comparison lastz.xml @ 3:c3767eaae954 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413

2:8e9252994649

<tool id="lastz_wrapper_2" name="LASTZ" version="1.3">
    <description>: align long sequences</description>
    <macros>
        <import>lastz_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@LASTZ_CONDA_VERSION@">lastz</requirement>
        <requirement type="package" version="1.7">samtools</requirement>
        <requirement type="package" version="3.4.2">r-base</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        lastz
        @TARGET_INPUT_COMMAND_LINE@
        ## If --self is set: perform self alignment and ignore the query

            '${where_to_look.self}'
            #if $where_to_look.nomirror
                '${where_to_look.nomirror}'
            #end if
        #else:
            '${query}'
        #end if

## WHERE TO LOOK --------------------------------

        '${where_to_look.strand}'

            ]]>
        </configfile>
    </configfiles>
    <inputs>
        <expand macro="target_input"/>
        <param name="query" format="fasta,fastq" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/>

        <section name="where_to_look" expanded="False" title="Where to look">
            <param name="strand" type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus">
                <option value="--strand=both" selected="True">Both</option>
                <option value="--strand=plus">Plus</option>

            <param name="strand" value="--strand=both" />
            <param name="score_file" value="score_file.txt" />
            <param name="format" value="general_def" />
            <output name="output" value="test3.out" />
        </test>
    </tests>

    <help><![CDATA[

        **What is does**

3:c3767eaae954

<tool id="lastz_wrapper_2" name="LASTZ" version="1.3.1">
    <description>: align long sequences</description>
    <macros>
        <import>lastz_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@LASTZ_CONDA_VERSION@">lastz</requirement>
        <requirement type="package" version="1.7">samtools</requirement>
        <requirement type="package" version="3.4.2">r-base</requirement>
        <requirement type="package" version="1.0.6">bzip2</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        lastz
        @TARGET_INPUT_COMMAND_LINE@
        ## If --self is set: perform self alignment and ignore the query

            '${where_to_look.self}'
            #if $where_to_look.nomirror
                '${where_to_look.nomirror}'
            #end if
        #else:
            @query_input@
        #end if

## WHERE TO LOOK --------------------------------

        '${where_to_look.strand}'

            ]]>
        </configfile>
    </configfiles>
    <inputs>
        <expand macro="target_input"/>
        <param name="query" format="fasta,fastq,fasta.gz,fastq.gz,fastq.bz2" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/>

        <section name="where_to_look" expanded="False" title="Where to look">
            <param name="strand" type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus">
                <option value="--strand=both" selected="True">Both</option>
                <option value="--strand=plus">Plus</option>

            <param name="strand" value="--strand=both" />
            <param name="score_file" value="score_file.txt" />
            <param name="format" value="general_def" />
            <output name="output" value="test3.out" />
        </test>
        <test>
            <param name="ref_source" value="history" />
            <param name="target" value="chrM_mouse.fa.gz" />
            <param name="query" value="chrM_human.fa.gz" />
            <param name="strand" value="--strand=both" />
            <param name="format" value="blastn" />
            <output name="output" value="test4.out" />
        </test>
        <test>
            <param name="ref_source" value="history" />
            <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
            <param name="query" ftype="fastq.bz2" value="chrM_mouse.fq.bz2" />
            <param name="strand" value="--strand=both" />
            <param name="format" value="blastn" />
            <output name="output" value="test5.out" />
        </test>
        <test>
            <param name="ref_source" value="history" />
            <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
            <param name="query" ftype="fastq.gz" value="chrM_mouse.fq.gz" />
            <param name="strand" value="--strand=both" />
            <param name="format" value="blastn" />
            <output name="output" value="test5.out" />
        </test>
        <test>
            <param name="ref_source" value="history" />
            <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
            <param name="query" ftype="fastq" value="chrM_mouse.fq" />
            <param name="strand" value="--strand=both" />
            <param name="format" value="blastn" />
            <output name="output" value="test5.out" />
        </test>
    </tests>

    <help><![CDATA[

        **What is does**