comparison augustus.xml @ 3:702d9e042295 draft

Uploaded

2:b8ccbad1b062

<tool id="augustus" name="Augustus" version="0.3">
    <description>gene prediction for eukaryotic genomes</description>
    <requirements>
        <requirement type="package" version="2.7">augustus</requirement>
    </requirements>
    <command>
        ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
        ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed
        ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external script is used to extract the sequences into additional files

            --genemodel=$genemodel
            --species=$organism
            ##--outfile=$output
        | tee $output 
        #if $protein or $codingseq:
            | python extract_features.py 
                #if $protein:
                    --protein $protein_output
                #end if
                #if $codingseq:
                    --codingseq $codingseq_output

            <change_format>
                <when input="gff" value="--gff3=on" format="gff" />
            </change_format>
        </data>
        <data format="fasta" name="protein_output">
            <filter>protein == "--protein=on"</filter>
        </data>
        <data format="fasta" name="codingseq_output">
            <filter>codingseq == "--codingseq=on"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />

            <param name="input_genome" value="arabidopsis_augustus.fa" ftype="fasta" />
            <param name="organism" value="arabidopsis" />
            <param name="singlestrand" value="--singlestrand=true" />
            <param name="mea" value="--mea=1" />
            <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on" ftype="gtf" />
        </test>
    </tests>
    <help>

**What it does**

3:702d9e042295

<tool id="augustus" name="Augustus" version="0.3">
    <description>gene prediction for eukaryotic genomes</description>
    <requirements>
        <requirement type="package" version="2.7">augustus</requirement>
        <requirement type="set_environment">SCRIPT_PATH</requirement>
    </requirements>
    <command>
        ## please set export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
        ## or use the --AUGUSTUS_CONFIG_PATH=path if you are not installing through the toolshed
        ## Augustus writes the protein and coding sequences as comment into the gff/gtf file an external script is used to extract the sequences into additional files

            --genemodel=$genemodel
            --species=$organism
            ##--outfile=$output
        | tee $output 
        #if $protein or $codingseq:
            | python \$SCRIPT_PATH/extract_features.py
                #if $protein:
                    --protein $protein_output
                #end if
                #if $codingseq:
                    --codingseq $codingseq_output

            <change_format>
                <when input="gff" value="--gff3=on" format="gff" />
            </change_format>
        </data>
        <data format="fasta" name="protein_output">
            <filter>protein == True</filter>
        </data>
        <data format="fasta" name="codingseq_output">
            <filter>codingseq == True</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />

            <param name="input_genome" value="arabidopsis_augustus.fa" ftype="fasta" />
            <param name="organism" value="arabidopsis" />
            <param name="singlestrand" value="--singlestrand=true" />
            <param name="mea" value="--mea=1" />
            <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on" ftype="gtf" />
        </test>
        <test>
            <param name="input_genome" value="HS04636_augustus.fa" ftype="fasta" />
            <param name="organism" value="human" />
            <param name="protein" value="--protein=on" />
            <param name="codingseq" value="--codingseq=on" />
            <param name="introns" value="--introns=on" />
            <param name="cds" value="--cds=on" />
            <output name="output" file="human_augustus_protein_codingseq_introns_cds_main.gtf" ftype="gff" />
            <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>

**What it does**