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comparison kobas_annotate.xml @ 4:dc84c4e1f9c4 draft

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planemo upload commit f6412ce479ec7ea8984e82ea1b226a039133eea4
author iuc
date Thu, 10 Nov 2016 16:21:29 -0500
parents e3308a2b63f4
children d1f8912a4796
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3:f562991cf6d5 4:dc84c4e1f9c4
1 <tool id="kobas_annotate" name="KOBAS Annotate" version="@WRAPPER_VERSION@"> 1 <tool id="kobas_annotate" name="KOBAS Annotate" version="@WRAPPER_VERSION@">
2 <description>KEGG Orthology Based Annotation System</description> 2 <description>KEGG Orthology Based Annotation System</description>
3 <macros> 3 <macros>
4 <import>kobas_macros.xml</import> 4 <import>kobas_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6
7 <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement> 7 <expand macro="requirements"/>
8 </requirements> 8
9 <stdio> 9 <stdio>
10 <exit_code range="0" level="warning" description="BiopythonDeprecationWarning"/> 10 <exit_code range="0" level="warning" description="BiopythonDeprecationWarning"/>
11 <exit_code range="1" level="fatal" description="Bad input settings or none of the entries was annotated successfully."/> 11 <exit_code range="1" level="fatal" description="Bad input settings or none of the entries was annotated successfully."/>
12 </stdio> 12 </stdio>
13 <command> 13 <command>
65 -i '$infile' 65 -i '$infile'
66 -t '$intype' 66 -t '$intype'
67 -s '$species' 67 -s '$species'
68 -e '$evalue' 68 -e '$evalue'
69 -r $rank 69 -r $rank
70 -n "\${GALAXY_SLOTS:-4}"
70 -c $coverage 71 -c $coverage
71 #if $ortholog.only == 'YES': 72 #if $ortholog.only == 'YES':
72 -z '$ortholog.species' 73 -z '$ortholog.species'
73 #end if 74 #end if
74 -y seq_pep 75 -y seq_pep
78 -o '$output' 79 -o '$output'
79 80
80 ]]> 81 ]]>
81 </command> 82 </command>
82 <inputs> 83 <inputs>
83 <param format="fasta" type="data" label="Input file" help="Input data file matching the input type." argument="--infile"/> 84 <param format="fasta,tabular,txt" type="data" label="Input file" help="Input data file matching the input type." argument="--infile"/>
84 <param type="select" label="Input type" argument="--intype" help="Input data type, default fasta:pro"> 85 <param type="select" label="Input type" argument="--intype" help="Input data type, default fasta:pro">
85 <option value="fasta:pro">FASTA protein sequence</option> 86 <option value="fasta:pro">FASTA protein sequence</option>
86 <option value="fasta:nuc">FASTA nucleotide sequence</option> 87 <option value="fasta:nuc">FASTA nucleotide sequence</option>
87 <option value="blastout:xml">XML BLAST output</option> 88 <option value="blastout:xml">XML BLAST output</option>
88 <option value="blastout:tab">Tabular BLAST output</option> 89 <option value="blastout:tab">Tabular BLAST output</option>