Mercurial > repos > iuc > trinity
comparison trinity.xml @ 26:26d5493b20b6 draft
"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 |
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| 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"/> |