Mercurial > repos > iuc > trinity_align_and_estimate_abundance
comparison align_and_estimate_abundance.xml @ 6:04bd98a9c751 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
author | iuc |
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date | Mon, 28 Aug 2017 16:54:12 -0400 |
parents | be3607a306af |
children | 3baf18bcf03e |
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5:be3607a306af | 6:04bd98a9c751 |
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1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.0"> | 1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.2"> |
2 <description>on a de novo assembly of RNA-Seq data</description> | 2 <description>on a 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"> |
7 <requirement type="package" version="1.3.0">rsem</requirement> | 7 <requirement type="package" version="1.3.0">rsem</requirement> |
8 <requirement type="package" version="1.5.1">express</requirement> | 8 <requirement type="package" version="1.5.1">express</requirement> |
9 <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 --> | 9 <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 --> |
10 <requirement type="package" version="0.8.1">salmon</requirement> | 10 <requirement type="package" version="0.8.1">salmon</requirement> |
11 <requirement type="package" version="0.43.1">kallisto</requirement> | |
11 </expand> | 12 </expand> |
12 <command detect_errors="aggressive"><![CDATA[ | 13 <command detect_errors="aggressive"><![CDATA[ |
13 ln -f -s '$transcripts' input.fa && | 14 ln -f -s '$transcripts' input.fa && |
14 | 15 |
15 #if $inputs.paired_or_single == "paired": | 16 #if $inputs.paired_or_single == "paired": |
123 <conditional name="method"> | 124 <conditional name="method"> |
124 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> | 125 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> |
125 <option value="RSEM">RSEM</option> | 126 <option value="RSEM">RSEM</option> |
126 <option value="eXpress">eXpress</option> | 127 <option value="eXpress">eXpress</option> |
127 <option value="salmon">Salmon</option> | 128 <option value="salmon">Salmon</option> |
129 <option value="kallisto">Kallisto</option> | |
128 </param> | 130 </param> |
129 <when value="RSEM"> | 131 <when value="RSEM"> |
130 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> | 132 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> |
131 <option value="bowtie">Bowtie</option> | 133 <option value="bowtie">Bowtie</option> |
132 <option value="bowtie2">Bowtie2</option> | 134 <option value="bowtie2">Bowtie2</option> |
141 <when value="salmon"> | 143 <when value="salmon"> |
142 <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type"> | 144 <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type"> |
143 <option value="quasi">Quasi</option> | 145 <option value="quasi">Quasi</option> |
144 <option value="fmd">FMD</option> | 146 <option value="fmd">FMD</option> |
145 </param> | 147 </param> |
148 </when> | |
149 <when value="kallisto"> | |
146 </when> | 150 </when> |
147 </conditional> | 151 </conditional> |
148 | 152 |
149 <section name="additional_params" title="Additional Options" expanded="False"> | 153 <section name="additional_params" title="Additional Options" expanded="False"> |
150 <conditional name="gene_map"> | 154 <conditional name="gene_map"> |
180 <filter>method['est_method'] == "salmon"</filter> | 184 <filter>method['est_method'] == "salmon"</filter> |
181 </data> | 185 </data> |
182 <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes"> | 186 <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes"> |
183 <filter>method['est_method'] == "salmon"</filter> | 187 <filter>method['est_method'] == "salmon"</filter> |
184 </data> | 188 </data> |
189 | |
190 <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/abundance.tsv"> | |
191 <filter>method['est_method'] == "kallisto"</filter> | |
192 </data> | |
193 <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/abundance.tsv.genes"> | |
194 <filter>method['est_method'] == "kallisto"</filter> | |
195 </data> | |
185 </outputs> | 196 </outputs> |
186 <tests> | 197 <tests> |
187 <test> | 198 <test> |
188 <param name="paired_or_single" value="paired"/> | 199 <param name="paired_or_single" value="paired"/> |
189 <param name="left_input" value="reads.left.fq"/> | 200 <param name="left_input" value="reads.left.fq"/> |
248 <has_line_matching expression="NA	TRINITY_DN3_c0_g1.*" /> | 259 <has_line_matching expression="NA	TRINITY_DN3_c0_g1.*" /> |
249 <has_n_columns n="15" /> | 260 <has_n_columns n="15" /> |
250 </assert_contents> | 261 </assert_contents> |
251 </output> | 262 </output> |
252 </test> | 263 </test> |
253 <!-- test disabled because broken in travis, probably due to conda/symlink problem--> | 264 <test> |
254 <!--test> | |
255 <param name="paired_or_single" value="paired"/> | 265 <param name="paired_or_single" value="paired"/> |
256 <param name="left_input" value="reads.left.fq"/> | 266 <param name="left_input" value="reads.left.fq"/> |
257 <param name="right_input" value="reads.right.fq"/> | 267 <param name="right_input" value="reads.right.fq"/> |
258 <param name="transcripts" value="raw/Trinity.fasta"/> | 268 <param name="transcripts" value="raw/Trinity.fasta"/> |
259 <param name="library_type" value="RF"/> | 269 <param name="library_type" value="RF"/> |
270 <assert_contents> | 280 <assert_contents> |
271 <has_line_matching expression="TRINITY_DN3_c0_g1.*" /> | 281 <has_line_matching expression="TRINITY_DN3_c0_g1.*" /> |
272 <has_n_columns n="5" /> | 282 <has_n_columns n="5" /> |
273 </assert_contents> | 283 </assert_contents> |
274 </output> | 284 </output> |
275 </test--> | 285 </test> |
286 <test> | |
287 <param name="paired_or_single" value="paired"/> | |
288 <param name="left_input" value="reads.left.fq"/> | |
289 <param name="right_input" value="reads.right.fq"/> | |
290 <param name="transcripts" value="raw/Trinity.fasta"/> | |
291 <param name="library_type" value="RF"/> | |
292 <param name="est_method" value="kallisto"/> | |
293 <param name="has_gene_map" value="yes"/> | |
294 <output name="isoforms_counts_kallisto"> | |
295 <assert_contents> | |
296 <has_line_matching expression="TRINITY_DN1_c0_g1_i1	.*" /> | |
297 <has_n_columns n="5" /> | |
298 </assert_contents> | |
299 </output> | |
300 <output name="genes_counts_kallisto"> | |
301 <assert_contents> | |
302 <has_line_matching expression="TRINITY_DN1_c0_g1	.*" /> | |
303 <has_n_columns n="5" /> | |
304 </assert_contents> | |
305 </output> | |
306 </test> | |
276 </tests> | 307 </tests> |
277 <help> | 308 <help> |
278 <![CDATA[ | 309 <![CDATA[ |
279 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. | 310 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. |
280 This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample. | 311 This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample. |