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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
author iuc
date Wed, 27 Jul 2016 08:43:07 -0400
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1 <tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.0">
2 <description>for a de novo assembly of RNA-Seq data by Trinity</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
8 <requirement type="package" version="0.6.0">salmon</requirement>
9 </expand>
10 <expand macro="stdio"/>
11 <command><![CDATA[
12 #for $entry in $samples:
13 ln -s "${entry.file}" "${entry.sample_name}" &&
14 #end for
15
16 abundance_estimates_to_matrix.pl
17
18 --est_method ${est_method}
19 --cross_sample_norm ${additional_params.cross_sample_norm}
20
21 #for $entry in $samples:
22 "${entry.sample_name}"
23 #end for
24 ]]></command>
25 <inputs>
26 <repeat name="samples" title="Abundance estimates for samples">
27 <param name="file" label="Add file" type="data" format="tabular"/>
28 <param name="sample_name" label="Sample name" type="text">
29 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
30 </param>
31 </repeat>
32
33 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
34 <option value="RSEM">RSEM</option>
35 <option value="eXpress">eXpress</option>
36 <option value="salmon">Salmon</option>
37 </param>
38
39 <section name="additional_params" title="Additional Options" expanded="False">
40 <param type="select" name="cross_sample_norm" argument="--cross_sample_norm" label="Cross sample normalization">
41 <option value="TMM">TMM</option>
42 <option value="UpperQuartile">UpperQuartile</option>
43 <option value="none">None</option>
44 </param>
45 </section>
46 </inputs>
47 <outputs>
48 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/>
49 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/>
50 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix">
51 <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
52 </data>
53 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix">
54 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
55 </data>
56 </outputs>
57 <tests>
58 <test>
59 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
60 <param name="samples_0|sample_name" value="sample_A"/>
61 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
62 <param name="samples_1|sample_name" value="sample_B"/>
63 <param name="est_method" value="RSEM"/>
64 <param name="cross_sample_norm" value="TMM"/>
65 <output name="trans_counts">
66 <assert_contents>
67 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
68 <has_n_columns n="3" />
69 </assert_contents>
70 </output>
71 <output name="TPM_no_norm">
72 <assert_contents>
73 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
74 <has_n_columns n="3" />
75 </assert_contents>
76 </output>
77 <output name="norm">
78 <assert_contents>
79 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
80 <has_n_columns n="3" />
81 </assert_contents>
82 </output>
83 </test>
84 <test>
85 <param name="samples_0|file" value="count/rsem_bowtie2/RSEM.genes.results"/>
86 <param name="samples_0|sample_name" value="sample_A"/>
87 <param name="samples_1|file" value="count/rsem_bowtie2/RSEM.genes_B.results"/>
88 <param name="samples_1|sample_name" value="sample_B"/>
89 <param name="est_method" value="RSEM"/>
90 <param name="cross_sample_norm" value="TMM"/>
91 <output name="trans_counts">
92 <assert_contents>
93 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
94 <has_n_columns n="3" />
95 </assert_contents>
96 </output>
97 <output name="TPM_no_norm">
98 <assert_contents>
99 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
100 <has_n_columns n="3" />
101 </assert_contents>
102 </output>
103 <output name="norm">
104 <assert_contents>
105 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
106 <has_n_columns n="3" />
107 </assert_contents>
108 </output>
109 </test>
110 <test>
111 <param name="samples_0|file" value="count/express_bowtie/results.xprs.genes"/>
112 <param name="samples_0|sample_name" value="sample_A"/>
113 <param name="samples_1|file" value="count/express_bowtie/results_B.xprs.genes"/>
114 <param name="samples_1|sample_name" value="sample_B"/>
115 <param name="est_method" value="eXpress"/>
116 <param name="cross_sample_norm" value="TMM"/>
117 <output name="trans_counts">
118 <assert_contents>
119 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
120 <has_n_columns n="3" />
121 </assert_contents>
122 </output>
123 <output name="TPM_no_norm">
124 <assert_contents>
125 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
126 <has_n_columns n="3" />
127 </assert_contents>
128 </output>
129 <output name="norm">
130 <assert_contents>
131 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
132 <has_n_columns n="3" />
133 </assert_contents>
134 </output>
135 </test>
136 <test>
137 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
138 <param name="samples_0|sample_name" value="sample_A"/>
139 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
140 <param name="samples_1|sample_name" value="sample_B"/>
141 <param name="est_method" value="RSEM"/>
142 <param name="cross_sample_norm" value="UpperQuartile"/>
143 <output name="trans_counts">
144 <assert_contents>
145 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
146 <has_n_columns n="3" />
147 </assert_contents>
148 </output>
149 <output name="TPM_no_norm">
150 <assert_contents>
151 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
152 <has_n_columns n="3" />
153 </assert_contents>
154 </output>
155 <output name="norm">
156 <assert_contents>
157 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
158 </assert_contents>
159 </output>
160 </test>
161 <test>
162 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
163 <param name="samples_0|sample_name" value="sample_A"/>
164 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
165 <param name="samples_1|sample_name" value="sample_B"/>
166 <param name="est_method" value="RSEM"/>
167 <param name="cross_sample_norm" value="none"/>
168 <output name="trans_counts">
169 <assert_contents>
170 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
171 <has_n_columns n="3" />
172 </assert_contents>
173 </output>
174 <output name="TPM_no_norm">
175 <assert_contents>
176 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
177 <has_n_columns n="3" />
178 </assert_contents>
179 </output>
180 </test>
181 <test>
182 <param name="samples_0|file" value="count/salmon/quant.sf"/>
183 <param name="samples_0|sample_name" value="sample_A"/>
184 <param name="samples_1|file" value="count/salmon/quant.sf.genes"/>
185 <param name="samples_1|sample_name" value="sample_B"/>
186 <param name="est_method" value="salmon"/>
187 <param name="cross_sample_norm" value="none"/>
188 <output name="trans_counts">
189 <assert_contents>
190 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
191 <has_n_columns n="3" />
192 </assert_contents>
193 </output>
194 <output name="TPM_no_norm">
195 <assert_contents>
196 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
197 <has_n_columns n="3" />
198 </assert_contents>
199 </output>
200 </test>
201 </tests>
202 <help>
203 <![CDATA[
204 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
205 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.
206 This matrix can then be used by 'RNASeq samples quality check for transcript quantification' and 'Differential Expression Analysis using a Trinity assembly' tools.
207
208 **Inputs**
209
210 It takes as input multiple results from 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool/
211 Each sample must have a name, that should be used in subsequent tools.
212
213 **Output**
214
215 This tool will produce a single matrix file. More details on this page:
216
217 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
218
219
220 .. _Trinity: http://trinityrnaseq.github.io
221 ]]>
222 </help>
223
224 <expand macro="citation" />
225 </tool>