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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author iuc
date Thu, 14 Jun 2018 03:11:11 -0400
parents cee61b3fcf78
children c9cfec002f71
comparison
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19:cee61b3fcf78 20:171b827eadf2
1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.2"> 1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@">
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="requirements" /> 6 <expand macro="requirements" />
20 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' && 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' && 21 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
22 #end if 22 #end if
23 Trinity --no_version_check 23 Trinity --no_version_check
24 24
25 ## Inputs. 25 ## Inputs
26 #if $inputs.paired_or_single == "paired": 26 #if $pool.pool_mode == "Yes":
27 27 #if str($pool.inputs.paired_or_single) == "single":
28 --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) } 28 --single ${ ','.join(['"%s"' % x for x in $pool.inputs.input]) }
29 29 #if $pool.inputs.input[0].is_of_type('fasta'):
30 --right ${ ','.join(['"%s"' % x for x in $inputs.right_input]) } 30 --seqType fa
31 31 #else:
32 #if $inputs.left_input[0].is_of_type('fasta'): 32 --seqType fq
33 --seqType fa 33 #end if
34 #else: 34
35 --seqType fq 35 #if $pool.inputs.strand.is_strand_specific:
36 #end if 36 --SS_lib_type $pool.inputs.strand.library_type
37 37 #end if
38 @COMMAND_PAIRED_STRAND_JACCARD@ 38 #elif str($pool.inputs.paired_or_single) == "paired":
39 39 --left ${ ','.join(['"%s"' % x for x in $pool.inputs.left_input]) }
40 #elif $inputs.paired_or_single == "paired_collection" 40
41 --left ${ ','.join(['"%s"' % x.forward for x in $inputs.pair_input]) } 41 --right ${ ','.join(['"%s"' % x for x in $pool.inputs.right_input]) }
42 42
43 --right ${ ','.join(['"%s"' % x.reverse for x in $inputs.pair_input]) } 43 #if $pool.inputs.left_input[0].is_of_type('fasta'):
44 44 --seqType fa
45 #if $inputs.pair_input[0].forward.is_of_type('fasta'): 45 #else:
46 --seqType fa 46 --seqType fq
47 #else: 47 #end if
48 --seqType fq 48 @COMMAND_PAIRED_STRAND_JACCARD@
49 #end if 49 #elif str($pool.inputs.paired_or_single) == "paired_collection":
50 50 --left ${ ','.join(['"%s"' % x.forward for x in $pool.inputs.pair_input]) }
51 @COMMAND_PAIRED_STRAND_JACCARD@ 51 --right ${ ','.join(['"%s"' % x.reverse for x in $pool.inputs.pair_input]) }
52 52 #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'):
53 #else: 53 --seqType fa
54 --single ${ ','.join(['"%s"' % x for x in $inputs.input]) } 54 #else:
55 55 --seqType fq
56 #if $inputs.input[0].is_of_type('fasta'): 56 #end if
57 --seqType fa 57 @COMMAND_PAIRED_STRAND_JACCARD@
58 #else: 58 #end if
59 --seqType fq 59 #elif $pool.pool_mode == "No":
60 #end if 60 #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
61 61 --left $pool.inputs.pair_input.forward
62 #if $inputs.strand.is_strand_specific: 62
63 --SS_lib_type $inputs.strand.library_type 63 --right $pool.inputs.pair_input.reverse
64 #end if 64
65 #end if 65 #if $pool.inputs.pair_input.forward.is_of_type('fasta'):
66 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
67 $norm 85 $norm
68 86
69 ## Additional parameters. 87 ## Additional parameters.
