Mercurial > repos > vipints > fml_mergeloci
diff fml_gff_groomer/galaxy/gff_loci_merge.xml @ 0:79726c328621 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | vipints |
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| date | Tue, 07 Jun 2011 17:29:24 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_groomer/galaxy/gff_loci_merge.xml Tue Jun 07 17:29:24 2011 -0400 @@ -0,0 +1,114 @@ +<tool id="fml_mergeloci" name="MergeLoci" version="1.0.0"> + <description>Merge feature annotation from same loci</description> + <command interpreter="python"> + gff_loci_merge.py + $gff_input + $gff_result + > $logfile + </command> + <inputs> + <param format="gff3" name="gff_input" type="data" label="Genome annotation in GFF3 format" help="Genome annotation in GFF3 format describing the known gene structures for the provided genome."/> + </inputs> + <outputs> + <data format="txt" name="logfile" label="Log file for MergeLoci" /> + <data format="gff3" name="gff_result" /> + </outputs> + <tests> + <test> + <param name="gff_input" value="ucsc_splitted_genes.gff3" /> + <output name="logfile" file="ucsc_merged_genes_log.txt" /> + <output name="gff_result" file="ucsc_merged_genes.gff3" /> + </test> + </tests> + <help> + +**What it does** + +This tool merge the feature annotation of same loci. MergeLoci will be able to merge several transcripts from single loci to a main feature instead of several features. For example, in UCSC genome annotation files the alternative splice model of the transcript are represented as individual gene models. + +-------- + +**Example** + +- data in GFF3 format:: + + ##gff-version 3 + chr19 hg19_knownGene gene 44764033 44779468 . + . ID=Gene:uc002oyy.1;Name=Gene:uc002oyy.1 + chr19 hg19_knownGene mRNA 44764033 44779468 . + . ID=Transcript:uc002oyy.1;Parent=Gene:uc002oyy.1 + chr19 hg19_knownGene protein 44777369 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44764033 44764091 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44768467 44768528 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44777052 44777368 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene CDS 44777369 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44764033 44764091 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44768467 44768528 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44777052 44779468 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene gene 44770351 44779468 . + . ID=Gene:uc002oyy.1;Name=Gene:uc002oyy.1 + chr19 hg19_knownGene mRNA 44770351 44779468 . + . ID=Transcript:uc002oyy.1;Parent=Gene:uc002oyy.1 + chr19 hg19_knownGene protein 44777052 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene CDS 44777052 44777368 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene CDS 44777489 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44777052 44777368 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44777489 44779468 . + . Parent=Transcript:uc002oyy.1 + +- Will be merged as:: + + ##gff-version 3 + chr19 hg19_knownGene gene 44764033 44779468 . + . ID=Gene_hg19_chr19_00001;Name=Gene_hg19_chr19_0001 + chr19 hg19_knownGene mRNA 44764033 44779468 . + . ID=Transcript:uc002oyy.1;Parent=Gene_hg19_chr19_0001 + chr19 hg19_knownGene protein 44777369 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44764033 44764091 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44768467 44768528 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44777052 44777368 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene CDS 44777369 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44764033 44764091 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44768467 44768528 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44777052 44779468 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene mRNA 44770351 44779468 . + . ID=Transcript:uc002oyy.1;Gene_hg19_chr19_0001 + chr19 hg19_knownGene protein 44777052 44778826 . + . ID=Protein:uc002oyy.1;Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44770351 44770477 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene five_prime_UTR 44771019 44771297 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene CDS 44777052 44777368 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene CDS 44777489 44778826 . + 0 Name=CDS:uc002oyy.1;Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene three_prime_UTR 44778827 44779468 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44770351 44770477 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44771019 44771297 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44777052 44777368 . + . Parent=Transcript:uc002oyy.1 + chr19 hg19_knownGene exon 44777489 44779468 . + . Parent=Transcript:uc002oyy.1 + +-------- + +**About formats** + +**GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields: + + 1. seqid - Must be a chromosome or scaffold. + 2. source - The program that generated this feature. + 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". + 4. start - The starting position of the feature in the sequence. The first base is numbered 1. + 5. stop - The ending position of the feature (inclusive). + 6. score - A score between 0 and 1000. If there is no score value, enter ".". + 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). + 8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'. + 9. attributes - All lines with the same group are linked together into a single item. + +-------- + +This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de) +</help> +</tool>