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comparison abundance_estimates_to_matrix.xml @ 2:de0af39266ef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
author iuc
date Mon, 25 Apr 2016 10:02:37 -0400
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children c7555bc21812
comparison
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1:0067c78f49dc 2:de0af39266ef
1 <tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1">
2 <description>for a de novo assembly of RNA-Seq data by Trinity</description>
3 <requirements>
4 <requirement type="package" version="2.1.1">trinity</requirement>
5 <requirement type="package" version="1.1.2">bowtie</requirement>
6 <requirement type="package" version="1.2">samtools</requirement>
7 <requirement type="package" version="3.12.0">edger</requirement>
8 <requirement type="package" version="3.12.0">bioconductor-edger</requirement>
9 <requirement type="package" version="1.2.28">rsem</requirement>
10 </requirements>
11 <stdio>
12 <exit_code range="1:"/>
13 </stdio>
14 <command><![CDATA[
15 #for $entry in $samples:
16 ln -s "${entry.file}" "${entry.sample_name}.tsv" &&
17 #end for
18
19 abundance_estimates_to_matrix.pl
20
21 --est_method ${est_method}
22 --cross_sample_norm ${additional_params.cross_sample_norm}
23
24 #for $entry in $samples:
25 "${entry.sample_name}.tsv"
26 #end for
27 ]]></command>
28 <inputs>
29 <repeat name="samples" title="RSEM abundance estimates for samples">
30 <param name="file" label="Add file" type="data" format="tabular"/>
31 <param name="sample_name" label="Sample name" type="text">
32 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
33 </param>
34 </repeat>
35
36 <param type="select" name="est_method" label="Abundance estimation method">
37 <option value="RSEM">RSEM</option>
38 <option value="eXpress">eXpress</option>
39 </param>
40
41 <section name="additional_params" title="Additional Options" expanded="False">
42 <param type="select" name="cross_sample_norm" label="Cross sample normalization">
43 <option value="TMM">TMM</option>
44 <option value="UpperQuartile">UpperQuartile</option>
45 <option value="none">None</option>
46 </param>
47 </section>
48 </inputs>
49 <outputs>
50 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/>
51 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/>
52 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix">
53 <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
54 </data>
55 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix">
56 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
57 </data>
58 </outputs>
59 <tests>
60 <test>
61 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
62 <param name="samples_0|sample_name" value="sample_A"/>
63 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
64 <param name="samples_1|sample_name" value="sample_B"/>
65 <param name="est_method" value="RSEM"/>
66 <param name="cross_sample_norm" value="TMM"/>
67 <output name="trans_counts">
68 <assert_contents>
69 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
70 <has_n_columns n="3" />
71 </assert_contents>
72 </output>
73 <output name="TPM_no_norm">
74 <assert_contents>
75 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
76 <has_n_columns n="3" />
77 </assert_contents>
78 </output>
79 <output name="norm">
80 <assert_contents>
81 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
82 <has_n_columns n="3" />
83 </assert_contents>
84 </output>
85 </test>
86 <test>
87 <param name="samples_0|file" value="count/rsem_bowtie2/RSEM.genes.results"/>
88 <param name="samples_0|sample_name" value="sample_A"/>
89 <param name="samples_1|file" value="count/rsem_bowtie2/RSEM.genes_B.results"/>
90 <param name="samples_1|sample_name" value="sample_B"/>
91 <param name="est_method" value="RSEM"/>
92 <param name="cross_sample_norm" value="TMM"/>
93 <output name="trans_counts">
94 <assert_contents>
95 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
96 <has_n_columns n="3" />
97 </assert_contents>
98 </output>
99 <output name="TPM_no_norm">
100 <assert_contents>
101 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
102 <has_n_columns n="3" />
103 </assert_contents>
104 </output>
105 <output name="norm">
106 <assert_contents>
107 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
108 <has_n_columns n="3" />
109 </assert_contents>
110 </output>
111 </test>
112 <test>
113 <param name="samples_0|file" value="count/express_bowtie/results.xprs.genes"/>
114 <param name="samples_0|sample_name" value="sample_A"/>
115 <param name="samples_1|file" value="count/express_bowtie/results_B.xprs.genes"/>
116 <param name="samples_1|sample_name" value="sample_B"/>
117 <param name="est_method" value="eXpress"/>
118 <param name="cross_sample_norm" value="TMM"/>
119 <output name="trans_counts">
120 <assert_contents>
121 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
122 <has_n_columns n="3" />
123 </assert_contents>
124 </output>
125 <output name="TPM_no_norm">
126 <assert_contents>
127 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
128 <has_n_columns n="3" />
129 </assert_contents>
130 </output>
131 <output name="norm">
132 <assert_contents>
133 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
134 <has_n_columns n="3" />
135 </assert_contents>
136 </output>
137 </test>
138 <test>
139 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
140 <param name="samples_0|sample_name" value="sample_A"/>
141 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
142 <param name="samples_1|sample_name" value="sample_B"/>
143 <param name="est_method" value="RSEM"/>
144 <param name="cross_sample_norm" value="UpperQuartile"/>
145 <output name="trans_counts">
146 <assert_contents>
147 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
148 <has_n_columns n="3" />
149 </assert_contents>
150 </output>
151 <output name="TPM_no_norm">
152 <assert_contents>
153 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
154 <has_n_columns n="3" />
155 </assert_contents>
156 </output>
157 <output name="norm" file="count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix" />
158 </test>
159 <test>
160 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
161 <param name="samples_0|sample_name" value="sample_A"/>
162 <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
163 <param name="samples_1|sample_name" value="sample_B"/>
164 <param name="est_method" value="RSEM"/>
165 <param name="cross_sample_norm" value="none"/>
166 <output name="trans_counts">
167 <assert_contents>
168 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
169 <has_n_columns n="3" />
170 </assert_contents>
171 </output>
172 <output name="TPM_no_norm">
173 <assert_contents>
174 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
175 <has_n_columns n="3" />
176 </assert_contents>
177 </output>
178 </test>
179 </tests>
180 <help>
181 <![CDATA[
182 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.
184 This matrix can then be used by 'RNASeq samples quality check for transcript quantification' and 'Differential Expression Analysis using a Trinity assembly' tools.
185
186 **Inputs**
187
188 It takes as input multiple results from 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool/
189 Each sample must have a name, that should be used in subsequent tools.
190
191 **Output**
192
193 This tool will produce a single matrix file. More details on this page:
194
195 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
196
197
198 .. _Trinity: http://trinityrnaseq.github.io
199 ]]>
200 </help>
201
202 <citations>
203 <citation type="doi">doi:10.1038/nbt.1883</citation>
204 </citations>
205 </tool>
206