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

annotate flaimapper-gtf-from-fasta.xml @ 30:25a96df047f7 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty

author	yhoogstrate
date	Wed, 03 Jun 2015 07:28:26 -0400
parents	19d1402611ef
children	ea855f0a689a

rev	line source
20 ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	1 <?xml version="1.0" encoding="UTF-8"?>
28 19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	2 <tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.2.1.w1">
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>
28 19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	5 <requirement type="package" version="1.2.1">flaimapper</requirement>
20 ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	6 </requirements>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	7
28 19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	8 <stdio>
19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	9 <regex
19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	10 match="[fai_load] build FASTA index."
19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	11 source="stderr"
19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	12 level="log"
19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	13 description="The FASTA file is being indexed." />
19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	14 </stdio>
19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	15
20 ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	16 <version_command>flaimapper --version</version_command>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	17
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	18 <command>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	19 gtf-from-fasta
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	20 -o $output
21 262d9457ad84 Uploaded yhoogstrate parents: 20 diff changeset	21 $fasta
20 ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	22 </command>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	23
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	24 <inputs>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	25 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	26 </inputs>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	27
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	28 <outputs>
23 e0c0fc569303 Suppressed stderr warning yhoogstrate parents: 22 diff changeset	29 <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" />
20 ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	30 </outputs>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	31
24 bd695d4cb7c4 Uploaded yhoogstrate parents: 23 diff changeset	32 <tests>
bd695d4cb7c4 Uploaded yhoogstrate parents: 23 diff changeset	33 <test>
28 19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	34 <param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" />
24 bd695d4cb7c4 Uploaded yhoogstrate parents: 23 diff changeset	35
28 19d1402611ef planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty yhoogstrate parents: 24 diff changeset	36 <output name="output" file="test3/reference.gtf" />
24 bd695d4cb7c4 Uploaded yhoogstrate parents: 23 diff changeset	37 </test>
bd695d4cb7c4 Uploaded yhoogstrate parents: 23 diff changeset	38 </tests>
bd695d4cb7c4 Uploaded yhoogstrate parents: 23 diff changeset	39
20 ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	40 <help>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	41 FlaiMapper wrapper for Galaxy
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	42 =============================
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	43
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	44 https://github.com/yhoogstrate/flaimapper
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	45 http://www.ncbi.nlm.nih.gov/pubmed/25338717
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	46 http://dx.doi.org/10.1093/bioinformatics/btu696
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	47
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	48 Fragment Location Annotation Identification Mapper
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	49
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	50 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	51
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	52 Input formats
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	53 -------------
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	54 To make FlaiMapper compatible with both an entire reference genome as a
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	55 separate ncRNA database, it requires an additional GTF file (mask file).
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	56 The major difference between an entire reference and a ncRNA database
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	57 is that an entire reference usually contains multiple ncRNAs per sequence
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	58 entry (chromosome). While for the ncRNA database, each entry should
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	59 represent one single mature ncRNA.
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 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	62 database will only contain the start- and end positions of each entry.
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	63 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	64 as long as the FASTA file doesn't contain entire chromosomes but
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	65 mature ncRNA.
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 An example input file is ncRNAdb09, available at the following URLs:
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	68 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	69
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	70 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	71 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	72
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	73 Installation
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
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	76 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	77 ensure you have easy_install installed.
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	78
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	79 License
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 flaimapper and wrapper:
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 GPL (>=3)
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	85
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	86 pysam:
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 The MIT License
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 Contact
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	91 -------
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 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	94 Medical Center (Rotterdam, Netherlands).
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	95
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	96
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	97 Development
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	98 -----------
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	99
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	100 * Repository-Maintainer: Youri Hoogstrate
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	101 * Repository-Developers: Youri Hoogstrate
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	102
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	103 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	104
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	105 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	106 Medical Center (Rotterdam, Netherlands).
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	107
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	108 </help>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	109
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	110 <citations>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	111 <citation type="doi">10.1093/bioinformatics/btu696</citation>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	112 </citations>
ac69be28e786 FlaiMapper: added wrapper for FASTA->GTF conversion yhoogstrate parents: diff changeset	113 </tool>

Mercurial > repos > yhoogstrate > flaimapper

annotate flaimapper-gtf-from-fasta.xml @ 30:25a96df047f7 draft