annotate psltobigpsl.xml @ 1:7cd07dd27927 draft default tip

planemo upload for repository https://github.com/Yating-L/psltobigpsl.git commit 517f74861bea50f74aa36e15cf3239bbcd353e4f-dirty

<tool id="pslToBigPsl" name="pslToBigPsl" version="0.1.0">
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        $__tool_directory__/pslToBigPsl 
            '${input}'
            #if $add_input.input_type == "both"
                -cds='${input_cds}'
                -fa='${input_fa}'
            #elif $add_input.input_type == "fa"
                -fa='${input_fa}'
            #elif $add_input.input_type == "cds"
                -cds='${input_cds}'
            #end if   
            output
            && sort -k1,1 -k2,2n output > '${output_sorted}'
    ]]></command>
    <inputs>
        <param name="input" label="Psl file" type="data" format="psl" />
        <conditional name="add_input">
            <param name="input_type" type="select" label="Provide FASTA and CDS files">
                <option value="no">No</option>
                <option value="both">Provide both FASTA and CDS files</option>
                <option value="fa">Provide FASTA file</option>
                <option value="cds">Provide CDS file</option>
            </param>
            <when value="both">
                <param name="input_fa" type="data" format="fasta" label="Input FASTA file" />
                <param name="input_cds" type="data" format="tabular" label="Input CDS file" />
            </when>
             <when value="fa">
                <param name="input_fa" type="data" format="fasta" label="Input FASTA file" />
            </when>
            <when value="cds">
                <param name="input_cds" type="data" format="tabular" label="Input CDS file" />
            </when>
            <when value="no">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_sorted" format="bed" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="amaVit1_Gallus_gallus.psl" />
            <param name="input_type" value="no" />
            <output name="output_sorted" value="out.bigpsl" />
        </test>
        <test>
            <param name="input" value="amaVit1_Gallus_gallus.psl" />
            <param name="input_type" value="fa" />
            <param name="input_fa" value="Gallus_gallus_RefSeq.fa" />
            <output name="output_sorted" value="out_fa.bigpsl" />
        </test>
        <test>
            <param name="input" value="amaVit1_Gallus_gallus.psl" />
            <param name="input_type" value="cds" />
            <param name="input_cds" value="Gallus_gallus_RefSeq.cds" />
            <output name="output_sorted" value="out_cds.bigpsl" />
        </test>
        <test>
            <param name="input" value="amaVit1_Gallus_gallus.psl" />
            <param name="input_type" value="both" />
            <param name="input_fa" value="Gallus_gallus_RefSeq.fa" />
            <param name="input_cds" value="Gallus_gallus_RefSeq.cds" />
            <output name="output_sorted" value="out_both.bigpsl" />
        </test>
    </tests>
    <help><![CDATA[
        Transform a Psl format file to a Bed format file.
        Input: Psl File
        Ouput: BigPsl File
    ]]></help>
    <citations>
            <citation type="bibtex">@article{kent2002blat,
                  title={BLAT—the BLAST-like alignment tool},
                  author={Kent, W James},
                  journal={Genome research},
                  volume={12},
                  number={4},
                  pages={656--664},
                  year={2002},
                  publisher={Cold Spring Harbor Lab}
            }</citation>
      </citations> 
</tool>