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comparison tools/effectiveT3/effectiveT3.xml @ 9:512530020360 draft

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v0.0.18 Internal changes to command line handling
author peterjc
date Tue, 16 May 2017 09:17:17 -0400
parents 60a9b3f760cc
children a46d7861c32c
comparison
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8:60a9b3f760cc 9:512530020360
1 <tool id="effectiveT3" name="Effective T3" version="0.0.17"> 1 <tool id="effectiveT3" name="Effective T3" version="0.0.18">
2 <description>Find bacterial effectors in protein sequences</description> 2 <description>Find bacterial effectors in protein sequences</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.1">effectiveT3</requirement> 4 <requirement type="package" version="1.0.1">effectiveT3</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <version_command>
7 <!-- Anything other than zero is an error --> 7 python $__tool_directory__/effectiveT3.py --version
8 <exit_code range="1:" /> 8 </version_command>
9 <exit_code range=":-1" /> 9 <command detect_errors="aggressive">
10 </stdio> 10 python $__tool_directory__/effectiveT3.py '$module.fields.path'
11 <version_command interpreter="python">effectiveT3.py --version</version_command>
12 <command interpreter="python">
13 effectiveT3.py $module.fields.path
14 #if $restrict.type=="cutoff": 11 #if $restrict.type=="cutoff":
15 cutoff=$restrict.cutoff 12 'cutoff=$restrict.cutoff'
16 #else: 13 #else:
17 $restrict.type 14 '$restrict.type'
18 #end if 15 #end if
19 $fasta_file $tabular_file</command> 16 '$fasta_file' '$tabular_file'
17 </command>
20 <inputs> 18 <inputs>
21 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 19 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
22 <param name="module" type="select" display="radio" label="Classification module"> 20 <param name="module" type="select" display="radio" label="Classification module">
23 <options from_file="effectiveT3.loc"> 21 <options from_file="effectiveT3.loc">
24 <column name="value" index="0"/> 22 <column name="value" index="0"/>