comparison das_tool.xml @ 4:7d997332582e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit b32e3a4bfaf7e014097eeb0b850b61bac218802d

3:e23e7bf8491b

<tool id="das_tool" name="DAS Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        for genome resolved metagenomics
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>

    #set $labels += "%s%s" %($sep, $s.labels)
    #set $sep = ","
#end for

#if $adv.proteins
ln -s $adv.proteins 'proteins' &&
#end if

DAS_Tool
    --contigs '$contigs'
    --outputbasename 'outputs'
    --bins '$bins'
    --labels '$labels'
    --search_engine '$adv.search_engine'
#if $adv.proteins
    --proteins 'proteins'
#end if
    --score_threshold $adv.score_threshold
    --duplicate_penalty $adv.duplicate_penalty
    --megabin_penalty $adv.megabin_penalty
    $output.write_bin_evals
    $output.write_bins.write_bins
#if str($output.write_bins.write_bins) != ''
    $output.write_bins.write_unbinned
#end if
    $output.debug
    --threads \${GALAXY_SLOTS:-1}
    ]]></command>
    <inputs>
        <param argument="--contigs" type="data" format="fasta" label="Contig sequences"/>

            </param>
            <param argument="--proteins" type="data" format="fasta" optional="true" label="Predicted proteins" help="The file should be prodigal fasta format: >contigID_geneNo"/>
            <param argument="--score_threshold" type="float" min="0" max="1" value="0.5" label="Score threshold until selection algorithm will keep selecting bins"/>
            <param argument="--duplicate_penalty" type="float" min="0" max="3" value="0.6" label="Penalty for duplicate single copy genes per bin (weight b)" help="Only change if you know what you are doing"/>
            <param argument="--megabin_penalty" type="float" min="0" max="3" value="0.5" label="Penalty for megabins (weight c)" help="Only change if you know what you are doing"/>
        </section>
        <section name="output" title="Outputs">
            <param name="proteins" type="boolean" checked="false" label="Output predicted proteins?"/>
            <param argument="--write_bin_evals" type="boolean" truevalue="--write_bin_evals" falsevalue="" checked="false" label="Write evaluation of input bin sets?"/>
            <conditional name="write_bins">

@HELP_HEADER@

Inputs
======

- Bins: Tab separated files of contig-IDs and bin-IDs. Contigs to bin file example: ::

    Contig_1	bin.01
    Contig_8	bin.01
    Contig_42	bin.02
    Contig_49	bin.03

    >Contig_1
    ATCATCGTCCGCATCGACGAATTCGGCGAACGAGTACCCCTGACCATCTCCGATTA...
    >Contig_2
    GATCGTCACGCAGGCTATCGGAGCCTCGACCCGCAAGCTCTGCGCCTTGGAGCAGG...

- [Optional] Proteins: Predicted proteins in prodigal fasta format. Header contains contig-ID and gene number: ::

    >Contig_1_1
    MPRKNKKLPRHLLVIRTSAMGDVAMLPHALRALKEAYPEVKVTVATKSLFHPFFEG...
    >Contig_1_2
    MANKIPRVPVREQDPKVRATNFEEVCYGYNVEEATLEASRCLNCKNPRCVAACPVN...

4:7d997332582e

<tool id="das_tool" name="DAS Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>for genome-resolved metagenomics</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>

    #set $labels += "%s%s" %($sep, $s.labels)
    #set $sep = ","
#end for

#if $adv.proteins
    ln -s '$adv.proteins' 'proteins' &&
#end if

DAS_Tool
    --contigs '$contigs'
    --outputbasename 'outputs'
    --bins '$bins'
    --labels '$labels'
    --search_engine '$adv.search_engine'
    #if $adv.proteins
        --proteins 'proteins'
    #end if
    --score_threshold $adv.score_threshold
    --duplicate_penalty $adv.duplicate_penalty
    --megabin_penalty $adv.megabin_penalty
    --max_iter_post_threshold $adv.max_iter_post_threshold

    $output.write_bin_evals
    $output.write_bins.write_bins
    #if str($output.write_bins.write_bins) != ''
        $output.write_bins.write_unbinned
    #end if
    $output.debug
    --threads \${GALAXY_SLOTS:-1}
    ]]></command>
    <inputs>
        <param argument="--contigs" type="data" format="fasta" label="Contig sequences"/>

            </param>
            <param argument="--proteins" type="data" format="fasta" optional="true" label="Predicted proteins" help="The file should be prodigal fasta format: >contigID_geneNo"/>
            <param argument="--score_threshold" type="float" min="0" max="1" value="0.5" label="Score threshold until selection algorithm will keep selecting bins"/>
            <param argument="--duplicate_penalty" type="float" min="0" max="3" value="0.6" label="Penalty for duplicate single copy genes per bin (weight b)" help="Only change if you know what you are doing"/>
            <param argument="--megabin_penalty" type="float" min="0" max="3" value="0.5" label="Penalty for megabins (weight c)" help="Only change if you know what you are doing"/>
            <param argument="--max_iter_post_threshold" type="integer" min="1" value="10" label="Maximum number of iterations after reaching score threshold"/>
        </section>
        <section name="output" title="Outputs">
            <param name="proteins" type="boolean" checked="false" label="Output predicted proteins?"/>
            <param argument="--write_bin_evals" type="boolean" truevalue="--write_bin_evals" falsevalue="" checked="false" label="Write evaluation of input bin sets?"/>
            <conditional name="write_bins">

@HELP_HEADER@

Inputs
======

- Bins: Tab-separated files of contig-IDs and bin-IDs. Contigs to bin file example: ::

    Contig_1	bin.01
    Contig_8	bin.01
    Contig_42	bin.02
    Contig_49	bin.03

    >Contig_1
    ATCATCGTCCGCATCGACGAATTCGGCGAACGAGTACCCCTGACCATCTCCGATTA...
    >Contig_2
    GATCGTCACGCAGGCTATCGGAGCCTCGACCCGCAAGCTCTGCGCCTTGGAGCAGG...

- [Optional] Proteins: Predicted proteins in prodigal fasta format. The header contains contig-ID and gene number: ::

    >Contig_1_1
    MPRKNKKLPRHLLVIRTSAMGDVAMLPHALRALKEAYPEVKVTVATKSLFHPFFEG...
    >Contig_1_2
    MANKIPRVPVREQDPKVRATNFEEVCYGYNVEEATLEASRCLNCKNPRCVAACPVN...