flaimapper: flaimapper-gtf-from-fasta.xml annotate

annotate flaimapper-gtf-from-fasta.xml @ 21:262d9457ad84 draft

Uploaded

author	yhoogstrate
date	Wed, 25 Mar 2015 16:07:51 -0400
parents	ac69be28e786
children	79b54b3c4472

rev	line source
20 ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	1 <?xml version="1.0" encoding="UTF-8"?>
21 262d9457ad84 Uploaded yhoogstrate parents: 20 diff changeset	2 <tool id="flaimapper-gtf-from-fasta" name="FlaiMapper" version="1.1.5.b">
20 ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	3 <description>Extract GTF file from FASTA file (as FlaiMapper reference).</description>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	4 <requirements>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	5 <requirement type="package" version="0.8.2.1">pysam</requirement>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	6 <requirement type="package" version="1.1.5">flaimapper</requirement>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	7 </requirements>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	8
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	9 <version_command>flaimapper --version</version_command>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	10
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	11 <command>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	12 gtf-from-fasta
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	13 -o $output
21 262d9457ad84 Uploaded yhoogstrate parents: 20 diff changeset	14 $fasta
20 ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	15 </command>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	16
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	17 <inputs>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	18 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	19 </inputs>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	20
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	21 <outputs>
21 262d9457ad84 Uploaded yhoogstrate parents: 20 diff changeset	22 <data format="gtf" name="output" label="${tool.name} on ${fasta}" />
20 ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	23 </outputs>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	24
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	25 <help>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	26 FlaiMapper wrapper for Galaxy
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	27 =============================
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	28
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	29 https://github.com/yhoogstrate/flaimapper
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	30 http://www.ncbi.nlm.nih.gov/pubmed/25338717
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	31 http://dx.doi.org/10.1093/bioinformatics/btu696
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	32
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	33 Fragment Location Annotation Identification Mapper
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	34
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	35 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	36
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	37 Input formats
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	38 -------------
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	39 To make FlaiMapper compatible with both an entire reference genome as a
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	40 separate ncRNA database, it requires an additional GTF file (mask file).
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	41 The major difference between an entire reference and a ncRNA database
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	42 is that an entire reference usually contains multiple ncRNAs per sequence
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	43 entry (chromosome). While for the ncRNA database, each entry should
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	44 represent one single mature ncRNA.
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	45
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	46 Therefore the mask file that represents to the FASTA file of a ncRNA
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	47 database will only contain the start- and end positions of each entry.
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	48 To generate this in an automated fashion, you can make use of this tool
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	49 as long as the FASTA file doesn't contain entire chromosomes but
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	50 mature ncRNA.
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	51
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	52 An example input file is ncRNAdb09, available at the following URLs:
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	53 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa (reference file)
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	54
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	55 It should generate a GTF/GFF file (mask file) similar to the following URL:
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	56 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf (mask file)
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	57
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	58 Installation
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	59 ------------
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	60
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	61 The wrapper makes use of easy_install to install a python egg. Please
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	62 ensure you have easy_install installed.
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	63
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	64 License
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	65 -------
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	66
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	67 flaimapper and wrapper:
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	68
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	69 GPL (>=3)
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	70
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	71 pysam:
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	72
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	73 The MIT License
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	74
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	75 Contact
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	76 -------
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	77
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	78 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	79 Medical Center (Rotterdam, Netherlands).
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	80
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	81
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	82 Development
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	83 -----------
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	84
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	85 * Repository-Maintainer: Youri Hoogstrate
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	86 * Repository-Developers: Youri Hoogstrate
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	87
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	88 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	89
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	90 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	91 Medical Center (Rotterdam, Netherlands).
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	92
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	93 </help>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	94
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	95 <citations>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	96 <citation type="doi">10.1093/bioinformatics/btu696</citation>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	97 </citations>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	98 </tool>

Mercurial > repos > yhoogstrate > flaimapper

annotate flaimapper-gtf-from-fasta.xml @ 21:262d9457ad84 draft