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comparison trinity.xml @ 26:26d5493b20b6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
author iuc
date Fri, 19 Mar 2021 21:43:30 +0000
parents c9cfec002f71
children 5b60313a6ce7
comparison
equal deleted inserted replaced
25:d84caa5a98ad 26:26d5493b20b6
1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@"> 1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy1">
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" />
137 <option value="single" selected="true">Single-end</option> 137 <option value="single" selected="true">Single-end</option>
138 <option value="paired">Paired-end</option> 138 <option value="paired">Paired-end</option>
139 <option value="paired_collection">Paired-end collection</option> 139 <option value="paired_collection">Paired-end collection</option>
140 </param> 140 </param>
141 <when value="single"> 141 <when value="single">
142 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/> 142 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" help=""/>
143 <conditional name="strand"> 143 <conditional name="strand">
144 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 144 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
145 <when value="false"> 145 <when value="false">
146 </when> 146 </when>
147 <when value="true"> 147 <when value="true">
151 </param> 151 </param>
152 </when> 152 </when>
153 </conditional> 153 </conditional>
154 </when> 154 </when>
155 <when value="paired"> 155 <when value="paired">
156 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" /> 156 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" 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" /> 157 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Right/Reverse strand reads" />
158 <expand macro="input_paired_strand_jaccard" /> 158 <expand macro="input_paired_strand_jaccard" />
159 </when> 159 </when>
160 <when value="paired_collection"> 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"/> 161 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger,fastqsanger.gz" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/>
162 <expand macro="input_paired_strand_jaccard" /> 162 <expand macro="input_paired_strand_jaccard" />
163 </when> 163 </when>
164 </conditional> 164 </conditional>
165 </when> 165 </when>
166 <when value="No"> 166 <when value="No">
168 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> 168 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
169 <option value="unmerged_single_collection">Single-end</option> 169 <option value="unmerged_single_collection">Single-end</option>
170 <option value="unmerged_paired_collection">Paired-end</option> 170 <option value="unmerged_paired_collection">Paired-end</option>
171 </param> 171 </param>
172 <when value="unmerged_single_collection"> 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"/> 173 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Single-end reads" help="Elements of collection will NOT be merged"/>
174 <conditional name="strand"> 174 <conditional name="strand">
175 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 175 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
176 <when value="false"> 176 <when value="false">
177 </when> 177 </when>
178 <when value="true"> 178 <when value="true">
182 </param> 182 </param>
183 </when> 183 </when>
184 </conditional> 184 </conditional>
185 </when> 185 </when>
186 <when value="unmerged_paired_collection"> 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"/> 187 <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"/>
188 <expand macro="input_paired_strand_jaccard" /> 188 <expand macro="input_paired_strand_jaccard" />
189 </when> 189 </when>
190 </conditional> 190 </conditional>
191 </when> 191 </when>
192 </conditional> 192 </conditional>
222 <test> 222 <test>
223 <param name="pool_mode" value="No" /> 223 <param name="pool_mode" value="No" />
224 <param name="paired_or_single" value="unmerged_paired_collection"/> 224 <param name="paired_or_single" value="unmerged_paired_collection"/>
225 <param name="pair_input"> 225 <param name="pair_input">
226 <collection type="paired"> 226 <collection type="paired">
227 <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> 227 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
228 <element name="reverse" value="reads.right.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_paired_collection"/>
240 <param name="pair_input">
241 <collection type="paired">
242 <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger" />
243 <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger"/>
229 </collection> 244 </collection>
230 </param> 245 </param>
231 <param name="is_strand_specific" value="true"/> 246 <param name="is_strand_specific" value="true"/>
232 <param name="norm" value="true"/> 247 <param name="norm" value="true"/>
233 <param name="library_type" value="RF"/> 248 <param name="library_type" value="RF"/>