comparison kc-align.xml @ 8:1c65ddbaeefa draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 000db9fd34a1056bbdd95b007acb5919873fa2b6"

7:8dc7708c3266

<tool id="kc-align" name="Kc-Align" version="0.2" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="0.6.1">kcalign</requirement>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
        kc-align
            --mode $position.mode
            --reference '$reference'
            --reads '$reads'
            #if $position.mode == "genome":
                --start $position.start
                --end $position.end
            #end if
            $compress
            --parallel
    ]]></command>
    <inputs>
        <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
        <param name="reads" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" />
        <conditional name="position" >
            <param name="mode" type="select" label="Mode" >
                <option value="genome">Genome</option>
                <option value="gene">Gene</option>
                <option value="mixed">Mixed</option>
            </param>
            <when value="genome" >
                <param name="start" type="text" value="0" label="Start Position(s)" help="The 1-indexed start position of the gene of interest in the reference sequence (For multi-segmented sequences, input each start site separated by a comma ex: 12562,12591)" />
                <param name="end" type="text" value="0" label="End Position(s)" help="The 1-indexed end position of the gene of interest in the reference sequence (For multi-segmented sequences, input each end site separated by a comma ex: 12592,13905)" />
            </when>
            <when value="gene" >
            </when>
            <when value="mixed" >
            </when>
        </conditional>
        <param name="compress" type="boolean" truevalue="--compress" falsevalue="" label="Compress" help="Compress identical sequences" />
    </inputs>
    <outputs>
        <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${tool.name}: fasta output" />
        <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${tool.name}: clustal output" />
    </outputs>
<tests>
    <test>
        <param name="reference" ftype="fasta" value="wuhan_ref.fasta" />
        <param name="reads" ftype="fasta" value="3.fasta" />
        <param name="mode" value="genome" />
        <param name="start" value="21563" />
        <param name="end" value="25384" />
        <output name="fasta" ftype="fasta" compare="diff" value="kc-align.fasta" />
        <output name="clustal" ftype="txt" compare="diff" value="kc-align.clustal" />
    </test>
</tests>
    <help><![CDATA[

============

8:1c65ddbaeefa

<tool id="kc-align" name="Kc-Align" version="1.0" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="1.0.2">kcalign</requirement>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
        kc-align
            --mode '$position.mode'
            --reference '$ref'
            --sequences '$seqs'
            #if $position.mode == "genome":
                --start '$position.start'
                --end '$position.end'
                -d '$position.dist'
            #end if
            #if $position.mode == "mixed":
                -d '$position.dist'
            #end if
            $compress
            -th '$threads'

    ]]></command>
    <inputs>
        <param name="ref" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
        <param name="seqs" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" />
        <conditional name="position" >
            <param name="mode" type="select" label="Mode" >
                <option value="genome">Genome</option>
                <option value="gene">Gene</option>
                <option value="mixed">Mixed</option>
            </param>
            <when value="genome" >
                <param name="start" type="text" value="0" label="Start Position(s)" help="The 1-indexed start position of the gene of interest in the reference sequence (For multi-segmented sequences, input each start site separated by a comma ex: 12562,12591)" />
                <param name="end" type="text" value="0" label="End Position(s)" help="The 1-indexed end position of the gene of interest in the reference sequence (For multi-segmented sequences, input each end site separated by a comma ex: 12592,13905)" />
                <param name="dist" type="select" label="Homology distance limit" help="Sequences that are more than an empirically determined distance from the reference are discarded before the final alignment">
                    <option value="none">None</option>
                    <option value="very-close">Very Close</option>
                    <option value="semi-close">Semi-Close</option>
                    <option value="less-close">Less Close</option>
                </param>
            </when>
            <when value="gene" >
            </when>
            <when value="mixed" >
            	<param name="dist" type="select" label="Homology distance limit" help="Sequences that are more than an empirically determined distance from the reference are discarded before the final alignment">
                    <option value="none">None</option>
                    <option value="very-close">Very Close</option>
                    <option value="semi-close">Semi Close</option>
                    <option value="less-close">Less Close</option>
                </param>
            </when>
        </conditional>
        <param name="compress" type="boolean" truevalue="--compress" falsevalue="" label="Compress" help="Compress identical sequences" />
        <param name="threads" type="integer" argument="-th" value="1" label="Cores" />
    </inputs>
    <outputs>
        <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${tool.name}: fasta output" />
        <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${tool.name}: clustal output" />
    </outputs>
<tests>
    <test>
        <param name="ref" ftype="fasta" value="wuhan_ref.fasta" />
        <param name="seqs" ftype="fasta" value="3.fasta" />
        <param name="mode" value="genome" />
        <param name="start" value="21563" />
        <param name="end" value="25384" />
        <param name="threads" value="15" />
        <output name="fasta" ftype="fasta" compare="contains" value="kc-align.fasta" />
        <output name="clustal" ftype="txt" compare="contains" value="kc-align.clustal" />
    </test>
</tests>
    <help><![CDATA[

============