Mercurial > repos > artbio > trinity

comparison trinity.xml @ 0:b3fe7c4ca5aa draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
author artbio
date Sat, 17 Mar 2018 17:43:58 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:b3fe7c4ca5aa
1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.3">
2 <description>de novo assembly of RNA-Seq data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="aggressive"><![CDATA[
8 if [ -z "\$GALAXY_MEMORY_MB" ] ; then
9 GALAXY_MEMORY_GB=1 ;
10 else
11 GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
12 fi ;
13
14 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
15 workdir=`pwd` ;
16 cd "\$TRINITY_SCRATCH_DIR" ;
17 fi ;
18
19 #if $additional_params.guided.is_guided == "yes":
20 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
21 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
22 #end if
23 Trinity --no_version_check
24
25 ## Inputs
26 #if $pool.pool_mode == "Yes":
27 #if str($pool.inputs.paired_or_single) == "single":
28 --single ${ ','.join(['"%s"' % x for x in $pool.inputs.input]) }
29 #if $pool.inputs.input[0].is_of_type('fasta'):
30 --seqType fa
31 #else:
32 --seqType fq
33 #end if
34
35 #if $pool.inputs.strand.is_strand_specific:
36 --SS_lib_type $pool.inputs.strand.library_type
37 #end if
38 #elif str($pool.inputs.paired_or_single) == "paired":
39 --left ${ ','.join(['"%s"' % x for x in $pool.inputs.left_input]) }
40
41 --right ${ ','.join(['"%s"' % x for x in $pool.inputs.right_input]) }
42
43 #if $pool.inputs.left_input[0].is_of_type('fasta'):
44 --seqType fa
45 #else:
46 --seqType fq
47 #end if
48 @COMMAND_PAIRED_STRAND_JACCARD@
49 #elif str($pool.inputs.paired_or_single) == "paired_collection":
50 --left ${ ','.join(['"%s"' % x.forward for x in $pool.inputs.pair_input]) }
51 --right ${ ','.join(['"%s"' % x.reverse for x in $pool.inputs.pair_input]) }
52 #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'):
53 --seqType fa
54 #else:
55 --seqType fq
56 #end if
57 @COMMAND_PAIRED_STRAND_JACCARD@
58 #end if
59 #elif $pool.pool_mode == "No":
60 #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
61 --left $pool.inputs.pair_input.forward
62
63 --right $pool.inputs.pair_input.reverse
64
65 #if $pool.inputs.pair_input.forward.is_of_type('fasta'):
66 --seqType fa
67 #else:
68 --seqType fq
69 #end if
70 @COMMAND_PAIRED_STRAND_JACCARD@
71 #elif $pool.inputs.paired_or_single == "unmerged_single_collection":
72 --single $pool.inputs.input
73
74 #if $pool.inputs.input.is_of_type('fasta'):
75 --seqType fa
76 #else:
77 --seqType fq
78 #end if
79
80 #if $pool.inputs.strand.is_strand_specific:
81 --SS_lib_type $pool.inputs.strand.library_type
82 #end if
83 #end if
84 #end if
85 $norm
86
87 ## Additional parameters.
88 #if $additional_params.min_contig_length:
89 --min_contig_length $additional_params.min_contig_length
90 #end if
91 #if $additional_params.long_reads:
92 --long_reads $additional_params.long_reads
93 #end if
94 #if $additional_params.guided.is_guided == "yes":
95 --genome_guided_bam 'localbam.bam'
96
97 #if $additional_params.guided.genome_guided_min_coverage:
98 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
99 #end if
100
101 #if $additional_params.guided.genome_guided_min_reads_per_partition:
102 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
103 #end if
104
105 #if $additional_params.guided.genome_guided_max_intron:
106 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron
107 #end if
108 #end if
109
110 #if $additional_params.min_kmer_cov:
111 --min_kmer_cov $additional_params.min_kmer_cov
112 #end if
113
114 ## CPU and butterfly options.
