comparison tools/get_orfs_or_cdss/get_orfs_or_cdss.xml @ 8:09a8be9247ca draft

v0.2.0 with GFF3 output

7:705a2e2df7fb

<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.1.1">
    <description>e.g. to get peptides from ESTs</description>
    <requirements>
        <requirement type="package" version="1.65">biopython</requirement>
        <requirement type="python-module">Bio</requirement>
    </requirements>

        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command>
    <command interpreter="python">
get_orfs_or_cdss.py -i $input_file -f $input_file.ext --table $table -t $ftype -e $ends -m $mode --min_len $min_len -s $strand --on $out_nuc_file --op $out_prot_file --ob $out_bed_file
    </command>
    <inputs>
        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." />
        <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
            <option value="1">1. Standard</option>

    </inputs>
    <outputs>
        <data name="out_nuc_file" format="fasta" label="${ftype.value}s (nucleotides)" />
        <data name="out_prot_file" format="fasta" label="${ftype.value}s (amino acids)" />
        <data name="out_bed_file" format="bed6" label="${ftype.value}s (bed)" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="get_orf_input.fasta" />
            <param name="table" value="1" />

            <param name="min_len" value="10" />
            <param name="strand" value="forward" />
            <output name="out_nuc_file" file="get_orf_input.t1_nuc_out.fasta" />
            <output name="out_prot_file" file="get_orf_input.t1_prot_out.fasta" />
            <output name="out_bed_file" file="get_orf_input.t1_bed_out.bed" />
        </test>
        <test>
            <param name="input_file" value="get_orf_input.fasta" />
            <param name="table" value="11" />
            <param name="ftype" value="CDS" />

            <param name="min_len" value="10" />
            <param name="strand" value="forward" />
            <output name="out_nuc_file" file="get_orf_input.t11_nuc_out.fasta" />
            <output name="out_prot_file" file="get_orf_input.t11_prot_out.fasta" />
            <output name="out_bed_file" file="get_orf_input.t11_bed_out.bed" />
        </test>
        <test>
            <param name="input_file" value="get_orf_input.fasta" />
            <param name="table" value="11" />
            <param name="ftype" value="CDS" />

            <param name="min_len" value="10" />
            <param name="strand" value="forward" />
            <output name="out_nuc_file" file="get_orf_input.t11_open_nuc_out.fasta" />
            <output name="out_prot_file" file="get_orf_input.t11_open_prot_out.fasta" />
            <output name="out_bed_file" file="get_orf_input.t11_open_bed_out.bed" />
        </test>
        <test>
            <param name="input_file" value="Ssuis.fasta" />
            <param name="table" value="11" />
            <param name="ftype" value="ORF" />

            <param name="min_len" value="100" />
            <param name="strand" value="both" />
            <output name="out_nuc_file" file="get_orf_input.Suis_ORF.nuc.fasta" />
            <output name="out_prot_file" file="get_orf_input.Suis_ORF.prot.fasta" />
            <output name="out_bed_file" file="get_orf_input.Suis_ORF.bed" />
        </test>
    </tests>
    <help>
**What it does**

8:09a8be9247ca

<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.0">
    <description>e.g. to get peptides from ESTs</description>
    <requirements>
        <requirement type="package" version="1.65">biopython</requirement>
        <requirement type="python-module">Bio</requirement>
    </requirements>

        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command>
    <command interpreter="python">
get_orfs_or_cdss.py -i $input_file -f $input_file.ext --table $table -t $ftype -e $ends -m $mode --min_len $min_len -s $strand --on $out_nuc_file --op $out_prot_file --ob $out_bed_file --og $out_gff3_file
    </command>
    <inputs>
        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." />
        <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
            <option value="1">1. Standard</option>

    </inputs>
    <outputs>
        <data name="out_nuc_file" format="fasta" label="${ftype.value}s (nucleotides)" />
        <data name="out_prot_file" format="fasta" label="${ftype.value}s (amino acids)" />
        <data name="out_bed_file" format="bed6" label="${ftype.value}s (bed)" />
        <data name="out_gff3_file" format="gff3" label="${ftype.value}s (gff3)" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="get_orf_input.fasta" />
            <param name="table" value="1" />

            <param name="min_len" value="10" />
            <param name="strand" value="forward" />
            <output name="out_nuc_file" file="get_orf_input.t1_nuc_out.fasta" />
            <output name="out_prot_file" file="get_orf_input.t1_prot_out.fasta" />
            <output name="out_bed_file" file="get_orf_input.t1_bed_out.bed" />
            <output name="out_gff3_file" file="get_orf_input.t1_gff3_out.gff3" />
        </test>
        <test>
            <param name="input_file" value="get_orf_input.fasta" />
            <param name="table" value="11" />
            <param name="ftype" value="CDS" />

            <param name="min_len" value="10" />
            <param name="strand" value="forward" />
            <output name="out_nuc_file" file="get_orf_input.t11_nuc_out.fasta" />
            <output name="out_prot_file" file="get_orf_input.t11_prot_out.fasta" />
            <output name="out_bed_file" file="get_orf_input.t11_bed_out.bed" />
            <output name="out_gff3_file" file="get_orf_input.t11_gff3_out.gff3" />
        </test>
        <test>
            <param name="input_file" value="get_orf_input.fasta" />
            <param name="table" value="11" />
            <param name="ftype" value="CDS" />

            <param name="min_len" value="10" />
            <param name="strand" value="forward" />
            <output name="out_nuc_file" file="get_orf_input.t11_open_nuc_out.fasta" />
            <output name="out_prot_file" file="get_orf_input.t11_open_prot_out.fasta" />
            <output name="out_bed_file" file="get_orf_input.t11_open_bed_out.bed" />
            <output name="out_gff3_file" file="get_orf_input.t11_open_gff3_out.gff3" />
        </test>
        <test>
            <param name="input_file" value="Ssuis.fasta" />
            <param name="table" value="11" />
            <param name="ftype" value="ORF" />

            <param name="min_len" value="100" />
            <param name="strand" value="both" />
            <output name="out_nuc_file" file="get_orf_input.Suis_ORF.nuc.fasta" />
            <output name="out_prot_file" file="get_orf_input.Suis_ORF.prot.fasta" />
            <output name="out_bed_file" file="get_orf_input.Suis_ORF.bed" />
            <output name="out_gff3_file" file="get_orf_input.Suis_ORF.gff3" />
        </test>
    </tests>
    <help>
**What it does**