Mercurial > repos > yhoogstrate > flaimapper
annotate flaimapper.xml @ 25:c9f0f918bef6 draft
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| author | yhoogstrate |
|---|---|
| date | Sun, 29 Mar 2015 02:54:20 -0400 |
| parents | bd695d4cb7c4 |
| children | 4e00cc7b97e5 |
| 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 $alignment | |
| 21 #end for | |
| 0 | 22 </command> |
| 23 | |
| 24 | 24 <stdio> |
| 25 | 25 <regex match="[fai_load] build FASTA index." source="stderr" level="log" /> |
| 24 | 26 </stdio> |
| 27 | |
| 0 | 28 <inputs> |
| 29 <param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" /> | |
| 30 | |
| 18 | 31 <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" /> |
| 8 | 32 |
| 2 | 33 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> |
| 34 | |
| 35 <param name="output_format" type="select" label="Output format"> | |
| 24 | 36 <option value="1">Tabular (1 fragment per column)</option> |
| 37 <option value="2">Tabular (1 precursor per column)</option> | |
| 38 <option value="3">GenBank</option> | |
| 39 <!-- option value="gtf">GTF/GFF</option --> | |
| 0 | 40 </param> |
| 41 </inputs> | |
| 42 | |
| 43 <outputs> | |
| 44 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> | |
| 45 </outputs> | |
| 46 | |
| 24 | 47 <tests> |
| 48 <test> | |
| 49 <param name="alignments" value="snord81.bam" /> | |
| 50 <param name="mask" value="ncrnadb09.gtf" format="gtf" /> | |
| 51 <param name="fasta" value="ncrnadb09.fa" format="fasta" /> | |
| 52 <param name="output_format" value="1" /> | |
| 53 | |
| 54 <output name="output" file="snord81.flaimapper.txt" /> | |
| 55 </test> | |
| 56 </tests> | |
| 57 | |
| 0 | 58 <help> |
| 14 | 59 FlaiMapper wrapper for Galaxy |
| 60 ============================= | |
| 61 | |
| 62 https://github.com/yhoogstrate/flaimapper | |
| 63 http://www.ncbi.nlm.nih.gov/pubmed/25338717 | |
| 64 http://dx.doi.org/10.1093/bioinformatics/btu696 | |
| 65 | |
| 66 Fragment Location Annotation Identification Mapper | |
| 67 | |
| 68 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. | |
| 69 | |
| 70 Input formats | |
| 71 ------------- | |
| 72 Alignments should be provided in BAM format. | |
| 73 Gene (MASK) regions should be provided in the GFF/GTF format: | |
| 74 | |
| 75 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3 | |
| 76 - http://www.ensembl.org/info/website/upload/gff.html | |
| 77 | |
|
20
ac69be28e786
FlaiMapper: added wrapper for FASTA->GTF conversion
yhoogstrate
parents:
19
diff
changeset
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78 The reference sequence should be provided in FASTA format. |
| 14 | 79 |
| 19 | 80 You can access **ncRNAdb09** at the following URLs: |
| 81 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)* | |
| 82 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)* | |
| 83 | |
| 84 Therefore you need bam files aligned to the same reference. We have made | |
| 85 the following available: | |
| 86 | |
| 87 - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz | |
| 88 - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz | |
| 89 | |
| 90 If you want to test flaimapper with example data you can obtain several | |
| 91 alignment files from this following directory tree: | |
| 92 | |
| 93 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments | |
| 94 | |
| 14 | 95 Installation |
| 96 ------------ | |
| 97 | |
| 98 The wrapper makes use of easy_install to install a python egg. Please | |
| 99 ensure you have easy_install installed. | |
| 100 | |
| 101 License | |
| 102 ------- | |
| 103 | |
| 104 **flaimapper** and **wrapper**: | |
| 105 | |
| 106 GPL (>=3) | |
| 107 | |
| 108 **pysam**: | |
| 109 | |
| 19 | 110 The MIT License |
| 14 | 111 |
| 112 Contact | |
| 113 ------- | |
| 114 | |
| 115 The tool wrapper has been written by Youri Hoogstrate from the Erasmus | |
| 116 Medical Center (Rotterdam, Netherlands). | |
| 117 | |
| 118 | |
| 119 Development | |
| 120 ----------- | |
| 121 | |
| 122 * Repository-Maintainer: Youri Hoogstrate | |
| 123 * Repository-Developers: Youri Hoogstrate | |
| 124 | |
| 125 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools | |
| 126 | |
| 127 The tool wrapper has been written by Youri Hoogstrate from the Erasmus | |
| 128 Medical Center (Rotterdam, Netherlands). | |
| 129 | |
| 0 | 130 </help> |
| 14 | 131 |
| 132 <citations> | |
| 133 <citation type="doi">10.1093/bioinformatics/btu696</citation> | |
| 134 </citations> | |
|
20
ac69be28e786
FlaiMapper: added wrapper for FASTA->GTF conversion
yhoogstrate
parents:
19
diff
changeset
|
135 </tool> |