comparison kc-align.xml @ 2:20bef04b5272 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 03afe9e2a97f86f13041214639112a80e9765a71"

1:60ed1c94f584

<tool id="kc-align" name="Kc-Align" version="0.1.2" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="0.5.8">kcalign</requirement>
        <requirement type="package" version="3.2.2">kalign3</requirement>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
        kc-align

            --reads '$reads'
            #if $position.mode == "genome":
                --start $position.start
                --end $position.end
            #end if
    ]]></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" />
        <param name="outname" type="text" value="out" label="Output Prefix" />

            <when value="gene" >
            </when>
            <when value="mixed" >
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${outname}.fasta" />
        <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${outname}.clustal" />
    </outputs>

2:20bef04b5272

<tool id="kc-align" name="Kc-Align" version="0.1.3" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="0.5.9">kcalign</requirement>
        <requirement type="package" version="3.2.2">kalign3</requirement>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
        kc-align

            --reads '$reads'
            #if $position.mode == "genome":
                --start $position.start
                --end $position.end
            #end if
            $compress
    ]]></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" />
        <param name="outname" type="text" value="out" label="Output Prefix" />

            <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="${outname}.fasta" />
        <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${outname}.clustal" />
    </outputs>