comparison kc-align.xml @ 9:0c0288a9d92c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit f3a0fbdcf97b2a8ef4b5cc9a8d4d59b7aab4db27"

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[

            #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" />

                    <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>

        <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[

9:0c0288a9d92c

<tool id="kc-align" name="Kc-Align" version="1.0.2" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="1.0.2">kcalign</requirement>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[

            #end if
            #if $position.mode == "mixed":
                -d '$position.dist'
            #end if
            $compress
            -th \${GALAXY_SLOTS:-1}

    ]]></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" />

                    <option value="less-close">Less Close</option>
                </param>
            </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>

        <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" />
        <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[