comparison gecko.xml @ 3:1de657a3198d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit b55cfca7f53d2eaa3f4c7c4ce09436371b088000

2:5efbd15675ca

<tool id="gecko" name="Gecko" version="@TOOL_VERSION@" profile="20.01">
    <description>Ungapped genome comparison</description>
    <macros>
        <token name="@TOOL_VERSION@">1.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">gecko</requirement>
    </requirements>
    <command><![CDATA[

    #set $dbName=re.sub('/', '\\/', str($db.element_identifier))
    cp $query query.fasta &&
    cp $db db.fasta &&
    workflow.sh query.fasta db.fasta $minlen $similarity $kmer 1 &&
    rm -rf intermediateFiles &&
    #if str($options['selection_mode']) == "alignments":
      frags2align.sh results/query-db.frags query.fasta db.fasta results/query-db.txt &&
      mv results/query-db.txt $alignments2 &&
    #end if
    sed -i 's/query.fasta/$queryName/g' results/query-db.csv &&
    sed -i 's/db.fasta/$dbName/g' results/query-db.csv &&

            <option value="12">12</option>
            <option value="8">8</option>
        </param>
        <param name="minlen" type="integer" value="40" min="8" label="Minimum length" help="The minimum length a fragment must achieve to be reported"/>
        <param name="similarity" type="integer" value="60" min="1" max="99" label="Minimum similarity" help="Percentage of similarity threshold (calculated as the attained score divided by the maximum possible score)"/>
        <conditional name="options">
            <param label="Generate alignments file?" name="selection_mode" type="select">
                <option selected="true" value="noalignments">Do not extract alignments (Only CSV file)</option>
                <option value="alignments">Extract alignments (CSV and alignments file)</option>
            </param>
        </conditional>
    </inputs>
    <outputs>
        <data name="csv_output1" format="csv" label="${tool.name} on ${on_string}: CSV"/> 
        <data name="alignments2" format="txt" label="${tool.name} on ${on_string}: Alignments">
            <filter> options['selection_mode'] == 'alignments'</filter>
        </data>
    </outputs>
    <tests>
        <!-- test run w defaults (no alignments) -->
        <test expect_num_outputs="1">

3:1de657a3198d

<tool id="gecko" name="Gecko" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
    <description>Ungapped genome comparison</description>
    <macros>
        <token name="@TOOL_VERSION@">1.2</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">gecko</requirement>
    </requirements>
    <command><![CDATA[

    #set $dbName=re.sub('/', '\\/', str($db.element_identifier))
    cp $query query.fasta &&
    cp $db db.fasta &&
    workflow.sh query.fasta db.fasta $minlen $similarity $kmer 1 &&
    rm -rf intermediateFiles &&
    #if str($selection_mode) == "alignments":
      frags2align.sh results/query-db.frags query.fasta db.fasta results/query-db.txt &&
      mv results/query-db.txt $alignments2 &&
    #end if
    sed -i 's/query.fasta/$queryName/g' results/query-db.csv &&
    sed -i 's/db.fasta/$dbName/g' results/query-db.csv &&

            <option value="12">12</option>
            <option value="8">8</option>
        </param>
        <param name="minlen" type="integer" value="40" min="8" label="Minimum length" help="The minimum length a fragment must achieve to be reported"/>
        <param name="similarity" type="integer" value="60" min="1" max="99" label="Minimum similarity" help="Percentage of similarity threshold (calculated as the attained score divided by the maximum possible score)"/>
        <param label="Generate alignments file?" name="selection_mode" type="select">
            <option selected="true" value="noalignments">Do not extract alignments (Only CSV file)</option>
            <option value="alignments">Extract alignments (CSV and alignments file)</option>
        </param>
    </inputs>
    <outputs>
        <data name="csv_output1" format="csv" label="${tool.name} on ${on_string}: CSV"/> 
        <data name="alignments2" format="txt" label="${tool.name} on ${on_string}: Alignments">
            <filter> selection_mode == 'alignments'</filter>
        </data>
    </outputs>
    <tests>
        <!-- test run w defaults (no alignments) -->
        <test expect_num_outputs="1">