Mercurial > repos > yhoogstrate > flaimapper
annotate flaimapper.xml @ 28:19d1402611ef 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 07:27:47 -0400 |
| parents | 19feb87f757d |
| children | 3074e91f9f80 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0" encoding="UTF-8"?> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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2 <tool id="flaimapper" name="FlaiMapper" version="1.2.1.w1"> |
| 0 | 3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description> |
| 4 <requirements> | |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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5 <requirement type="package" version="1.2.1">flaimapper</requirement> |
| 0 | 6 </requirements> |
| 8 | 7 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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8 <stdio> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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9 <regex match="in parse_gff.*?ValueError: invalid literal for int\(\) with base 10" source="stderr" level="fatal" description="The GTF file is corrupt: double check the columns of your GTF/GFF file.\n" /> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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10 <regex match="[fai_load] build FASTA index." source="stderr" level="log" /> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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11 </stdio> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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12 |
| 8 | 13 <version_command>flaimapper --version</version_command> |
| 14 | |
| 0 | 15 <command> |
| 16 flaimapper | |
| 17 -v | |
| 18 -f $output_format | |
| 19 -o $output | |
| 20 -m $mask | |
| 21 -r $fasta | |
| 8 | 22 |
| 23 #for $alignment in $alignments | |
| 24 $alignment | |
| 25 #end for | |
| 0 | 26 </command> |
| 27 | |
| 28 <inputs> | |
| 26 | 29 <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" /> |
| 0 | 30 |
| 18 | 31 <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" /> |
| 8 | 32 |
| 2 | 33 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> |
| 34 | |
| 35 <param name="output_format" type="select" label="Output format"> | |
| 24 | 36 <option value="1">Tabular (1 fragment per column)</option> |
| 37 <option value="2">Tabular (1 precursor per column)</option> | |
| 38 <option value="3">GenBank</option> | |
| 39 <!-- option value="gtf">GTF/GFF</option --> | |
| 0 | 40 </param> |
| 41 </inputs> | |
| 42 | |
| 43 <outputs> | |
| 44 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> | |
| 45 </outputs> | |
| 46 | |
| 24 | 47 <tests> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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48 <test><!-- Testing "ncRNAdb09 alignment"-type analysis --> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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49 <param name="alignments" value="test1/snord81.bam" ftype="bam" /> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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50 <param name="mask" value="test1/ncrnadb09.v2.gtf" ftype="gtf" /> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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51 <param name="fasta" value="test1/ncrnadb09.fa" ftype="fasta" /> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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52 <param name="output_format" value="1" /> |
| 24 | 53 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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54 <output name="output" file="test1/snord81.flaimapper.txt" /> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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55 </test> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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56 <test><!-- Testing "Full genome alignment"-type analysis --> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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57 <param name="alignments" value="test2/test_genomic_alignment.bam" ftype="bam" /> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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58 <param name="mask" value="test2/test_genomic_genes.gtf" ftype="gtf" /> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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59 <param name="fasta" value="test2/test_genomic_all_chromosomes.fa" ftype="fasta" /> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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60 <param name="output_format" value="1" /> |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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61 |
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19d1402611ef
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
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62 <output name="output" file="test2/test_genomic_flaimapper_output.txt" /> |
| 24 | 63 </test> |
| 64 </tests> | |
| 65 | |
| 0 | 66 <help> |
| 14 | 67 FlaiMapper wrapper for Galaxy |
| 68 ============================= | |
| 69 | |
| 70 https://github.com/yhoogstrate/flaimapper | |
| 71 http://www.ncbi.nlm.nih.gov/pubmed/25338717 | |
| 72 http://dx.doi.org/10.1093/bioinformatics/btu696 | |
| 73 | |
| 74 Fragment Location Annotation Identification Mapper | |
| 75 | |
| 76 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. | |
| 77 | |
| 26 | 78 |
| 79 Input | |
| 80 ----- | |
| 81 | |
| 82 Alignments | |
| 83 ********** | |
| 84 | |
| 85 Aligned reads from small RNA-Seq experiments have to be provided in the BAM format. | |
| 86 In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments. | |
| 87 | |
| 88 Mask File | |
| 89 ********* | |
| 90 | |
| 91 There are two strategies to analyze using FlaiMapper: | |
| 92 | |
| 93 - Relative to mature ncRNA sequences | |
| 94 - Relative to chromosomes | |
| 95 | |
| 96 Therefore FlaiMapper requires a list of ncRNA annotations relative to the used reference genome for the alignment files. These ncRNA locations within the sequences provided in the FASTA file (MASK) regions should be provided in the GFF/GTF format: | |
| 14 | 97 |
| 98 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3 | |
| 99 - http://www.ensembl.org/info/website/upload/gff.html | |
| 100 | |
| 26 | 101 If you are making use of a ncRNA database that has no GTF file available you can make use of the galaxy tool **flaimapper-gtf-from-fasta** to create one. |
| 102 | |
| 103 | |
| 104 You can access **ncRNAdb09** GTF file at the following URL: | |
| 105 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)* | |
| 106 | |
| 107 Fasta sequence | |
| 108 ************** | |
| 109 | |
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110 The reference sequence should be provided in FASTA format. |
| 14 | 111 |
| 26 | 112 You can access **ncRNAdb09** FASTA file at the following URL: |
| 19 | 113 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)* |
| 114 | |
| 26 | 115 Example- and reference data |
| 116 *************************** | |
| 117 | |
| 118 To align reads to ncRNA you need aligner specific indexed version of the reference. We have made | |
| 119 the following available for ncRNAdb09: | |
| 19 | 120 |
| 121 - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz | |
| 122 - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz | |
| 123 | |
| 26 | 124 If you want to test FlaiMapper with example data you can obtain several |
| 125 alignment files from the following directory tree: | |
| 19 | 126 |
| 127 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments | |
| 128 | |
| 14 | 129 Installation |
| 130 ------------ | |
| 131 | |
| 132 The wrapper makes use of easy_install to install a python egg. Please | |
| 133 ensure you have easy_install installed. | |
| 134 | |
| 135 License | |
| 136 ------- | |
| 137 | |
| 138 **flaimapper** and **wrapper**: | |
| 139 | |
| 140 GPL (>=3) | |
| 141 | |
| 142 **pysam**: | |
| 143 | |
| 19 | 144 The MIT License |
| 14 | 145 |
| 146 Contact | |
| 147 ------- | |
| 148 | |
| 149 The tool wrapper has been written by Youri Hoogstrate from the Erasmus | |
| 150 Medical Center (Rotterdam, Netherlands). | |
| 151 | |
| 152 | |
| 153 Development | |
| 154 ----------- | |
| 155 | |
| 156 * Repository-Maintainer: Youri Hoogstrate | |
| 157 * Repository-Developers: Youri Hoogstrate | |
| 158 | |
| 159 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools | |
| 160 | |
| 161 The tool wrapper has been written by Youri Hoogstrate from the Erasmus | |
| 162 Medical Center (Rotterdam, Netherlands). | |
| 163 | |
| 0 | 164 </help> |
| 14 | 165 |
| 166 <citations> | |
| 167 <citation type="doi">10.1093/bioinformatics/btu696</citation> | |
| 168 </citations> | |
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169 </tool> |