comparison lasttrain.xml @ 4:8705e0d74a0f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"

3:3de2195f32c0

<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy2" profile="18.01">

    <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>

    <macros>
        <import>macros_last.xml</import>

    <requirements>
        <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        #if $db_opts.db_opts_input == 'lastdb'
            ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
        #end if

        last-train

        -Q $init_options.Q
        -r $init_options.r
        -q $init_options.q
        -a $init_options.cost_opt.a

            '${"' '".join(str($db_opts.database.fields.path).split(","))}'
        #else if $db_opts.db_opts_input == 'lastdb'
            'db_files/lastdb'
        #end if

        '$query_fasta'

        >'$outfile'

    ]]></command>

    <inputs>
        <expand macro="input_db" />
        <param name="query_fasta" type="data" format="fasta,fastqsanger" label="Queries input files" />
        <conditional name="init_options">            
            <param argument="-Q" type="select" multiple="false" label="Query input format">
                <option value="0" selected="true">FASTA</option>
                <option value="1">Fastq-sanger</option>
            </param>

            <section name="last_train_opt">
                <section name="align_opt">
                    <param name="E" value="10"/>
                </section>
            </section>
            <param name="query_fasta" value="fuguMito.fa"/>
            <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="22"/>
        </test>
        <test>
            <conditional name="db_opts">
                <param name="db_opts_input" value="db"/>
                <param name="database" value="humdb"/>
            </conditional>
            <param name="query_fasta" value="fuguMito.fa"/>
            <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
        </test>
    </tests>

    <help>@LAST_HELP@</help>

4:8705e0d74a0f

<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">

    <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>

    <macros>
        <import>macros_last.xml</import>

    <requirements>
        <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        set -e -o pipefail; 
        #if $db_opts.db_opts_input == 'lastdb'
            ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
        #end if
        #if $query_fasta.ext.endswith('.gz')
        zcat 
        #else
        cat 
        #end if
        '$query_fasta' | last-train

        -Q $init_options.Q
        -r $init_options.r
        -q $init_options.q
        -a $init_options.cost_opt.a

            '${"' '".join(str($db_opts.database.fields.path).split(","))}'
        #else if $db_opts.db_opts_input == 'lastdb'
            'db_files/lastdb'
        #end if

        >'$outfile'

    ]]></command>

    <inputs>
        <expand macro="input_db" />
        <param name="query_fasta" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Queries input files" />
        <conditional name="init_options">            
            <param argument="-Q" type="select" multiple="false" label="Query input format">
                <option value="0" selected="true">FASTA</option>
                <option value="1">Fastq-sanger</option>
            </param>

            <section name="last_train_opt">
                <section name="align_opt">
                    <param name="E" value="10"/>
                </section>
            </section>
            <param name="query_fasta" value="fuguMito.fa.gz" ftype="fasta.gz"/>
            <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="28"/>
        </test>
        <test>
            <conditional name="db_opts">
                <param name="db_opts_input" value="db"/>
                <param name="database" value="humdb"/>
            </conditional>
            <param name="query_fasta" value="fuguMito.fq.gz" ftype="fastqsanger.gz"/>
            <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
        </test>
    </tests>

    <help>@LAST_HELP@</help>