115 --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr'
116
117 ## > $trinity_log 2>&1
118
119 &&
120
121 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
122 mkdir -p "\$workdir/trinity_out_dir";
123 cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir";
124 cd "\$workdir";
125 fi ;
126
127 ]]></command>
128 <inputs>
129 <conditional name="pool">
130 <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" >
131 <option value="No">No</option>
132 <option value="Yes" selected="True">Yes</option>
133 </param>
134 <when value="Yes" >
135 <conditional name="inputs">
136 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
137 <option value="single" selected="true">Single-end</option>
138 <option value="paired">Paired-end</option>
139 <option value="paired_collection">Paired-end collection</option>
140 </param>
141 <when value="single">
142 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/>
143 <conditional name="strand">
144 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
145 <when value="false">
146 </when>
147 <when value="true">
148 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
149 <option value="F">F</option>
150 <option value="R">R</option>
151 </param>
152 </when>
153 </conditional>
154 </when>
155 <when value="paired">
156 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" />
157 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" />
158 <expand macro="input_paired_strand_jaccard" />
159 </when>
160 <when value="paired_collection">
161 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/>
162 <expand macro="input_paired_strand_jaccard" />
163 </when>
164 </conditional>
165 </when>
166 <when value="No">
167 <conditional name="inputs">
168 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
169 <option value="unmerged_single_collection">Single-end</option>
170 <option value="unmerged_paired_collection">Paired-end</option>
171 </param>
172 <when value="unmerged_single_collection">
173 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" label="Single-end reads" help="Elements of collection will NOT be merged"/>
174 <conditional name="strand">
175 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
176 <when value="false">
177 </when>
178 <when value="true">
179 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
180 <option value="F">F</option>
181 <option value="R">R</option>
182 </param>
183 </when>
184 </conditional>
185 </when>
186 <when value="unmerged_paired_collection">
187 <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/>
188 <expand macro="input_paired_strand_jaccard" />
189 </when>
190 </conditional>
191 </when>
192 </conditional>
193 <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
194 <section name="additional_params" title="Additional Options" expanded="False">
195 <param name="min_contig_length" argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
196
197 <conditional name="guided">
198 <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information">
199 <option value="no">No</option>
200 <option value="yes">Yes</option>
201 </param>
202 <when value="no">
203 </when>
204 <when value="yes">
205 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
206 <param name="genome_guided_max_intron" argument="--genome_guided_max_intron" type="integer" value="" min="1" label="Maximum allowed intron length (also maximum fragment span on genome)"/>
207 <param name="genome_guided_min_coverage" argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
208 <param name="genome_guided_min_reads_per_partition" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
209 </when>
210 </conditional>
211
212 <param name="long_reads" argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
213
214 <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
215 </section>
216 </inputs>
217 <outputs>
218 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
219 </outputs>
220 <tests>
221 <test>
222 <param name="pool_mode" value="No" />
223 <param name="paired_or_single" value="unmerged_paired_collection"/>
224 <param name="pair_input">
225 <collection type="paired">
226 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
227 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
228 </collection>
229 </param>
230 <param name="is_strand_specific" value="true"/>
231 <param name="norm" value="true"/>
232 <param name="library_type" value="RF"/>
233 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
234 </test>
235 <test>
236 <param name="pool_mode" value="No" />
237 <param name="paired_or_single" value="unmerged_single_collection"/>
238 <param name="input" value="reads.left.fq" ftype="fastqsanger"/>
239 <param name="is_strand_specific" value="true"/>
240 <param name="norm" value="false"/>
241 <param name="library_type" value="F"/>
242 <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" />
243 </test>
244 <test>
245 <param name="pool_mode" value="Yes" />
246 <param name="paired_or_single" value="paired"/>
247 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
248 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
249 <param name="is_strand_specific" value="true"/>
250 <param name="norm" value="false"/>
251 <param name="library_type" value="RF"/>
252 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
253 </test>
254 <test>
255 <param name="pool_mode" value="Yes" />
256 <param name="paired_or_single" value="paired"/>
257 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
258 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
259 <param name="is_strand_specific" value="true"/>
260 <param name="norm" value="true"/>
261 <param name="library_type" value="RF"/>
262 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
263 </test>
264 <test>
265 <param name="pool_mode" value="Yes" />
266 <param name="paired_or_single" value="paired_collection"/>
267 <param name="pair_input">
268 <collection type="list:paired">
269 <element name="pair1">
270 <collection type="paired">
271 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
272 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
273 </collection>
274 </element>
275 <element name="pair2">
276 <collection type="paired">
277 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
278 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
279 </collection>
280 </element>
281 </collection>
282 </param>
283 <param name="is_strand_specific" value="true"/>
284 <param name="norm" value="true"/>
285 <param name="library_type" value="RF"/>
286 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
287 </test>
288 </tests>
289 <help>
290 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
291
292 .. _Trinity: http://trinityrnaseq.github.io
293 </help>
294 <expand macro="citation" />
295 </tool>