annotate gff3_to_json.xml @ 1:befe6021e476 draft default tip

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gff3_to_json commit 5e5fbe362ed5a4714debda0f2c0834cbbfd34147

<tool id="gff3_to_json" name="GFF3 to JSON" version="0.1.1">
    <description>converter</description>
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    <command>
<![CDATA[
python '$__tool_directory__/gff3_to_json.py'
#for $q in $queries
    --gff3 '${q.genome}:${q.gff3_input}'
#end for
#if str($json) != 'None'
    #for $v in $json
        --json '$v'
    #end for
#end if
$sort
-o '$output'
]]>
    </command>

    <inputs>
        <repeat name="queries" title="GFF3 dataset">
            <param name="gff3_input" type="data" format="gff3" label="GFF3 dataset" />
            <param name="genome" type="text" label="Genome name" help="Genome name without whitespaces or special characters">
                <validator type="empty_field" />
            </param>
        </repeat>
        <param name="json" type="data" format="json" multiple="true" optional="true" label="JSON datasets to merge" />
        <param name="sort" type="boolean" truevalue="-s" falsevalue="" label="Sort the keys in the JSON output" help="Ensure reproducibility, but can slow down the JSON creation for big files" />
    </inputs>

    <outputs>
         <data name="output" format="json" label="${tool.name} on ${on_string}" />
    </outputs>

    <tests>
        <test>
            <param name="gff3_input" ftype="gff3" value="ENSCAFT00000026349.gff" />
            <param name="genome" ftype="text" value="canisfamiliaris" />
 
            <param name="gff3_input" ftype="gff3" value="ENSMUST00000005671.gff" />
            <param name="genome" ftype="text" value="musmusculus" />

            <param name="gff3_input" ftype="gff3" value="ENSMUST00000091291.gff" />
            <param name="genome" ftype="text" value="musmusculus" />

            <param name="gff3_input" ftype="gff3" value="ENSPTRT00000013802.gff" />
            <param name="genome" ftype="text" value="pantroglodytes" />

            <param name="gff3_input" ftype="gff3" value="ENSRNOT00000019267.gff" />
            <param name="genome" value="rattusnorvegicus" />

            <param name="sort" value="-s" />
            <output name="output" file="test.json" ftype="json" />
        </test>
        <test>
            <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.gff3" />
            <param name="genome" value="caenorhabditiselegans" />
            <param name="sort" value="-s" />
            <output name="output" file="Caenorhabditis_elegans.WBcel235.33.chromosome.I_shortened.json" ftype="json" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Simple tool to convert a set of GFF3 datasets into JSON format and to merge with other JSON files.

Example GFF3 file::

    scaffold_0  MYZPE13164_Clone_G006_v1.0  gene            44968   69413   .   -   .   ID=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030;biotype=protein_coding
    scaffold_0  MYZPE13164_Clone_G006_v1.0  mRNA            44968   69413   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1;Parent=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030.1;biotype=protein_coding;_AED=0.31
    scaffold_0  MYZPE13164_Clone_G006_v1.0  three_prime_utr 44968   46637   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.3utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  exon            44968   47432   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.exon1;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  CDS             46638   47432   .   -   0   ID=MYZPE13164_G006_v1.0_000000030.1.cds1;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  exon            53325   53539   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.exon2;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  CDS             53325   53539   .   -   2   ID=MYZPE13164_G006_v1.0_000000030.1.cds2;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  exon            54614   54719   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.exon3;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  CDS             54614   54719   .   -   0   ID=MYZPE13164_G006_v1.0_000000030.1.cds3;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  CDS             54852   55106   .   -   0   ID=MYZPE13164_G006_v1.0_000000030.1.cds4;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  exon            54852   55117   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.exon4;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  five_prime_utr  55107   55117   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.5utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  five_prime_utr  68851   69413   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.5utr2;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  exon            68851   69413   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.exon5;Parent=MYZPE13164_G006_v1.0_000000030.1

Warning: **Gene**, **mRNA** and **exon** features are mandatory, UTR and CDS are optional. Also, **ID** and **Parent** tags are needed to create relations.
]]>
    </help>
    <citations>
    </citations>
</tool>