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comparison trinity.xml @ 32:77cf519a812e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author iuc
date Tue, 11 Apr 2023 19:57:45 +0000
parents 3772d9a10f27
children 9fa24d5aac68
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31:d2bc35f3d1c5 32:77cf519a812e
1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy2"> 1 <tool id="trinity" name="Trinity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>de novo assembly of RNA-Seq data</description> 2 <description>de novo assembly of RNA-Seq data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="8.32">coreutils</requirement> 8 <requirement type="package" version="3.2.7">rsync</requirement>
9 <requirement type="package" version="3.2.3">rsync</requirement>
10 </expand> 9 </expand>
11 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
12 if [ -z "\$GALAXY_MEMORY_MB" ] ; then 11 if [ -z "\$GALAXY_MEMORY_MB" ] ; then
13 GALAXY_MEMORY_GB=1 ; 12 GALAXY_MEMORY_GB=1 ;
14 else 13 else
52 ln -s '$pool.inputs.input' 'input.${pool.inputs.input.ext}' && 51 ln -s '$pool.inputs.input' 'input.${pool.inputs.input.ext}' &&
53 #end if 52 #end if
54 #end if 53 #end if
55 54
56 Trinity --no_version_check 55 Trinity --no_version_check
57 56 --output ./trinity_out_dir
57 ## do not try to run the high-mem normalization stats generator in parallel for paired-end fastqs
58 --no_parallel_norm_stats
58 ## Inputs 59 ## Inputs
59 #if $pool.pool_mode == "Yes": 60 #if $pool.pool_mode == "Yes":
60 #if str($pool.inputs.paired_or_single) == "single": 61 #if str($pool.inputs.paired_or_single) == "single":
61 --single ${ ','.join(["'input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.input)]) } 62 --single ${ ','.join(["'input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.input)]) }
62 #if $pool.inputs.input[0].is_of_type('fasta'): 63 #if $pool.inputs.input[0].is_of_type('fasta'):
63 --seqType fa 64 --seqType fa
64 #else: 65 #else:
65 --seqType fq 66 --seqType fq
66 #end if 67 #end if
67 68
68 #if $pool.inputs.strand.is_strand_specific: 69 #if $pool.inputs.strand.is_strand_specific == 'true':
69 --SS_lib_type $pool.inputs.strand.library_type 70 --SS_lib_type $pool.inputs.strand.library_type
70 #end if 71 #end if
71 #elif str($pool.inputs.paired_or_single) == "paired": 72 #elif str($pool.inputs.paired_or_single) == "paired":
72 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.left_input)]) } 73 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.left_input)]) }
73 74
108 --seqType fa 109 --seqType fa
109 #else: 110 #else:
110 --seqType fq 111 --seqType fq
111 #end if 112 #end if
112 113
113 #if $pool.inputs.strand.is_strand_specific: 114 #if $pool.inputs.strand.is_strand_specific == 'true':
114 --SS_lib_type $pool.inputs.strand.library_type 115 --SS_lib_type $pool.inputs.strand.library_type
115 #end if 116 #end if
116 #end if 117 #end if
117 #end if 118 #end if
118 $norm 119 $no_normalize_reads
119 120
120 ## Additional parameters. 121 ## Additional parameters.
