comparison macros.xml @ 2:a6f004bc73bf draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84

1:5ae13a156271

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.5.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">21.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">semibin</xref>

            <requirement type="package" version="@TOOL_VERSION@">semibin</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="version">
        <version_command>SemiBin -v</version_command>
    </xml>
    <xml name="mode_fasta_bam">
        <conditional name="mode">
            <expand macro="mode_select"/>
            <when value="single">

            #else
ln -s '$e' '${identifier}.fasta' &&
            #end if
        #end for
#set $separator = ':'
SemiBin concatenate_fasta
    --input-fasta *.fasta
    --output 'output'
    --separator '$separator'
    -m $mode.multi_fasta.min_len
&&
ln -s 'output/concatenated.fa' 'contigs.fasta' &&
    #end if
#end if

    <xml name="batch-size">
        <param argument="--batch-size" type="integer" min="0" value="2048" label="Batch size used in the training process"/>
    </xml>
    <xml name="orf-finder">
        <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">
            <option value="prodigal" selected="true">Prodigal</option>
            <option value="fraggenescan">Fraggenescan</option>
        </param>
    </xml>
    <xml name="max-node">
        <param argument="--max-node" type="float" min="0" max="1" value="1" label="Fraction of contigs that considered to be binned"/>

        </param>
    </xml>
    <xml name="minfasta-kbs">
        <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/>
    </xml>
    <xml name="no-recluster">
        <param argument="--no-recluster" type="boolean" truevalue="--no-recluster" falsevalue="" checked="false" label="Do not recluster bins?"/>
    </xml>
    <xml name="data">
        <param argument="--data" type="data" format="csv" label="Train data"/>
    </xml>
    <xml name="data_output_single">

        </collection>
        <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
            <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
        </collection>
    </xml>
    <xml name="train_output">
        <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />
    </xml>
    <xml name="cannot_link_output">

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>

            <requirement type="package" version="@TOOL_VERSION@">semibin</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="version">
        <version_command>SemiBin2 -v</version_command>
    </xml>
    <xml name="mode_fasta_bam">
        <conditional name="mode">
            <expand macro="mode_select"/>
            <when value="single">

            #else
ln -s '$e' '${identifier}.fasta' &&
            #end if
        #end for
#set $separator = ':'
SemiBin2 concatenate_fasta
    --input-fasta *.fasta
    --output 'output'
    --separator '$separator'
    --compression none
    -m $mode.multi_fasta.min_len
&&
ln -s 'output/concatenated.fa' 'contigs.fasta' &&
    #end if
#end if

    <xml name="batch-size">
        <param argument="--batch-size" type="integer" min="0" value="2048" label="Batch size used in the training process"/>
    </xml>
    <xml name="orf-finder">
        <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">
            <option value="fast-naive" selected="true">Fast-Naive</option>
            <option value="prodigal">Prodigal</option>
            <option value="fraggenescan">Fraggenescan</option>
        </param>
    </xml>
    <xml name="max-node">
        <param argument="--max-node" type="float" min="0" max="1" value="1" label="Fraction of contigs that considered to be binned"/>

        </param>
    </xml>
    <xml name="minfasta-kbs">
        <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/>
    </xml>
    <xml name="write_pre_reclustering_bins">
        <param argument="--write-pre-reclustering-bins" type="boolean" truevalue="--write-pre-reclustering-bins" falsevalue="" checked="false" label="Return also the pre reclustered bins?"/>
    </xml>
    <xml name="data">
        <param argument="--data" type="data" format="csv" label="Train data"/>
    </xml>
    <xml name="data_output_single">

        </collection>
        <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
            <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
        </collection>
        
    </xml>
    <xml name="train_output">
        <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />
    </xml>
    <xml name="cannot_link_output">