comparison validate_fasta_database.xml @ 9:d7f67cc9a9e7 draft default tip

planemo upload commit ea998f84bf4eb1f6f6ece4eb7fc725920f9c78c4-dirty

8:ba8bbfd8933e

<tool id="validate_fasta_database" name="Validate FASTA Database" version="0.1.3">
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1" level="fatal" description="Invalid FASTA headers detected, was asked to fail"/>
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        java -jar $__tool_directory__/validate_fasta_database-0.2.jar
        '$inFasta'
        '$goodFastaOut'
        '$badFastaOut'
        '$crashIfInvalid'
        '$checkIsProtein'

               label="Only pass sequences with accession numbers?"
               value="false"/>
        <param type="integer" name="minimumLength"
               label="Minimum length for sequences to pass"
               value="0"/>


        <!--<conditional name="checkLength">-->
            <!--<param type="boolean" name="checkLength" label="Filter out sequences below a minimum sequenceLength?">-->
                <!--<option value="true"></option>-->
                <!--<option value="false"></option>-->
            <!--</param>-->
            <!--<when value="true">-->
                <!--<param name="minimumLength" type="integer" value="0" label="Minimum sequenceLength that AA sequence must have"/>-->
            <!--</when>-->
            <!--<when value="false">-->
            <!--</when>-->
        <!--</conditional>-->

    </inputs>
    <outputs>
        <data name="goodFastaOut" format="fasta" label="Validate FASTA: Passed Sequences"/>
        <data name="badFastaOut" format="fasta" label="Validate FASTA: Failed Sequences"/>
    </outputs>
    <tests>
        <!-- test general filtering -->
        <test>
            <param name="inFasta" value="fastaFilteringTest_IN.fasta"/>

9:d7f67cc9a9e7

<tool id="validate_fasta_database" name="Validate FASTA Database" version="0.1.4">
    <requirements>
        <requirement type="package" version="1.0">validate-fasta-database</requirement>
    </requirements>
    <stdio>
        <exit_code range="1" level="fatal" description="Invalid FASTA headers detected, was asked to fail"/>
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        validate-fasta-database
        '$inFasta'
        '$goodFastaOut'
        '$badFastaOut'
        '$crashIfInvalid'
        '$checkIsProtein'

               label="Only pass sequences with accession numbers?"
               value="false"/>
        <param type="integer" name="minimumLength"
               label="Minimum length for sequences to pass"
               value="0"/>
    </inputs>
    <outputs>
        <data name="goodFastaOut" format="fasta" label="Validate FASTA ${on_string}: passed"/>
        <data name="badFastaOut" format="fasta" label="Validate FASTA ${on_string}: failed"/>
    </outputs>
    <tests>
        <!-- test general filtering -->
        <test>
            <param name="inFasta" value="fastaFilteringTest_IN.fasta"/>