Mercurial > repos > iuc > trinity_align_and_estimate_abundance

comparison align_and_estimate_abundance.xml @ 13:6d6b72d14170 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3b8670ad0ce9dd90d6a24429bca131362e56d17d"
author iuc
date Fri, 01 Nov 2019 08:09:49 -0400
parents aed859a021c0
children 56162e446004
comparison
equal deleted inserted replaced
12:478f36effca1 13:6d6b72d14170
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="1.3.2">rsem</requirement>
8 <requirement type="package" version="1.5.1">express</requirement> 8 <requirement type="package" version="0.46.0">kallisto</requirement>
9 <requirement type="package" version="0.43.1">kallisto</requirement>
10 </expand> 9 </expand>
11 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
12 ln -f -s '$transcripts' input.fa && 11 ln -f -s '$transcripts' input.fa &&
13 12
14 #if $additional_params.gene_map.has_gene_map == "yes": 13 #if $additional_params.gene_map.has_gene_map == "yes":
38 align_and_estimate_abundance.pl 37 align_and_estimate_abundance.pl
39 38
40 --transcripts input.fa 39 --transcripts input.fa
41 40
42 --est_method $method.est_method 41 --est_method $method.est_method
43 #if $method.est_method == "RSEM" or $method.est_method == "eXpress": 42 #if $method.est_method == "RSEM":
44 --aln_method $method.aln_method 43 --aln_method $method.aln_method
45 #else if $method.est_method == "salmon": 44 #else if $method.est_method == "salmon":
46 --salmon_idx_type $method.salmon_idx_type 45 --salmon_idx_type $method.salmon_idx_type
47 #end if 46 #end if
48 47
122 </conditional> 121 </conditional>
123 122
124 <conditional name="method"> 123 <conditional name="method">
125 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> 124 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
126 <option value="RSEM">RSEM</option> 125 <option value="RSEM">RSEM</option>
127 <option value="eXpress">eXpress</option>
128 <option value="salmon">Salmon</option> 126 <option value="salmon">Salmon</option>
129 <option value="kallisto">Kallisto</option> 127 <option value="kallisto">Kallisto</option>
130 </param> 128 </param>
131 <when value="RSEM"> 129 <when value="RSEM">
132 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method">
133 <option value="bowtie">Bowtie</option>
134 <option value="bowtie2">Bowtie2</option>
135 </param>
136 </when>
137 <when value="eXpress">
138 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> 130 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method">
139 <option value="bowtie">Bowtie</option> 131 <option value="bowtie">Bowtie</option>
140 <option value="bowtie2">Bowtie2</option> 132 <option value="bowtie2">Bowtie2</option>
141 </param> 133 </param>
142 </when> 134 </when>
171 </data> 163 </data>
172 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/RSEM.genes.results"> 164 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/RSEM.genes.results">
173 <filter>method['est_method'] == "RSEM"</filter> 165 <filter>method['est_method'] == "RSEM"</filter>
174 </data> 166 </data>
175 167
176 <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/results.xprs">
177 <filter>method['est_method'] == "eXpress"</filter>
178 </data>
179 <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/results.xprs.genes">
180 <filter>method['est_method'] == "eXpress"</filter>
181 </data>
182 168
183 <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf"> 169 <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf">
184 <filter>method['est_method'] == "salmon"</filter> 170 <filter>method['est_method'] == "salmon"</filter>
185 </data> 171 </data>
186 <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes"> 172 <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes">
246 <param name="left_input" value="reads.left.fq"/> 232 <param name="left_input" value="reads.left.fq"/>
247 <param name="right_input" value="reads.right.fq"/> 233 <param name="right_input" value="reads.right.fq"/>
248 <param name="transcripts" value="raw/Trinity.fasta"/> 234 <param name="transcripts" value="raw/Trinity.fasta"/>
249 <param name="gene_to_trans" value="raw/Trinity.map" /> 235 <param name="gene_to_trans" value="raw/Trinity.map" />
250 <param name="library_type" value="RF"/> 236 <param name="library_type" value="RF"/>
251 <param name="est_method" value="eXpress"/>
252 <param name="aln_method" value="bowtie"/>
253 <param name="has_gene_map" value="yes"/>
254 <output name="isoforms_counts_express">
255 <assert_contents>
256 <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" />
257 <has_n_columns n="15" />
258 </assert_contents>
259 </output>
260 <output name="genes_counts_express">
261 <assert_contents>
262 <has_line_matching expression="NA&#009;TRINITY_DN3_c0_g1.*" />
263 <has_n_columns n="15" />
264 </assert_contents>
265 </output>
266 </test>
267 <test>
268 <param name="paired_or_single" value="paired"/>
269 <param name="left_input" value="reads.left.fq"/>
270 <param name="right_input" value="reads.right.fq"/>
271 <param name="transcripts" value="raw/Trinity.fasta"/>
272 <param name="gene_to_trans" value="raw/Trinity.map" />
273 <param name="library_type" value="RF"/>
274 <param name="est_method" value="salmon"/> 237 <param name="est_method" value="salmon"/>
275 <param name="aln_method" value="bowtie"/> 238 <param name="aln_method" value="bowtie"/>
276 <param name="has_gene_map" value="yes"/> 239 <param name="has_gene_map" value="yes"/>
277 <output name="isoforms_counts_salmon"> 240 <output name="isoforms_counts_salmon">
278 <assert_contents> 241 <assert_contents>