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comparison abundance_estimates_to_matrix.xml @ 6:74217fbfba4d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
author iuc
date Mon, 28 Aug 2017 16:55:13 -0400
parents 8b5039bdf1f6
children 34cefa17a764
comparison
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5:8b5039bdf1f6 6:74217fbfba4d
1 <tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.0"> 1 <tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1">
2 <description>for a de novo assembly of RNA-Seq data by Trinity</description> 2 <description>for a de novo assembly of RNA-Seq data by Trinity</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="3.16.5">bioconductor-edger</requirement> 7 <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
8 <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 --> 8 <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 -->
9 <requirement type="package" version="0.8.1">salmon</requirement> 9 <requirement type="package" version="0.8.1">salmon</requirement>
10 <requirement type="package" version="0.43.1">kallisto</requirement>
10 </expand> 11 </expand>
11 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
12 #import re 13 #import re
13 #for $entry in $samples: 14 #for $entry in $samples:
14 ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && 15 ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' &&
28 29
29 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> 30 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
30 <option value="RSEM">RSEM</option> 31 <option value="RSEM">RSEM</option>
31 <option value="eXpress">eXpress</option> 32 <option value="eXpress">eXpress</option>
32 <option value="salmon">Salmon</option> 33 <option value="salmon">Salmon</option>
34 <option value="kallisto">Kallisto</option>
33 </param> 35 </param>
34 36
35 <section name="additional_params" title="Additional Options" expanded="False"> 37 <section name="additional_params" title="Additional Options" expanded="False">
36 <param type="select" name="cross_sample_norm" argument="--cross_sample_norm" label="Cross sample normalization"> 38 <param type="select" name="cross_sample_norm" argument="--cross_sample_norm" label="Cross sample normalization">
37 <option value="TMM">TMM</option> 39 <option value="TMM">TMM</option>
174 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 176 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
175 <has_n_columns n="3" /> 177 <has_n_columns n="3" />
176 </assert_contents> 178 </assert_contents>
177 </output> 179 </output>
178 </test> 180 </test>
181 <test>
182 <param name="samples" ftype="tabular" value="count/kallisto/abundance.tsv.genes,count/kallisto/abundance_B.tsv.genes"/>
183 <param name="est_method" value="kallisto"/>
184 <param name="cross_sample_norm" value="TMM"/>
185 <output name="trans_counts">
186 <assert_contents>
187 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
188 <has_n_columns n="3" />
189 </assert_contents>
190 </output>
191 <output name="TPM_no_norm">
192 <assert_contents>
193 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
194 <has_n_columns n="3" />
195 </assert_contents>
196 </output>
197 <output name="norm">
198 <assert_contents>
199 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
200 <has_n_columns n="3" />
201 </assert_contents>
202 </output>
203 </test>
179 </tests> 204 </tests>
180 <help> 205 <help>
181 <![CDATA[ 206 <![CDATA[
182 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. 207 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
183 This tool will combine abundance estimations (produced by 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool) from multiple samples into a single tabular file. 208 This tool will combine abundance estimations (produced by 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool) from multiple samples into a single tabular file.