121 #if $additional_params.min_contig_length: 122 #if $additional_params.min_contig_length:
122 --min_contig_length $additional_params.min_contig_length 123 --min_contig_length $additional_params.min_contig_length
123 #end if 124 #end if
177 <option value="paired">Paired-end</option> 178 <option value="paired">Paired-end</option>
178 <option value="paired_collection">Paired-end collection</option> 179 <option value="paired_collection">Paired-end collection</option>
179 </param> 180 </param>
180 <when value="single"> 181 <when value="single">
181 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" help=""/> 182 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" help=""/>
182 <conditional name="strand"> 183 <expand macro="is_strand_specific_f_r"/>
183 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
184 <when value="false">
185 </when>
186 <when value="true">
187 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
188 <option value="F">F</option>
189 <option value="R">R</option>
190 </param>
191 </when>
192 </conditional>
193 </when> 184 </when>
194 <when value="paired"> 185 <when value="paired">
195 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" /> 186 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" />
196 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Right/Reverse strand reads" /> 187 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Right/Reverse strand reads" />
197 <expand macro="input_paired_strand_jaccard" /> 188 <expand macro="input_paired_strand_jaccard" />
208 <option value="unmerged_single_collection">Single-end</option> 199 <option value="unmerged_single_collection">Single-end</option>
209 <option value="unmerged_paired_collection">Paired-end</option> 200 <option value="unmerged_paired_collection">Paired-end</option>
210 </param> 201 </param>
211 <when value="unmerged_single_collection"> 202 <when value="unmerged_single_collection">
212 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Single-end reads" help="Elements of collection will NOT be merged"/> 203 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Single-end reads" help="Elements of collection will NOT be merged"/>
213 <conditional name="strand"> 204 <expand macro="is_strand_specific_f_r"/>
214 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
215 <when value="false">
216 </when>
217 <when value="true">
218 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
219 <option value="F">F</option>
220 <option value="R">R</option>
221 </param>
222 </when>
223 </conditional>
224 </when> 205 </when>
225 <when value="unmerged_paired_collection"> 206 <when value="unmerged_paired_collection">
226 <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger,fastqsanger.gz" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/> 207 <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger,fastqsanger.gz" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/>
227 <expand macro="input_paired_strand_jaccard" /> 208 <expand macro="input_paired_strand_jaccard" />
228 </when> 209 </when>
229 </conditional> 210 </conditional>
230 </when> 211 </when>
231 </conditional> 212 </conditional>
232 <param name="norm" type="boolean" argument="--no_normalize_reads" truevalue="" falsevalue="--no_normalize_reads" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/> 213 <param argument="--no_normalize_reads" type="boolean" truevalue="" falsevalue="--no_normalize_reads" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
233 <section name="additional_params" title="Additional Options" expanded="False"> 214 <section name="additional_params" title="Additional Options" expanded="False">
234 <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"/> 215 <param 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"/>
235 216
236 <conditional name="guided"> 217 <conditional name="guided">
237 <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"> 218 <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">
238 <option value="no">No</option> 219 <option value="no">No</option>
239 <option value="yes">Yes</option> 220 <option value="yes">Yes</option>
240 </param> 221 </param>
241 <when value="no"> 222 <when value="no">
242 </when> 223 </when>
243 <when value="yes"> 224 <when value="yes">
244 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" /> 225 <param argument="--genome_guided_bam" type="data" format="bam" label="Coordinate-sorted BAM file" />
245 <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)"/> 226 <param argument="--genome_guided_max_intron" type="integer" value="" min="1" label="Maximum allowed intron length (also maximum fragment span on genome)"/>
246 <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"/> 227 <param 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"/>
247 <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"/> 228 <param argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
248 </when> 229 </when>
249 </conditional> 230 </conditional>
250 231
251 <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"/> 232 <param argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads"
252 233 help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
253 <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"/> 234 <param argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
254 </section> 235 </section>
255 </inputs> 236 </inputs>
256 <outputs> 237 <outputs>
257 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> 238 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir.Trinity.fasta"/>
258 <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map" from_work_dir="trinity_out_dir/Trinity.fasta.gene_trans_map"/> 239 <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map" from_work_dir="trinity_out_dir.Trinity.fasta.gene_trans_map"/>
259 </outputs> 240 </outputs>
