Mercurial > repos > earlhaminst > gff3_to_json
diff gff3_to_json.xml @ 0:be6cec883b02 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gff3_to_json commit 822c798d43a72724eeab174043fdaafcfdac845f-dirty
| author | earlhaminst |
|---|---|
| date | Wed, 21 Dec 2016 10:02:59 -0500 |
| parents | |
| children | befe6021e476 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff3_to_json.xml Wed Dec 21 10:02:59 2016 -0500 @@ -0,0 +1,92 @@ +<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 +$sort +> "$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>