comparison extract_genomic_dna.xml @ 11:80414c33a59a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296

10:5cc8e93ee98f

<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.3+galaxy2">
    <description>using coordinates from assembled/unassembled genomes</description>
    <requirements>
        <requirement type="package" version="0.7.1">bx-python</requirement>
        <requirement type="package" version="1.13.0">six</requirement>
        <requirement type="package" version="377">ucsc-fatotwobit</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#set genome = $input.metadata.dbkey
#set datatype = $input.datatype
mkdir -p output_dir &&
python '$__tool_directory__/extract_genomic_dna.py'

    <tests>
        <test>
            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
            <param name="interpret_features" value="no"/>
            <param name="reference_genome_source" value="history"/>
            <param name="reference_genome" value="mm9.fasta"/>
            <param name="output_format" value="fasta"/>
            <param name="fasta_header_type" value="char_delimited"/>
            <param name="fasta_header_delimiter" value="tilde"/>
            <output name="output" file="extract_genomic_dna_out1.fasta" compare="contains" />
        </test>
        <test>
            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
            <param name="interpret_features" value="yes"/>
            <param name="reference_genome_source" value="history"/>
            <param name="reference_genome" value="mm9.fasta"/>
            <param name="output_format" value="fasta"/>
            <param name="fasta_header_type" value="bedtools_getfasta_default"/>
            <output name="output" file="extract_genomic_dna_out2.fasta" compare="contains" />
        </test>
        <test>
            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
            <param name="interpret_features" value="no"/>
            <param name="reference_genome_source" value="history"/>
            <param name="reference_genome" value="mm9.fasta"/>
            <param name="output_format" value="interval"/>
            <output name="output" file="extract_genomic_dna_out3.gff" compare="contains" />
        </test>
        <test>
            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
            <param name="interpret_features" value="yes"/>
            <param name="reference_genome_source" value="history"/>
            <param name="reference_genome" value="mm9.fasta"/>
            <param name="output_format" value="interval"/>
            <output name="output" file="extract_genomic_dna_out4.gff" compare="contains" />
        </test>
    </tests>
    <help>

11:80414c33a59a

<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.3+galaxy3">
    <description>using coordinates from assembled/unassembled genomes</description>
    <requirements>
        <requirement type="package" version="0.7.1">bx-python</requirement>
        <requirement type="package" version="1.13.0">six</requirement>
        <requirement type="package" version="377">ucsc-fatotwobit</requirement>
    </requirements>
    <required_files>
        <include path="extract_genomic_dna_utils.py" />
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
#set genome = $input.metadata.dbkey
#set datatype = $input.datatype
mkdir -p output_dir &&
python '$__tool_directory__/extract_genomic_dna.py'

    <tests>
        <test>
            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
            <param name="interpret_features" value="no"/>
            <param name="reference_genome_source" value="history"/>
            <param name="reference_genome" value="mm9.fasta" dbkey="mm9" ftype="fasta"/>
            <param name="output_format" value="fasta"/>
            <param name="fasta_header_type" value="char_delimited"/>
            <param name="fasta_header_delimiter" value="tilde"/>
            <output name="output" file="extract_genomic_dna_out1.fasta" compare="contains" />
        </test>
        <test>
            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
            <param name="interpret_features" value="yes"/>
            <param name="reference_genome_source" value="history"/>
            <param name="reference_genome" value="mm9.fasta" dbkey="mm9"/>
            <param name="output_format" value="fasta"/>
            <param name="fasta_header_type" value="bedtools_getfasta_default"/>
            <output name="output" file="extract_genomic_dna_out2.fasta" compare="contains" />
        </test>
        <test>
            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
            <param name="interpret_features" value="no"/>
            <param name="reference_genome_source" value="history"/>
            <param name="reference_genome" value="mm9.fasta" dbkey="mm9"/>
            <param name="output_format" value="interval"/>
            <output name="output" file="extract_genomic_dna_out3.gff" compare="contains" />
        </test>
        <test>
            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
            <param name="interpret_features" value="yes"/>
            <param name="reference_genome_source" value="history"/>
            <param name="reference_genome" value="mm9.fasta" dbkey="mm9"/>
            <param name="output_format" value="interval"/>
            <output name="output" file="extract_genomic_dna_out4.gff" compare="contains" />
        </test>
    </tests>
    <help>