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comparison annotateMyIDs.xml @ 13:c99c6e951106 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 669d17e476ed4e3a57c697e42f690f9650e855d8
author iuc
date Sat, 21 Jan 2023 14:57:51 +0000
parents 6feec02cf814
children dec0e9dbe336
comparison
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12:6feec02cf814 13:c99c6e951106
2 <description>annotate a generic set of identifiers</description> 2 <description>annotate a generic set of identifiers</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">annotatemyids</xref> 4 <xref type="bio.tools">annotatemyids</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
7 <token name="@TOOL_VERSION@">3.14.0</token> 7 <token name="@TOOL_VERSION@">3.16.0</token>
8 <token name="@VERSION_SUFFIX@">1</token> 8 <token name="@VERSION_SUFFIX@">1</token>
9 </macros> 9 </macros>
10 <requirements> 10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.hs.eg.db</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.hs.eg.db</requirement>
12 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.mm.eg.db</requirement> 12 <requirement type="package" version="@TOOL_VERSION@">bioconductor-org.mm.eg.db</requirement>
145 <test expect_num_outputs="1"> 145 <test expect_num_outputs="1">
146 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/> 146 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
147 <param name="id_type" value="ENSEMBL"/> 147 <param name="id_type" value="ENSEMBL"/>
148 <param name="organism" value="Hs"/> 148 <param name="organism" value="Hs"/>
149 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" /> 149 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
150 <output name="out_tab" file="out_gokegg.tab" /> 150 <output name="out_tab">
151 <assert_contents>
152 <has_n_columns n="4"/>
153 <has_n_lines min="700"/>
154 <has_text_matching expression="ENSG00000012048" min="80"/>
155 </assert_contents>
156 </output>
151 </test> 157 </test>
152 <!-- Ensure duplicate Gene ID removal works --> 158 <!-- Ensure duplicate Gene ID removal works -->
153 <test expect_num_outputs="1"> 159 <test expect_num_outputs="1">
154 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/> 160 <param name="id_file" value="ensembl_ids.tab" ftype="tabular"/>
155 <param name="id_type" value="ENSEMBL"/> 161 <param name="id_type" value="ENSEMBL"/>
156 <param name="organism" value="Hs"/> 162 <param name="organism" value="Hs"/>
157 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" /> 163 <param name="output_cols" value="ENSEMBL,GO,ONTOLOGY,EVIDENCE" />
158 <param name="remove_dups" value="True" /> 164 <param name="remove_dups" value="True" />
159 <output name="out_tab" file="out_gokegg_dupsrem.tab" /> 165 <output name="out_tab">
166 <assert_contents>
167 <has_n_columns n="4"/>
168 <has_n_lines n="9"/>
169 <has_text_matching expression="ENSG00000012048" n="1"/>
170 </assert_contents>
171 </output>
160 </test> 172 </test>
161 <!-- Arabidopsis database --> 173 <!-- Arabidopsis database -->
162 <test expect_num_outputs="1"> 174 <test expect_num_outputs="1">
163 <param name="id_file" value="genelist_arabidopsis.txt" ftype="tabular"/> 175 <param name="id_file" value="genelist_arabidopsis.txt" ftype="tabular"/>
164 <param name="id_type" value="SYMBOL"/> 176 <param name="id_type" value="SYMBOL"/>
165 <param name="organism" value="At"/> 177 <param name="organism" value="At"/>
166 <param name="output_cols" value="GO,ENTREZID" /> 178 <param name="output_cols" value="GO,ENTREZID" />
167 <output name="out_tab" file="out_arabidopsis.tab" /> 179 <output name="out_tab">
180 <assert_contents>
181 <has_n_columns n="5"/>
182 <has_n_lines min="20"/>
183 <has_text_matching expression="CLE13" min="5"/>
184 </assert_contents>
185 </output>
168 </test> 186 </test>
169 <!-- Gallus gallus database --> 187 <!-- Gallus gallus database -->
170 <test expect_num_outputs="1"> 188 <test expect_num_outputs="1">
171 <param name="id_file" value="genelist_gallus.txt" ftype="tabular"/> 189 <param name="id_file" value="genelist_gallus.txt" ftype="tabular"/>
172 <param name="id_type" value="SYMBOL"/> 190 <param name="id_type" value="SYMBOL"/>
173 <param name="organism" value="Gg"/> 191 <param name="organism" value="Gg"/>
174 <param name="output_cols" value="GO,ENTREZID" /> 192 <param name="output_cols" value="GO,ENTREZID" />
175 <output name="out_tab" file="out_gallus.tab" /> 193 <output name="out_tab">
194 <assert_contents>
195 <has_n_columns n="5"/>
196 <has_n_lines min="40"/>
197 <has_text_matching expression="TENM2" min="20"/>
198 </assert_contents>
199 </output>
176 </test> 200 </test>
177 </tests> 201 </tests>
178 <help><![CDATA[ 202 <help><![CDATA[
179 203
180 .. class:: infomark 204 .. class:: infomark