view fasta_extract.xml @ 11:48f6e9f1c19d draft

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<tool id="fasta_extract" name="Extract fasta sequences" version="1.0.0">
    <description>using coordinates from assembled genomes</description>
    <macros>
        <import>fasta_extract_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
        <![CDATA[
            mkdir -p output_dir &&
            mkdir -p output_orphan_dir &&
            python $__tool_directory__/fasta_extract.py
            #for $i in $inputs:
                --input "$i" ${i.hid}
            #end for
            #if str($reference_genome_cond.reference_genome_source) == "cached":
                #set genome_file = $reference_genome_cond.reference_genome.fields.path
            #else:
                #set genome_file = $reference_genome_cond.reference_genome
            #end if
            --genome_file "$genome_file"
            --subtract_from_start $subtract_from_start
            --add_to_end $add_to_end
            --extend_existing $extend_existing
            --strand $strand
        ]]>
    </command>
    <inputs>
        <param name="inputs" type="data" format="gff" multiple="True" label="Fetch sequences for intervals in">
            <validator type="unspecified_build" />
        </param>
        <conditional name="reference_genome_cond">
            <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
                <option value="cached">Locally Cached</option>
                <option value="history">From History</option>
            </param>
            <when value="cached">
                <param name="reference_genome" type="select" label="Using reference genome">
                    <options from_data_table="all_fasta" />
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="reference_genome" type="data" format="fasta" label="Using reference genome"/>
            </when>
        </conditional>
        <param name="subtract_from_start" type="integer" value="50" min="0" label="Distance to subtract from start" />
        <param name="add_to_end" type="integer" value="50" min="0" label="Distance to add to end" />
        <param name="extend_existing" type="select" label="Extend existing start and end coordinates or extend from computed midpoint?">
            <option value="midpoint" selected="True">Extend from computed midpoint</option>
            <option value="existing">Extend from existing start and end coordinates</option>
        </param>
        <param name="strand" type="select" label="Extract reverse complement sequence on reverse strand?">
            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
    </inputs>
    <outputs>
        <collection name="fasta_extract_output_orphan" type="list" label="Extract fasta sequences (orphans) on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output_orphan_dir" ext="gff" visible="false" />
        </collection>
        <collection name="fasta_extract_output" type="list" label="Extract fasta sequences on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output_dir" ext="fasta" visible="false" />
        </collection>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>

**What it does**

   </help>
   <expand macro="citations" />
</tool>