260 <tests> 241 <tests>
261 <test> 242 <test>
262 <param name="pool_mode" value="No" /> 243 <param name="pool_mode" value="No" />
263 <param name="paired_or_single" value="unmerged_paired_collection"/> 244 <param name="paired_or_single" value="unmerged_paired_collection"/>
266 <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> 247 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
267 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> 248 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
268 </collection> 249 </collection>
269 </param> 250 </param>
270 <param name="is_strand_specific" value="true"/> 251 <param name="is_strand_specific" value="true"/>
271 <param name="norm" value="true"/> 252 <param name="no_normalize_reads" value="true"/>
272 <param name="library_type" value="RF"/> 253 <param name="library_type" value="RF"/>
273 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" /> 254 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
274 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" /> 255 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
275 </test> 256 </test>
276 <test> 257 <test>
281 <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger.gz" /> 262 <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger.gz" />
282 <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger.gz" /> 263 <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger.gz" />
283 </collection> 264 </collection>
284 </param> 265 </param>
285 <param name="is_strand_specific" value="true"/> 266 <param name="is_strand_specific" value="true"/>
286 <param name="norm" value="true"/> 267 <param name="no_normalize_reads" value="true"/>
287 <param name="library_type" value="RF"/> 268 <param name="library_type" value="RF"/>
288 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" /> 269 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
289 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" /> 270 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
290 </test> 271 </test>
291 <test> 272 <test>
292 <param name="pool_mode" value="No" /> 273 <param name="pool_mode" value="No" />
293 <param name="paired_or_single" value="unmerged_single_collection"/> 274 <param name="paired_or_single" value="unmerged_single_collection"/>
294 <param name="input" value="reads.left.fq" ftype="fastqsanger"/> 275 <param name="input" value="reads.left.fq" ftype="fastqsanger"/>
295 <param name="is_strand_specific" value="true"/> 276 <param name="is_strand_specific" value="true"/>
296 <param name="norm" value="false"/> 277 <param name="no_normalize_reads" value="false"/>
297 <param name="library_type" value="F"/> 278 <param name="library_type" value="F"/>
298 <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" /> 279 <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" />
299 <output name="gene_to_trans" file="raw/Trinity_single_unmerged_1.map" compare="sim_size" /> 280 <output name="gene_to_trans" file="raw/Trinity_single_unmerged_1.map" compare="sim_size" />
300 </test> 281 </test>
301 <test> 282 <test>
302 <param name="pool_mode" value="Yes" /> 283 <param name="pool_mode" value="Yes" />
303 <param name="paired_or_single" value="paired"/> 284 <param name="paired_or_single" value="paired"/>
304 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> 285 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
305 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> 286 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
306 <param name="is_strand_specific" value="true"/> 287 <param name="is_strand_specific" value="true"/>
307 <param name="norm" value="false"/> 288 <param name="no_normalize_reads" value="false"/>
308 <param name="library_type" value="RF"/> 289 <param name="library_type" value="RF"/>
309 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" /> 290 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
310 <output name="gene_to_trans" file="raw/Trinity.map" compare="sim_size" /> 291 <output name="gene_to_trans" file="raw/Trinity.map" compare="sim_size" />
311 </test> 292 </test>
312 <test> 293 <test>
313 <param name="pool_mode" value="Yes" /> 294 <param name="pool_mode" value="Yes" />
314 <param name="paired_or_single" value="paired"/> 295 <param name="paired_or_single" value="paired"/>
315 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> 296 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
316 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> 297 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
317 <param name="is_strand_specific" value="true"/> 298 <param name="is_strand_specific" value="true"/>
318 <param name="norm" value="true"/> 299 <param name="no_normalize_reads" value="true"/>
319 <param name="library_type" value="RF"/> 300 <param name="library_type" value="RF"/>
320 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> 301 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
321 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" /> 302 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
322 </test> 303 </test>
323 <test> 304 <test>
338 </collection> 319 </collection>
339 </element> 320 </element>
340 </collection> 321 </collection>
341 </param> 322 </param>
342 <param name="is_strand_specific" value="true"/> 323 <param name="is_strand_specific" value="true"/>
343 <param name="norm" value="true"/> 324 <param name="no_normalize_reads" value="true"/>
344 <param name="library_type" value="RF"/> 325 <param name="library_type" value="RF"/>
345 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> 326 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
346 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" /> 327 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
347 </test> 328 </test>
348 </tests> 329 </tests>