Mercurial > repos > yhoogstrate > flaimapper
annotate flaimapper.xml @ 24:bd695d4cb7c4 draft
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| author | yhoogstrate |
|---|---|
| date | Sun, 29 Mar 2015 02:43:11 -0400 |
| parents | ac69be28e786 |
| children | c9f0f918bef6 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0" encoding="UTF-8"?> |
| 19 | 2 <tool id="flaimapper" name="FlaiMapper" version="1.1.5.a"> |
| 0 | 3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description> |
| 4 <requirements> | |
| 19 | 5 <requirement type="package" version="0.8.2.1">pysam</requirement> |
| 6 <requirement type="package" version="1.1.5">flaimapper</requirement> | |
| 0 | 7 </requirements> |
| 8 | 8 |
| 9 <version_command>flaimapper --version</version_command> | |
| 10 | |
| 0 | 11 <command> |
| 12 flaimapper | |
| 13 -v | |
| 14 -f $output_format | |
| 15 -o $output | |
| 16 -m $mask | |
| 17 -r $fasta | |
| 8 | 18 |
| 19 #for $alignment in $alignments | |
| 20 $alignment | |
| 21 #end for | |
| 0 | 22 </command> |
| 23 | |
| 24 | 24 <stdio> |
| 25 </stdio> | |
| 26 | |
| 0 | 27 <inputs> |
| 28 <param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" /> | |
| 29 | |
| 18 | 30 <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" /> |
| 8 | 31 |
| 2 | 32 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> |
| 33 | |
| 34 <param name="output_format" type="select" label="Output format"> | |
| 24 | 35 <option value="1">Tabular (1 fragment per column)</option> |
| 36 <option value="2">Tabular (1 precursor per column)</option> | |
| 37 <option value="3">GenBank</option> | |
| 38 <!-- option value="gtf">GTF/GFF</option --> | |
| 0 | 39 </param> |
| 40 </inputs> | |
| 41 | |
| 42 <outputs> | |
| 43 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> | |
| 44 </outputs> | |
| 45 | |
| 24 | 46 <tests> |
| 47 <test> | |
| 48 <param name="alignments" value="snord81.bam" /> | |
| 49 <param name="mask" value="ncrnadb09.gtf" format="gtf" /> | |
| 50 <param name="fasta" value="ncrnadb09.fa" format="fasta" /> | |
| 51 <param name="output_format" value="1" /> | |
| 52 | |
| 53 <output name="output" file="snord81.flaimapper.txt" /> | |
| 54 </test> | |
| 55 </tests> | |
| 56 | |
| 0 | 57 <help> |
| 14 | 58 FlaiMapper wrapper for Galaxy |
| 59 ============================= | |
| 60 | |
| 61 https://github.com/yhoogstrate/flaimapper | |
| 62 http://www.ncbi.nlm.nih.gov/pubmed/25338717 | |
| 63 http://dx.doi.org/10.1093/bioinformatics/btu696 | |
| 64 | |
| 65 Fragment Location Annotation Identification Mapper | |
| 66 | |
| 67 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. | |
| 68 | |
| 69 Input formats | |
| 70 ------------- | |
| 71 Alignments should be provided in BAM format. | |
| 72 Gene (MASK) regions should be provided in the GFF/GTF format: | |
| 73 | |
| 74 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3 | |
| 75 - http://www.ensembl.org/info/website/upload/gff.html | |
| 76 | |
|
20
ac69be28e786
FlaiMapper: added wrapper for FASTA->GTF conversion
yhoogstrate
parents:
19
diff
changeset
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77 The reference sequence should be provided in FASTA format. |
| 14 | 78 |
| 19 | 79 You can access **ncRNAdb09** at the following URLs: |
| 80 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)* | |
| 81 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)* | |
| 82 | |
| 83 Therefore you need bam files aligned to the same reference. We have made | |
| 84 the following available: | |
| 85 | |
| 86 - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz | |
| 87 - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz | |
| 88 | |
| 89 If you want to test flaimapper with example data you can obtain several | |
| 90 alignment files from this following directory tree: | |
| 91 | |
| 92 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments | |
| 93 | |
| 14 | 94 Installation |
| 95 ------------ | |
| 96 | |
| 97 The wrapper makes use of easy_install to install a python egg. Please | |
| 98 ensure you have easy_install installed. | |
| 99 | |
| 100 License | |
| 101 ------- | |
| 102 | |
| 103 **flaimapper** and **wrapper**: | |
| 104 | |
| 105 GPL (>=3) | |
| 106 | |
| 107 **pysam**: | |
| 108 | |
| 19 | 109 The MIT License |
| 14 | 110 |
| 111 Contact | |
| 112 ------- | |
| 113 | |
| 114 The tool wrapper has been written by Youri Hoogstrate from the Erasmus | |
| 115 Medical Center (Rotterdam, Netherlands). | |
| 116 | |
| 117 | |
| 118 Development | |
| 119 ----------- | |
| 120 | |
| 121 * Repository-Maintainer: Youri Hoogstrate | |
| 122 * Repository-Developers: Youri Hoogstrate | |
| 123 | |
| 124 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools | |
| 125 | |
| 126 The tool wrapper has been written by Youri Hoogstrate from the Erasmus | |
| 127 Medical Center (Rotterdam, Netherlands). | |
| 128 | |
| 0 | 129 </help> |
| 14 | 130 |
| 131 <citations> | |
| 132 <citation type="doi">10.1093/bioinformatics/btu696</citation> | |
| 133 </citations> | |
|
20
ac69be28e786
FlaiMapper: added wrapper for FASTA->GTF conversion
yhoogstrate
parents:
19
diff
changeset
|
134 </tool> |