70 #if $additional_params.min_contig_length: 88 #if $additional_params.min_contig_length:
71 --min_contig_length $additional_params.min_contig_length 89 --min_contig_length $additional_params.min_contig_length
85 #end if 103 #end if
86 104
87 #if $additional_params.guided.genome_guided_max_intron: 105 #if $additional_params.guided.genome_guided_max_intron:
88 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron 106 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron
89 #end if 107 #end if
90
91 #end if 108 #end if
92 109
93 #if $additional_params.min_kmer_cov: 110 #if $additional_params.min_kmer_cov:
94 --min_kmer_cov $additional_params.min_kmer_cov 111 --min_kmer_cov $additional_params.min_kmer_cov
95 #end if 112 #end if
107 cd "\$workdir"; 124 cd "\$workdir";
108 fi ; 125 fi ;
109 126
110 ]]></command> 127 ]]></command>
111 <inputs> 128 <inputs>
112 <conditional name="inputs"> 129 <conditional name="pool">
113 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> 130 <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" >
114 <option value="single">Single-end</option> 131 <option value="No">No</option>
115 <option value="paired" selected="true">Paired-end</option> 132 <option value="Yes" selected="True">Yes</option>
116 <option value="paired_collection">Paired-end collection</option>
117 </param> 133 </param>
118 <when value="single"> 134 <when value="Yes" >
119 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/> 135 <conditional name="inputs">
120 <conditional name="strand"> 136 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
121 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 137 <option value="single" selected="true">Single-end</option>
122 <when value="false"> 138 <option value="paired">Paired-end</option>
123 </when> 139 <option value="paired_collection">Paired-end collection</option>
124 <when value="true"> 140 </param>
125 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> 141 <when value="single">
126 <option value="F">F</option> 142 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/>
127 <option value="R">R</option> 143 <conditional name="strand">
128 </param> 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" />
129 </when> 163 </when>
130 </conditional> 164 </conditional>
131 </when> 165 </when>
132 <when value="paired"> 166 <when value="No">
133 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" /> 167 <conditional name="inputs">
134 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" /> 168 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
135 <expand macro="input_paired_strand_jaccard" /> 169 <option value="unmerged_single_collection">Single-end</option>
136 </when> 170 <option value="unmerged_paired_collection">Paired-end</option>
137 <when value="paired_collection"> 171 </param>
138 <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"/> 172 <when value="unmerged_single_collection">
139 <expand macro="input_paired_strand_jaccard" /> 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>
140 </when> 191 </when>
141 </conditional> 192 </conditional>
142
143 <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."/> 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."/>
144
145 <section name="additional_params" title="Additional Options" expanded="False"> 194 <section name="additional_params" title="Additional Options" expanded="False">
146 <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"/> 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"/>
147 196
148 <conditional name="guided"> 197 <conditional name="guided">
149 <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"> 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">
165 <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"/> 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"/>
166 </section> 215 </section>
167 </inputs> 216 </inputs>
168 <outputs> 217 <outputs>
169 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> 218 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
219 <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map" from_work_dir="trinity_out_dir/Trinity.fasta.gene_trans_map"/>
170 </outputs> 220 </outputs>
171 <tests> 221 <tests>
172 <test> 222 <test>
223 <param name="pool_mode" value="No" />
224 <param name="paired_or_single" value="unmerged_paired_collection"/>
225 <param name="pair_input">
226 <collection type="paired">
227 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
228 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
229 </collection>
230 </param>
231 <param name="is_strand_specific" value="true"/>
232 <param name="norm" value="true"/>
233 <param name="library_type" value="RF"/>
234 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
235 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
236 </test>
237 <test>
238 <param name="pool_mode" value="No" />
239 <param name="paired_or_single" value="unmerged_single_collection"/>
240 <param name="input" value="reads.left.fq" ftype="fastqsanger"/>
241 <param name="is_strand_specific" value="true"/>
242 <param name="norm" value="false"/>
243 <param name="library_type" value="F"/>
244 <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" />
245 <output name="gene_to_trans" file="raw/Trinity_single_unmerged_1.map" compare="sim_size" />
246 </test>
247 <test>
248 <param name="pool_mode" value="Yes" />
173 <param name="paired_or_single" value="paired"/> 249 <param name="paired_or_single" value="paired"/>
174 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> 250 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
175 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> 251 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
176 <param name="is_strand_specific" value="true"/> 252 <param name="is_strand_specific" value="true"/>
177 <param name="norm" value="false"/> 253 <param name="norm" value="false"/>
178 <param name="library_type" value="RF"/> 254 <param name="library_type" value="RF"/>
179 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" /> 255 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
180 </test> 256 <output name="gene_to_trans" file="raw/Trinity.map" compare="sim_size" />
181 <test> 257 </test>
258 <test>
259 <param name="pool_mode" value="Yes" />
182 <param name="paired_or_single" value="paired"/> 260 <param name="paired_or_single" value="paired"/>
183 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> 261 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
184 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> 262 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
185 <param name="is_strand_specific" value="true"/> 263 <param name="is_strand_specific" value="true"/>
186 <param name="norm" value="true"/> 264 <param name="norm" value="true"/>
187 <param name="library_type" value="RF"/> 265 <param name="library_type" value="RF"/>
188 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> 266 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
189 </test> 267 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
190 <test> 268 </test>
269 <test>
270 <param name="pool_mode" value="Yes" />
191 <param name="paired_or_single" value="paired_collection"/> 271 <param name="paired_or_single" value="paired_collection"/>
192 <param name="pair_input"> 272 <param name="pair_input">
193 <collection type="list:paired"> 273 <collection type="list:paired">
194 <element name="pair1"> 274 <element name="pair1">
195 <collection type="paired"> 275 <collection type="paired">
207 </param> 287 </param>
208 <param name="is_strand_specific" value="true"/> 288 <param name="is_strand_specific" value="true"/>
209 <param name="norm" value="true"/> 289 <param name="norm" value="true"/>
210 <param name="library_type" value="RF"/> 290 <param name="library_type" value="RF"/>
211 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> 291 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
292 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
212 </test> 293 </test>
213 </tests> 294 </tests>
214 <help> 295 <help>
215 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. 296 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
216 297
217 .. _Trinity: http://trinityrnaseq.github.io 298 .. _Trinity: http://trinityrnaseq.github.io
218 </help> 299 </help>
219
220 <expand macro="citation" /> 300 <expand macro="citation" />
221 </tool> 301 </tool>