comparison macros.xml @ 3:68d2cd0be567 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b

2:a6f004bc73bf

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">2.0.2</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">semibin</xref>
        </xrefs>

        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
ln -s '$e' '${identifier}.bam' &&
    #end for
#end if
    ]]></token>
    <xml name="ref_select">
        <param name="select" type="select" label="Reference database">
            <option value="cached" selected="true">Cached database</option>
            <option value="taxonomy">Pre-computed taxonomy</option>
        </param>
    </xml>
    <xml name="cached_db">
        <param name="cached_db" label="Cached databases" type="select">
            <options from_data_table="gtdb">
                <validator message="No GTDB database is available" type="no_options" />
            </options>
        </param>
    </xml>
    <xml name="ref-single">
        <conditional name="ref">
            <expand macro="ref_select"/>
            <when value="cached">
                <expand macro="cached_db"/>
            </when>
            <when value="taxonomy">
                <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
            </when>
        </conditional>
    </xml>
    <xml name="ref-multi">
        <conditional name="ref">
            <expand macro="ref_select"/>

                <expand macro="cached_db"/>
            </when>
            <when value="taxonomy">
                <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/>
            </when>
        </conditional>
    </xml>
    <xml name="ref_single">
        <conditional name="ref">
            <expand macro="ref_select"/>

                <expand macro="cached_db"/>
            </when>
            <when value="taxonomy">
                <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
            </when>
        </conditional>
    </xml>
    <xml name="min_len">
        <conditional name="min_len">
            <param name="method" type="select" label="Method to set up the minimal length for contigs in binning">

3:68d2cd0be567

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">2.0.2</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">semibin</xref>
        </xrefs>

        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
ln -s '$e' '${identifier}.bam' &&
    #end for
#end if
    ]]></token>
    <xml name="ref_select_cannot">
        <param name="select" type="select" label="Reference database">
            <option value="cached">Cached database</option>
            <option value="taxonomy">Pre-computed taxonomy</option>
        </param>
    </xml>
    <xml name="ref_select">
        <param name="select" type="select" label="Reference database">
            <option value="ml" selected="true">Use SemiBin ML function</option>
            <option value="cached">Cached database</option>
            <option value="taxonomy">Pre-computed taxonomy</option>
        </param>
    </xml>
    <xml name="cached_db">
        <param name="cached_db" label="Cached databases" type="select">
            <options from_data_table="gtdb">
                <validator message="No GTDB database is available" type="no_options" />
            </options>
        </param>
    </xml>
    <xml name="ref-single-cannot">
        <conditional name="ref">
            <expand macro="ref_select_cannot"/>
            <when value="cached">
                <expand macro="cached_db"/>
            </when>
            <when value="taxonomy">
                <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
            </when>
        </conditional>
    </xml>
    <xml name="ref-multi-cannot">
        <conditional name="ref">
            <expand macro="ref_select_cannot"/>
            <when value="cached">
                <expand macro="cached_db"/>
            </when>
            <when value="taxonomy">
                <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/>
            </when>
        </conditional>
    </xml>
    <xml name="ref-single">
        <conditional name="ref">
            <expand macro="ref_select"/>
            <when value="cached">
                <expand macro="cached_db"/>
            </when>
            <when value="taxonomy">
                <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
            </when>
            <when value="ml"/>
        </conditional>
    </xml>
    <xml name="ref-multi">
        <conditional name="ref">
            <expand macro="ref_select"/>

                <expand macro="cached_db"/>
            </when>
            <when value="taxonomy">
                <param argument="--taxonomy-annotation-table" type="data" format="tabular" multiple="true" label="Pre-computed mmseqs2 format taxonomy TSV file" help="One per bin file"/>
            </when>
            <when value="ml"/>
        </conditional>
    </xml>
    <xml name="ref_single">
        <conditional name="ref">
            <expand macro="ref_select"/>

                <expand macro="cached_db"/>
            </when>
            <when value="taxonomy">
                <param argument="--taxonomy-annotation-table" type="data" format="tabular" label="Pre-computed mmseqs2 format taxonomy TSV file"/>
            </when>
            <when value="ml"/>
        </conditional>
    </xml>
    <xml name="min_len">
        <conditional name="min_len">
            <param name="method" type="select" label="Method to set up the minimal length for contigs in binning">