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comparison eggnog_mapper.xml @ 7:4e4c6329f6cd draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
author galaxyp
date Fri, 19 Feb 2021 18:54:25 +0000
parents 3cb37af59360
children 96cac424c870
comparison
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6:3cb37af59360 7:4e4c6329f6cd
1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@"> 1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@+galaxy1">
2 <description>functional sequence annotation by orthology</description> 2 <description>functional sequence annotation by orthology</description>
3 <macros> 3 <macros>
4 <import>eggnog_macros.xml</import> 4 <import>eggnog_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
40 --cpu "\${GALAXY_SLOTS:-4}" 40 --cpu "\${GALAXY_SLOTS:-4}"
41 ]]></command> 41 ]]></command>
42 <inputs> 42 <inputs>
43 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/> 43 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
44 <param name="eggnog_data" type="select" label="Version of eggNOG Database"> 44 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
45 <options from_data_table="eggnog_mapper_db"/> 45 <options from_data_table="eggnog_mapper_db_versioned">
46 <filter type="static_value" column="3" value="@IDX_VERSION@" />
47 </options>
46 </param> 48 </param>
47 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" 49 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
48 label="Are these coding DNA sequences that need to be translated?"/> 50 label="Are these coding DNA sequences that need to be translated?"/>
49 51
50 <section name="diamond" expanded="true" title="Diamond Options"> 52 <section name="diamond" expanded="true" title="Diamond Options">
241 <test> 243 <test>
242 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> 244 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
243 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> 245 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
244 <param name="no_annot" value="true"/> 246 <param name="no_annot" value="true"/>
245 <param name="no_file_comments" value="true"/> 247 <param name="no_file_comments" value="true"/>
246 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/> 248 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
247 </test> 249 </test>
248 <test> 250 <test>
249 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> 251 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
250 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> 252 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
251 <param name="report_orthologs" value="true"/> 253 <param name="report_orthologs" value="true"/>
252 <param name="no_file_comments" value="true"/> 254 <param name="no_file_comments" value="true"/>
253 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/> 255 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
254 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular"/> 256 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
255 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/> 257 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
256 </test> 258 </test>
257 <test> 259 <test>
258 <param name="input" value="Nmar_0135.fa" ftype="fasta"/> 260 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
259 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work --> 261 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
260 <param name="report_orthologs" value="true"/> 262 <param name="report_orthologs" value="true"/>
261 <param name="no_file_comments" value="true"/> 263 <param name="no_file_comments" value="true"/>
262 <section name="annotation_options"> 264 <section name="annotation_options">
263 <param name="tax_scope" value="651137" /> 265 <param name="tax_scope" value="651137" />
264 </section> 266 </section>
265 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular"/> 267 <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
266 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular"/> 268 <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/>
267 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/> 269 <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/>
268 </test> 270 </test>
269 </tests> 271 </tests>
270 <help><![CDATA[ 272 <help><![CDATA[
271 273