comparison augustus.xml @ 5:b3f5d0879dab draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d

4:4de31938431b

            $singlestrand
            $input_genome
            $utr
            --genemodel=$genemodel


            #if $model.augustus_mode == 'history'
                --species=local
            #else
                --species=$model.organism

            <option value="forward">forward</option>
            <option value="backward">backward</option>
        </param>

        <param name="genemodel" label="Gene Model" type="select"
            help="Gene Model to predict, for more information please refere to the help.">
            <option value="complete">complete</option>
            <option value="partial">partial</option>
            <option value="intronless">intronless</option>
            <option value="atleastone">atleastone</option>
            <option value="exactlyone">exactlyone</option>
        </param>

        <param name="gff" type="boolean" label="GFF formated output"
            help="Standard output is GTF."
            truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />

            <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
            <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/>
            <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
            <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

5:b3f5d0879dab

            $singlestrand
            $input_genome
            $utr
            --genemodel=$genemodel

            #if $hints.usehints == 'T'
                --hintsfile='$hints.hintsfile' --extrinsicCfgFile='$hints.extrinsiccfg'
            #end if

            #if $range.userange == 'T'
                --predictionStart=$range.start --predictionEnd=$range.stop
            #end if

            #if $model.augustus_mode == 'history'
                --species=local
            #else
                --species=$model.organism

            <option value="forward">forward</option>
            <option value="backward">backward</option>
        </param>

        <param name="genemodel" label="Gene Model" type="select"
            help="Gene Model to predict, for more information please refer to the help.">
            <option value="complete">complete</option>
            <option value="partial">partial</option>
            <option value="intronless">intronless</option>
            <option value="atleastone">atleastone</option>
            <option value="exactlyone">exactlyone</option>
        </param>

        <conditional name="hints">
            <param name="usehints" label="Use hints (extrinsic information)?" type="select" display="radio">
                <option value="F">No</option>
                <option value="T">Yes</option>
            </param>
            <when value="T">
                <param name="hintsfile" label="Select hints file from history" type="data" format="gff"
                    help="A file containing hints in gff format (--hintsfile)"/>
                <param name="extrinsiccfg" label="Select extrinsic configuration file from history" type="data" format="txt"
                    help="A .cfg file listing hint sources and their boni and mali (--extrinsicCfgFile)"/>
            </when>
            <when value="F">
            </when>
    	</conditional>

        <conditional name="range">
            <param name="userange" label="Specify prediction sequence range?" type="select" display="radio">
                <option value="F">No</option>
                <option value="T">Yes</option>
            </param>
            <when value="T">
                <param name="start" label="Starting position" type="integer" value=""
                    help="The beginning of the search range (--predictionStart)"/>
                <param name="stop" label="Ending position" type="integer" value=""
                    help="The end of the search range (--predictionEnd); must be greater than starting position"/>
            </when>
            <when value="F">
            </when>
        </conditional>

        <param name="gff" type="boolean" label="GFF formated output"
            help="Standard output is GTF."
            truevalue="--gff3=on" falsevalue="--gff3=off" checked="false" />

            <param name="outputs" value="protein,codingseq,introns,cds,start,stop" />
            <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gtf" lines_diff="6"/>
            <output name="codingseq_output" file="human_augustus_protein_codingseq_introns_cds_codingseq.fasta" ftype="fasta" />
            <output name="protein_output" file="human_augustus_protein_codingseq_introns_cds_protein.fasta" ftype="fasta" />
        </test>
        <test>
            <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
            <param name="organism" value="fly" />
            <param name="usehints" value="T" />
            <param name="hintsfile" value="hints.truncated.adjusted.gff" />
            <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
            <param name="outputs" value="" />
            <output name="output" file="augustus.hints.output.gtf" ftype="gtf" lines_diff="12">
                <assert_contents>
                    <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1" />
                    <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t9303\t0\.(7[8-9]|8[0-5])\t-\t.\tchr2R.g1.t1" />
                </assert_contents>
            </output>

        </test>
        <test>
            <param name="input_genome" value="chr2R.truncated.fa" ftype="fasta" />
            <param name="organism" value="fly" />
            <param name="usehints" value="T" />
            <param name="hintsfile" value="hints.truncated.adjusted.gff" />
            <param name="extrinsiccfg" value="extrinsic.truncated.cfg" />
            <param name="userange" value="T" />
            <param name="start" value="7000" />
            <param name="stop" value="9000" />
            <param name="outputs" value="" />
            <output name="output" file="augustus.hints_and_range.output.gtf" ftype="gtf" lines_diff="12">
                <assert_contents>
                    <has_text_matching expression="chr2R\tAUGUSTUS\tgene\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1" />
                    <has_text_matching expression="chr2R\tAUGUSTUS\ttranscript\t7560\t8931\t0.8[2-5]\t-\t.\tchr2R.g1.t1" />
                </assert_contents>
            </output>
        </test>

    </tests>
    <help>
<![CDATA[

**What it does**