Mercurial > repos > yhoogstrate > flaimapper
annotate flaimapper.xml @ 17:be98a7b6c94e draft
Fixed capturing a non-critical warning that's being send to stderr.
| author | yhoogstrate |
|---|---|
| date | Fri, 20 Mar 2015 06:33:35 -0400 |
| parents | ae3e699a4ae5 |
| children | 0e9520cf7587 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0" encoding="UTF-8"?> |
|
17
be98a7b6c94e
Fixed capturing a non-critical warning that's being send to stderr.
yhoogstrate
parents:
15
diff
changeset
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2 <tool id="flaimapper" name="FlaiMapper" version="1.1.2.d"> |
| 0 | 3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description> |
| 4 <requirements> | |
| 15 | 5 <requirement type="package" version="0.8.2.1">pysam</requirement><!-- pysam 0.7.7 ABSOLUTELY CRASHES !!! --> |
| 8 | 6 <requirement type="package" version="1.1.2">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 $alignment | |
| 21 #end for | |
|
17
be98a7b6c94e
Fixed capturing a non-critical warning that's being send to stderr.
yhoogstrate
parents:
15
diff
changeset
|
22 |
|
be98a7b6c94e
Fixed capturing a non-critical warning that's being send to stderr.
yhoogstrate
parents:
15
diff
changeset
|
23 2> stderr.txt ; |
|
be98a7b6c94e
Fixed capturing a non-critical warning that's being send to stderr.
yhoogstrate
parents:
15
diff
changeset
|
24 |
|
be98a7b6c94e
Fixed capturing a non-critical warning that's being send to stderr.
yhoogstrate
parents:
15
diff
changeset
|
25 grep -v '[fai_load] build FASTA index.' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; |
|
be98a7b6c94e
Fixed capturing a non-critical warning that's being send to stderr.
yhoogstrate
parents:
15
diff
changeset
|
26 |
|
be98a7b6c94e
Fixed capturing a non-critical warning that's being send to stderr.
yhoogstrate
parents:
15
diff
changeset
|
27 cat stderr.txt >&2 |
| 0 | 28 </command> |
| 29 | |
| 30 <inputs> | |
| 31 <param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" /> | |
| 32 | |
| 33 <param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" /> | |
| 8 | 34 |
| 2 | 35 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> |
| 36 | |
| 37 <param name="output_format" type="select" label="Output format"> | |
| 8 | 38 <option value="1">Tabular (1 fragment per column)</option> |
| 39 <option value="2">Tabular (1 precursor per column)</option> | |
| 40 <option value="3">GenBank</option> | |
| 41 <!-- option value="gtf">GTF/GFF</option --> | |
| 0 | 42 </param> |
| 43 </inputs> | |
| 44 | |
| 45 <outputs> | |
| 46 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> | |
| 47 </outputs> | |
| 48 | |
| 49 <help> | |
| 14 | 50 FlaiMapper wrapper for Galaxy |
| 51 ============================= | |
| 52 | |
| 53 https://github.com/yhoogstrate/flaimapper | |
| 54 http://www.ncbi.nlm.nih.gov/pubmed/25338717 | |
| 55 http://dx.doi.org/10.1093/bioinformatics/btu696 | |
| 56 | |
| 57 Fragment Location Annotation Identification Mapper | |
| 58 | |
| 59 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. | |
| 60 | |
| 61 Input formats | |
| 62 ------------- | |
| 63 Alignments should be provided in BAM format. | |
| 64 Gene (MASK) regions should be provided in the GFF/GTF format: | |
| 65 | |
| 66 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3 | |
| 67 - http://www.ensembl.org/info/website/upload/gff.html | |
| 68 | |
| 69 The reference sequence should be provided in FASTSA format. | |
| 70 | |
| 71 Installation | |
| 72 ------------ | |
| 73 | |
| 74 The wrapper makes use of easy_install to install a python egg. Please | |
| 75 ensure you have easy_install installed. | |
| 76 | |
| 77 License | |
| 78 ------- | |
| 79 | |
| 80 **flaimapper** and **wrapper**: | |
| 81 | |
| 82 GPL (>=3) | |
| 83 | |
| 84 **pysam**: | |
| 85 | |
| 86 The MIT License (>=3) | |
| 87 | |
| 88 Contact | |
| 89 ------- | |
| 90 | |
| 91 The tool wrapper has been written by Youri Hoogstrate from the Erasmus | |
| 92 Medical Center (Rotterdam, Netherlands). | |
| 93 | |
| 94 | |
| 95 Development | |
| 96 ----------- | |
| 97 | |
| 98 * Repository-Maintainer: Youri Hoogstrate | |
| 99 * Repository-Developers: Youri Hoogstrate | |
| 100 | |
| 101 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools | |
| 102 | |
| 103 The tool wrapper has been written by Youri Hoogstrate from the Erasmus | |
| 104 Medical Center (Rotterdam, Netherlands). | |
| 105 | |
| 106 References | |
| 107 ---------- | |
| 108 **FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.** | |
| 109 | |
| 110 *Hoogstrat* - Bioinformatics. 2014 Apr 1;30(7):923-30. | |
| 111 | |
| 112 *Youri Hoogstrate, Guido Jenster, and Elena S. Martens-Uzunova* - Bioinformatics (2015) 31 (5): 665-673 | |
| 113 | |
| 114 - http://www.ncbi.nlm.nih.gov/pubmed/25338717 | |
| 115 - http://dx.doi.org/10.1093/bioinformatics/btu696 | |
| 0 | 116 </help> |
| 14 | 117 |
| 118 <citations> | |
| 119 <citation type="doi">10.1093/bioinformatics/btu696</citation> | |
| 120 </citations> | |
| 0 | 121 </tool> |