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comparison abundance_estimates_to_matrix.xml @ 1:fba77b1f69b4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
author iuc
date Fri, 18 Nov 2016 06:07:28 -0500
parents 77fc547df6ff
children 8b5039bdf1f6
comparison
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0:77fc547df6ff 1:fba77b1f69b4
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="3.14.0">bioconductor-edger</requirement> 7 <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
8 <requirement type="package" version="0.6.0">salmon</requirement> 8 <requirement type="package" version="0.7.2">salmon</requirement>
9 </expand> 9 </expand>
10 <expand macro="stdio"/> 10 <expand macro="stdio"/>
11 <command><![CDATA[ 11 <command><![CDATA[
12 #import re
12 #for $entry in $samples: 13 #for $entry in $samples:
13 ln -s "${entry.file}" "${entry.sample_name}" && 14 ln -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' &&
14 #end for 15 #end for
15 16
16 abundance_estimates_to_matrix.pl 17 abundance_estimates_to_matrix.pl
17 18
18 --est_method ${est_method} 19 --est_method ${est_method}
19 --cross_sample_norm ${additional_params.cross_sample_norm} 20 --cross_sample_norm ${additional_params.cross_sample_norm}
20 21
21 #for $entry in $samples: 22 #for $entry in $samples:
22 "${entry.sample_name}" 23 '${re.sub('[^\w\-_]', '_', entry.element_identifier)}'
23 #end for 24 #end for
24 ]]></command> 25 ]]></command>
25 <inputs> 26 <inputs>
26 <repeat name="samples" title="Abundance estimates for samples"> 27 <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" />
27 <param name="file" label="Add file" type="data" format="tabular"/>
28 <param name="sample_name" label="Sample name" type="text">
29 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
30 </param>
31 </repeat>
32 28
33 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> 29 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
34 <option value="RSEM">RSEM</option> 30 <option value="RSEM">RSEM</option>
35 <option value="eXpress">eXpress</option> 31 <option value="eXpress">eXpress</option>
36 <option value="salmon">Salmon</option> 32 <option value="salmon">Salmon</option>
54 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter> 50 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
55 </data> 51 </data>
56 </outputs> 52 </outputs>
57 <tests> 53 <tests>
58 <test> 54 <test>
59 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> 55 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
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"/> 56 <param name="est_method" value="RSEM"/>
64 <param name="cross_sample_norm" value="TMM"/> 57 <param name="cross_sample_norm" value="TMM"/>
65 <output name="trans_counts"> 58 <output name="trans_counts">
66 <assert_contents> 59 <assert_contents>
67 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 60 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
80 <has_n_columns n="3" /> 73 <has_n_columns n="3" />
81 </assert_contents> 74 </assert_contents>
82 </output> 75 </output>
83 </test> 76 </test>
84 <test> 77 <test>
85 <param name="samples_0|file" value="count/rsem_bowtie2/RSEM.genes.results"/> 78 <param name="samples" ftype="tabular" value="count/rsem_bowtie2/sample_A,count/rsem_bowtie2/sample_B"/>
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"/> 79 <param name="est_method" value="RSEM"/>
90 <param name="cross_sample_norm" value="TMM"/> 80 <param name="cross_sample_norm" value="TMM"/>
91 <output name="trans_counts"> 81 <output name="trans_counts">
92 <assert_contents> 82 <assert_contents>
93 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 83 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
106 <has_n_columns n="3" /> 96 <has_n_columns n="3" />
107 </assert_contents> 97 </assert_contents>
108 </output> 98 </output>
109 </test> 99 </test>
110 <test> 100 <test>
111 <param name="samples_0|file" value="count/express_bowtie/results.xprs.genes"/> 101 <param name="samples" ftype="tabular" value="count/express_bowtie/sample_A,count/express_bowtie/sample_B"/>
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"/> 102 <param name="est_method" value="eXpress"/>
116 <param name="cross_sample_norm" value="TMM"/> 103 <param name="cross_sample_norm" value="TMM"/>
117 <output name="trans_counts"> 104 <output name="trans_counts">
118 <assert_contents> 105 <assert_contents>
119 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 106 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
132 <has_n_columns n="3" /> 119 <has_n_columns n="3" />
133 </assert_contents> 120 </assert_contents>
134 </output> 121 </output>
135 </test> 122 </test>
136 <test> 123 <test>
137 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> 124 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
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"/> 125 <param name="est_method" value="RSEM"/>
142 <param name="cross_sample_norm" value="UpperQuartile"/> 126 <param name="cross_sample_norm" value="UpperQuartile"/>
143 <output name="trans_counts"> 127 <output name="trans_counts">
144 <assert_contents> 128 <assert_contents>
145 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 129 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
157 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 141 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
158 </assert_contents> 142 </assert_contents>
159 </output> 143 </output>
160 </test> 144 </test>
161 <test> 145 <test>
162 <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/> 146 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
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"/> 147 <param name="est_method" value="RSEM"/>
167 <param name="cross_sample_norm" value="none"/> 148 <param name="cross_sample_norm" value="none"/>
168 <output name="trans_counts"> 149 <output name="trans_counts">
169 <assert_contents> 150 <assert_contents>
170 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 151 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
177 <has_n_columns n="3" /> 158 <has_n_columns n="3" />
178 </assert_contents> 159 </assert_contents>
179 </output> 160 </output>
180 </test> 161 </test>
181 <test> 162 <test>
182 <param name="samples_0|file" value="count/salmon/quant.sf"/> 163 <param name="samples" ftype="tabular" value="count/salmon/sample_A,count/salmon/sample_B"/>
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"/> 164 <param name="est_method" value="salmon"/>
187 <param name="cross_sample_norm" value="none"/> 165 <param name="cross_sample_norm" value="none"/>
188 <output name="trans_counts"> 166 <output name="trans_counts">
189 <assert_contents> 167 <assert_contents>
190 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 168 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />