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comparison abundance_estimates_to_matrix.xml @ 10:13ab393ba794 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author iuc
date Thu, 14 Jun 2018 03:12:12 -0400
parents 34cefa17a764
children 0f445c315a08
comparison
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9:67906d99d3c0 10:13ab393ba794
1 <tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.2"> 1 <tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@">
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="3.20.1">bioconductor-edger</requirement> 7 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
8 <requirement type="package" version="0.9.1">salmon</requirement> 8 <requirement type="package" version="0.9.1">salmon</requirement>
9 <requirement type="package" version="0.43.1">kallisto</requirement> 9 <requirement type="package" version="0.44.0">kallisto</requirement>
10 </expand> 10 </expand>
11 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
12 #import re 12 #import re
13 #for $entry in $samples: 13 #for $entry in $samples:
14 ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && 14 ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' &&
17 abundance_estimates_to_matrix.pl 17 abundance_estimates_to_matrix.pl
18 18
19 --est_method ${est_method} 19 --est_method ${est_method}
20 --cross_sample_norm ${additional_params.cross_sample_norm} 20 --cross_sample_norm ${additional_params.cross_sample_norm}
21 21
22 #if $gene_trans_map:
23 --gene_trans_map '$gene_trans_map'
24 #else:
25 --gene_trans_map 'none'
26 #end if
27
22 #for $entry in $samples: 28 #for $entry in $samples:
23 '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' 29 '${re.sub('[^\w\-_]', '_', entry.element_identifier)}'
24 #end for 30 #end for
31
32 && mv *.isoform.counts.matrix '$trans_counts'
33 && mv *.isoform.TPM.not_cross_norm '$TPM_no_norm'
34 #if $gene_trans_map:
35 && mv *.gene.counts.matrix '$trans_counts_gene'
36 && mv *.gene.TPM.not_cross_norm '$TPM_no_norm_gene'
37 #end if
38
39 #if $additional_params.cross_sample_norm == "TMM":
40 && mv *.isoform.TMM.EXPR.matrix '$norm_TMM'
41 #if $gene_trans_map:
42 && mv *.gene.TMM.EXPR.matrix '$norm_TMM_gene'
43 #end if
44 #else if $additional_params.cross_sample_norm == "UpperQuartile":
45 && mv *.isoform.UpperQuartile.EXPR.matrix '$norm_UQ'
46 #if $gene_trans_map:
47 && mv *.gene.UpperQuartile.EXPR.matrix '$norm_UQ_gene'
48 #end if
49 #end if
25 ]]></command> 50 ]]></command>
26 <inputs> 51 <inputs>
27 <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" /> 52 <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" />
28 53 <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" optional="true" help="Only needed for gene level estimates" />
29 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> 54 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
30 <option value="RSEM">RSEM</option> 55 <option value="RSEM">RSEM</option>
31 <option value="eXpress">eXpress</option> 56 <option value="eXpress">eXpress</option>
32 <option value="salmon">Salmon</option> 57 <option value="salmon">Salmon</option>
33 <option value="kallisto">Kallisto</option> 58 <option value="kallisto">Kallisto</option>
40 <option value="none">None</option> 65 <option value="none">None</option>
41 </param> 66 </param>
42 </section> 67 </section>
43 </inputs> 68 </inputs>
44 <outputs> 69 <outputs>
45 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/> 70 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment isoform counts (raw counts)"/>
46 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/> 71 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of isoform TPM expression values (not cross-sample normalized)"/>
47 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix"> 72
73 <data format="tabular" name="trans_counts_gene" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment gene counts (raw counts)">
74 <filter>gene_trans_map</filter>
75 </data>
76 <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: matrix of gene TPM expression values (not cross-sample normalized)">
77 <filter>gene_trans_map</filter>
78 </data>
79
80 <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
48 <filter>additional_params['cross_sample_norm'] == "TMM"</filter> 81 <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
49 </data> 82 </data>
50 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix"> 83 <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
51 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter> 84 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
85 </data>
86
87 <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
88 <filter>additional_params['cross_sample_norm'] == "TMM" and gene_trans_map</filter>
89 </data>
90 <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
91 <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter>
52 </data> 92 </data>
53 </outputs> 93 </outputs>
54 <tests> 94 <tests>
55 <test> 95 <test>
56 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> 96 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/>
66 <assert_contents> 106 <assert_contents>
67 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 107 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
68 <has_n_columns n="3" /> 108 <has_n_columns n="3" />
69 </assert_contents> 109 </assert_contents>
70 </output> 110 </output>
71 <output name="norm"> 111 <output name="norm_TMM">
72 <assert_contents> 112 <assert_contents>
73 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 113 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
74 <has_n_columns n="3" /> 114 <has_n_columns n="3" />
75 </assert_contents> 115 </assert_contents>
76 </output> 116 </output>
89 <assert_contents> 129 <assert_contents>
90 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 130 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
91 <has_n_columns n="3" /> 131 <has_n_columns n="3" />
92 </assert_contents> 132 </assert_contents>
93 </output> 133 </output>
94 <output name="norm"> 134 <output name="norm_TMM">
95 <assert_contents> 135 <assert_contents>
96 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 136 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
97 <has_n_columns n="3" /> 137 <has_n_columns n="3" />
98 </assert_contents> 138 </assert_contents>
99 </output> 139 </output>
112 <assert_contents> 152 <assert_contents>
113 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 153 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
114 <has_n_columns n="3" /> 154 <has_n_columns n="3" />
115 </assert_contents> 155 </assert_contents>
116 </output> 156 </output>
117 <output name="norm"> 157 <output name="norm_TMM">
118 <assert_contents> 158 <assert_contents>
119 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 159 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
120 <has_n_columns n="3" /> 160 <has_n_columns n="3" />
121 </assert_contents> 161 </assert_contents>
122 </output> 162 </output>
135 <assert_contents> 175 <assert_contents>
136 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 176 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
137 <has_n_columns n="3" /> 177 <has_n_columns n="3" />
138 </assert_contents> 178 </assert_contents>
139 </output> 179 </output>
140 <output name="norm"> 180 <output name="norm_UQ">
141 <assert_contents> 181 <assert_contents>
142 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 182 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
143 </assert_contents> 183 </assert_contents>
144 </output> 184 </output>
145 </test> 185 </test>
191 <assert_contents> 231 <assert_contents>
192 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 232 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
193 <has_n_columns n="3" /> 233 <has_n_columns n="3" />
194 </assert_contents> 234 </assert_contents>
195 </output> 235 </output>
196 <output name="norm"> 236 <output name="norm_TMM">
197 <assert_contents> 237 <assert_contents>
198 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" /> 238 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
199 <has_n_columns n="3" /> 239 <has_n_columns n="3" />
200 </assert_contents> 240 </assert_contents>
201 </output> 241 </output>