Mercurial > repos > iuc > trinotate

comparison trinotate.xml @ 3:4383070d29ed draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 7d7285e1c16a9058178a51c804409319e6685454"
author iuc
date Fri, 14 Aug 2020 16:54:16 -0400
parents 6fd16fad465d
children 2b093007fab9
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2:6fd16fad465d 3:4383070d29ed
1 <tool id="trinotate" name="Trinotate" version="3.1.1"> 1 <tool id="trinotate" name="Trinotate" version="3.2.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="3.1.1">trinotate</requirement> 3 <requirement type="package" version="3.2.1">trinotate</requirement>
4 <requirement type="package" version="1.18">gnu-wget</requirement> 4 <requirement type="package" version="1.18">gnu-wget</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <version_command> 9 <version_command><![CDATA[
10 <![CDATA[ 10 Trinotate version 3.2.1
11 Trinotate version 3.1.1 11 ]]></version_command>
12 ]]>
13 </version_command>
14 <command><![CDATA[ 12 <command><![CDATA[
15 13
16 #if str($cond_download.select_download) == "yes": 14 #if str($cond_download.select_download) == "yes":
17 Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate && 15 Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate &&
18 #else: 16 #else:
94 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" /> 92 <param name="blastx" ftype="tabular" value="swissprot.blastx.outfmt6" />
95 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" /> 93 <param name="hmmscan" ftype="txt" value="TrinotatePFAM.out" />
96 <param name="tmhmm" ftype="tabular" value="tmhmm.out" /> 94 <param name="tmhmm" ftype="tabular" value="tmhmm.out" />
97 <param name="signalp" ftype="tabular" value="signalp.out" /> 95 <param name="signalp" ftype="tabular" value="signalp.out" />
98 <output name="trinotate_out" file="trinotate_annotation_report.xls" /> 96 <output name="trinotate_out" file="trinotate_annotation_report.xls" />
99 <output name="trinotate_out" file="trinotate_annotation_report.xls" />
100 </test> 97 </test>
101 <test> 98 <test>
102 <param name="trinity" ftype="fasta" value="Trinity.fasta" /> 99 <param name="trinity" ftype="fasta" value="Trinity.fasta" />
103 <param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" /> 100 <param name="transdecoder" ftype="fasta" value="Trinity.fasta.transdecoder.pep" />
104 <param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" /> 101 <param name="gene_trans_map" ftype="tabular" value="Trinity.fasta.gene_to_trans_map" />