comparison metabat2.xml @ 3:eb50e7eca3dc draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 3a3dfd676076438bea1518eb731790edfb4da3c0

2:708abf08a626

<tool id="metabat2" name="MetaBAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>metagenome binning</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
mkdir bins &&
metabat2
    --inFile '$inFile'

                <option value="log">Process log file</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
            <filter>not out['saveCls'] and not out['onlyLabel']</filter>
            <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)\.fa" format="fasta" directory="bins"/>
        </collection>
        <data name="bin_saveCls" format="tabular" from_work_dir="bins/bin" label="${tool.name} on ${on_string}: Bins">
            <filter>out['saveCls'] and not out['onlyLabel']</filter>
        </data>
        <collection name="bin_onlyLabel" type="list" label="${tool.name} on ${on_string}: Bins">
            <filter>not out['saveCls'] and out['onlyLabel']</filter>
            <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)" format="tabular" directory="bins"/>
        </collection>
        <data name="lowDepth" format="fasta" from_work_dir="bins/bin.lowDepth.fa" label="${tool.name} on ${on_string}: Low depth bins">
            <filter>not out['saveCls'] and not out['onlyLabel'] and 'lowDepth' in out['extra_outputs']</filter>

3:eb50e7eca3dc

<tool id="metabat2" name="MetaBAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>metagenome binning</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
mkdir bins &&
metabat2
    --inFile '$inFile'

                <option value="log">Process log file</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bin sequences">
            <filter>not out['saveCls'] and not out['onlyLabel']</filter>
            <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)\.fa" format="fasta" directory="bins"/>
        </collection>
        <data name="bin_saveCls" format="tabular" from_work_dir="bins/bin" label="${tool.name} on ${on_string}: Bins with cluster memberships">
            <filter>out['saveCls'] and not out['onlyLabel']</filter>
        </data>
        <collection name="bin_onlyLabel" type="list" label="${tool.name} on ${on_string}: Bin labels">
            <filter>not out['saveCls'] and out['onlyLabel']</filter>
            <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)" format="tabular" directory="bins"/>
        </collection>
        <data name="lowDepth" format="fasta" from_work_dir="bins/bin.lowDepth.fa" label="${tool.name} on ${on_string}: Low depth bins">
            <filter>not out['saveCls'] and not out['onlyLabel'] and 'lowDepth' in out['extra_outputs']</filter>