sequencer quality filtering (ignored by default).
181 inputBinding:
182 prefix: --nonpf
183 position: 8
184 targets:
185 type: string?
186 doc: |
187 Only process the specified target(s). Targets are comma-separated, and each target
188 is a fasta element name optionally followed by a base range.
189 Example: "scaffold00001,scaffold00002:10000-20000" would result in processing all of
190 scaffold00001 and coordinates 10000-20000 of scaffold00002.
191 If "targetlist" is the name of a file, each line will be treated as a target
192 specification.
193 inputBinding:
194 prefix: --targets
195 position: 8
196 threads:
197 type: int?
198 doc: Degree of parallelism to use for certain processing (default 1). Experimental.
199 default: 1
200 inputBinding:
201 prefix: --threads
202 position: 8
203 verbose:
204 type: boolean
205 default: false
206 doc: More verbose output
207 inputBinding:
208 prefix: --verbose
209 position: 8
210 debug:
211 type: boolean
212 default: false
213 doc: Debugging output (implies verbose)
214 inputBinding:
215 prefix: --debug
216 position: 8
217 defaultqual:
218 type: int?
219 doc: Assumes bases are of this quality if quals are no present in input BAMs (default 15).
220 inputBinding:
221 prefix: --defaultqual
222 position: 9
223 flank:
224 type: int?
225 doc: Controls how much of the well-aligned reads will be used; this many bases at each end of the good reads will be ignored (default 10).
226 inputBinding:
227 prefix: --flank
228 position: 9
229 gapmargin:
230 type: int?
231 doc: Closed gaps must be within this number of bases of true size to be closed (100000)
232 inputBinding:
233 prefix: --gapmargin
234 position: 9
235 kmersize:
236 type: int?
237 doc: Kmer size used by internal assembler (default 47).
238 inputBinding:
239 prefix: --K
240 position: 9
241 mindepth:
242 type: float?
243 doc: |
244 Variants (snps and indels) will only be called if there is coverage of good pairs
245 at this depth or more; if this value is >= 1, it is an absolute depth, if it is a
246 fraction < 1, then minimum depth is computed by multiplying this value by the mean
247 coverage for the region, with a minumum value of 5 (default 0.1: min depth to call
248 is 10% of mean coverage or 5, whichever is greater).
249 inputBinding:
250 prefix: --mindepth
251 position: 9
252 mingap:
253 type: int?
254 doc: Minimum size for unclosed gaps (default 10)
255 inputBinding:
256 prefix: --mingap
257 position: 9
258 minmq:
259 type: int?
260 doc: Minimum alignment mapping quality for a read to count in pileups (default 0)
261 inputBinding:
262 prefix: --minmq
263 position: 9
264 minqual:
265 type: int?
266 doc: Minimum base quality to consider for pileups (default 0)
267 inputBinding:
268 prefix: --minqual
269 position: 9
270 nostrays:
271 type: boolean
272 default: false
273 doc: |
274 Skip making a pass through the input BAM files to identify stray pairs, that is,
275 those pairs in which both reads are aligned but not marked valid because they have
276 inconsistent orientation or separation. Identifying stray pairs can help fill gaps
277 and assemble larger insertions, especially of repeat content. However, doing so
278 sometimes consumes considerable memory.
279 inputBinding:
280 prefix: --nostrays
281 position: 9
282
283 outputs:
284 pilon_output:
285 type: stdout
286 fasta_output:
287 type: File?
288 outputBinding:
289 glob: $(inputs.output_prefix).fasta
290 vcf_output:
291 type: File?
292 outputBinding:
293 glob: $(inputs.output_prefix).vcf
294 track_outputs:
295 type: File[]?
296 outputBinding:
297 glob:
298 - $(inputs.output_prefix)Pilon.bed
299 - $(inputs.output_prefix)Changes.wig
300 - $(inputs.output_prefix)Unconfirmed.wig
301 - $(inputs.output_prefix)CopyNumber.wig
302 - $(inputs.output_prefix)Coverage.wig
303 - $(inputs.output_prefix)BadCoverage.wig
304 - $(inputs.output_prefix)PctBad.wig
305 - $(inputs.output_prefix)DeltaCoverage.wig
306 - $(inputs.output_prefix)DipCoverage.wig
307 - $(inputs.output_prefix)PhysicalCoverage.wig
308 - $(inputs.output_prefix)ClippedAlignments.wig
309 - $(inputs.output_prefix)WeightedQual.wig
310 - $(inputs.output_prefix)WeightedMq.wig
311 - $(inputs.output_prefix)GC.wig
312
313 changes_output:
314 type: File?
315 outputBinding:
316 glob: $(inputs.output_prefix).changes
317
318 baseCommand: [java]
319
320 arguments:
321 - valueFrom: "com.simontuffs.onejar.Boot"
322 position: 2