comparison ensembl_cdna_translate.xml @ 8:5c92d0be6514 draft

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7:d59e3ce10e74

        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.4.10">requests-cache</requirement>
        <requirement type="package" version="1.62">biopython</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[

                --transcripts '-'
            #end if
        #end if
        #if str($output_choice).find('translation') >= 0:
          | python '$__tool_directory__/ensembl_cdna_translate.py' -i '-' 
            --min_length $min_length
            #if $enzyme:
                --enzyme '$enzyme'
            #end if
            #if $input and str($output_choice).find('transcript_bed') >= 0:
                --transcripts '$transcript_bed'
            #end if
            #if str($output_choice).find('translation_bed') >= 0: 
                --bed '$translation_bed'
            #end if
            #if str($output_choice).find('translation_fasta') >= 0: 
                --fasta '$translation_fasta'
            #end if
            ###if $features.biotypes:
            ##    --biotypes '$features.biotypes'
            ###end if
        #end if
       
    ]]></command>
    <inputs>
        <param name="species" type="text" value="" label="Ensembl species" >
            <help>
            </help>

                <param name="biotypes" type="text" value="" optional="true" label="Restrict Feature translation to these biotypes" >
                    <expand macro="biotypes_help" />
                </param>
            </when>
        </conditional>
        <!--
        <conditional name="translations">
        </conditional>
        -->


        <param name="translate_all" type="boolean" truevalue="--all" falsevalue="" checked="false" 
            label="Report all translations (Default is non reference protein sequences)"/>
        <param name="output_choice" type="select" multiple="true" display="checkboxes" label="Outputs">
            <option value="transcript_bed">transcripts.bed</option>
            <option value="translation_bed">translation.bed</option>
            <option value="translation_fasta">translation.fasta</option>
        </param>
        <param name="min_length" type="integer" value="7" min="1" label="Minimum length of protein translation to report"/>
        <param name="enzyme" type="select" optional="true" label="Digest enzyme" 
             help="Remove frags that are in a reference protein">
            <option value="trypsin">trypsin:       ([KR](?=[^P]))|((?&lt;=W)K(?=P))|((?&lt;=M)R(?=P))</option>
        </param>
    </inputs>
    <outputs>
        <data name="transcript_bed" format="bed" label="Ensembl $species transcripts.bed">
            <filter>'transcript_bed' in output_choice</filter>
        </data>
        <data name="translation_bed" format="bed" label="Ensembl $species translation.bed">
            <filter>'translation_bed' in output_choice</filter>
        </data>
        <data name="translation_fasta" format="fasta" label="Ensembl $species translation.fasta">
            <filter>'translation_fasta' in output_choice</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="species" value="human"/>
            <param name="input" value="human_transcripts.bed" ftype="bed"/>
            <param name="output_choice" value="translation_bed,translation_fasta"/>
            <output name="translation_bed">
                <assert_contents>
                    <has_text text="ENST00000641515" />
                </assert_contents>

8:5c92d0be6514

        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.4.10">requests-cache</requirement>
        <requirement type="package" version="1.62">biopython</requirement>
        <requirement type="package" version="3.1.4">twobitreader</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[

                --transcripts '-'
            #end if
        #end if
        #if str($output_choice).find('translation') >= 0:
          | python '$__tool_directory__/ensembl_cdna_translate.py' -i '-' 
            #if $ref.ref_source == 'cached':
                --twobit='$ref.ref_loc.fields.path'
            #elif $ref.ref_source == 'history':
                --twobit='$ref.ref_file'
            #end if
            --min_length $translations.min_length
            #if $translations.enzyme:
                --enzyme '$translations.enzyme'
            #end if
            $translations.translate_all
            #if $features.feature_src == 'history_bed' and str($output_choice).find('transcript_bed') >= 0:
                --transcripts '$transcript_bed'
            #end if
            #if str($output_choice).find('translation_bed') >= 0: 
                --bed '$translation_bed'
            #end if
            #if str($output_choice).find('translation_fasta') >= 0: 
                --fasta '$translation_fasta'
            #end if
            #if $features.biotypes:
                --biotypes '$features.biotypes'
            #end if
        #end if
    ]]></command>
    <inputs>
        <param name="species" type="text" value="" label="Ensembl species" >
            <help>
            </help>

                <param name="biotypes" type="text" value="" optional="true" label="Restrict Feature translation to these biotypes" >
                    <expand macro="biotypes_help" />
                </param>
            </when>
        </conditional>
        <conditional name="ref">
            <param name="ref_source" type="select" label="Source for Genomic Sequence Data">
                <option value="cached">Locally cached twobit</option>
                <option value="history">History dataset twobit</option>
                <option value="ensembl_rest">Retrieve sequences from Ensembl (Slow and only for Ensembl Transcripts)</option>
            </param>
            <when value="cached">
                <param name="ref_loc" type="select" label="Select reference 2bit file">
                    <options from_data_table="twobit" />
                </param>
            </when>
            <when value="history">
                <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />
            </when>
            <when value="ensembl_rest"/>
        </conditional>
        <section name="translations" expanded="false" title="Translation  Options">
            <param name="min_length" type="integer" value="10" min="1" label="Minimum length of protein translation to report"/>
            <param name="translate_all" type="boolean" truevalue="--all" falsevalue="" checked="false" 
                label="Report all translations (Default is non reference protein sequences)"/>
            <param name="enzyme" type="select" optional="true" label="Digest enzyme" 
                 help="Remove frags that are in a reference protein">
                <option value="trypsin">trypsin:       ([KR](?=[^P]))|((?&lt;=W)K(?=P))|((?&lt;=M)R(?=P))</option>
            </param>
        </section>
        <param name="output_choice" type="select" multiple="true" display="checkboxes" label="Outputs">
            <option value="transcript_bed">transcripts.bed</option>
            <option value="translation_bed">translation.bed</option>
            <option value="translation_fasta">translation.fasta</option>
        </param>
    </inputs>
    <outputs>
        <data name="transcript_bed" format="bed" label="Ensembl ${species} transcripts.bed">
            <filter>'transcript_bed' in output_choice</filter>
        </data>
        <data name="translation_bed" format="bed" label="Ensembl ${species} translation.bed">
            <filter>'translation_bed' in output_choice</filter>
        </data>
        <data name="translation_fasta" format="fasta" label="Ensembl ${species} translation.fasta">
            <filter>'translation_fasta' in output_choice</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="species" value="human"/>
            <param name="feature_src" value="history_bed"/>
            <param name="input" value="human_transcripts.bed" ftype="bed"/>
            <param name="ref_source" value="ensembl_rest"/>
            <param name="output_choice" value="translation_bed,translation_fasta"/>
            <output name="translation_bed">
                <assert_contents>
                    <has_text text="ENST00000641515" />
                </assert_contents>