comparison tools/effectiveT3/effectiveT3.xml @ 6:0f6eb4a75000 draft

v0.0.15 internal changes; v0.0.14 fixed error handling

5:1ea715da1879

<tool id="effectiveT3" name="Effective T3" version="0.0.13">
    <description>Find bacterial effectors in protein sequences</description>
    <requirements>
        <requirement type="package" version="1.0.1">effectiveT3</requirement>
    </requirements>
    <version_command interpreter="python">effectiveT3.py --version</version_command>
    <command interpreter="python">
effectiveT3.py $module.fields.path
#if $restrict.type=="cutoff":
  cutoff=$restrict.cutoff
#else:
  $restrict.type
#end if
$fasta_file $tabular_file</command>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <inputs>
        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
        <param name="module" type="select" display="radio" label="Classification module">
            <options from_file="effectiveT3.loc">
                <column name="value" index="0"/>

6:0f6eb4a75000

<tool id="effectiveT3" name="Effective T3" version="0.0.15">
    <description>Find bacterial effectors in protein sequences</description>
    <requirements>
        <requirement type="package" version="1.0.1">effectiveT3</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command interpreter="python">effectiveT3.py --version</version_command>
    <command interpreter="python">
effectiveT3.py $module.fields.path
#if $restrict.type=="cutoff":
  cutoff=$restrict.cutoff
#else:
  $restrict.type
#end if
$fasta_file $tabular_file</command>
    <inputs>
        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
        <param name="module" type="select" display="radio" label="Classification module">
            <options from_file="effectiveT3.loc">
                <column name="value" index="0"/>