|
0
|
1 <?xml version="1.0" encoding="UTF-8"?>
|
|
|
2 <tool id="flaimapper" name="FlaiMapper">
|
|
|
3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="1.1.0">flaimapper</requirement>
|
|
1
|
6 <requirement type="package" version="0.7.7">pysam</requirement>
|
|
0
|
7 </requirements>
|
|
|
8 <command>
|
|
2
|
9 ##rm $mask".tbi"
|
|
|
10 ##rm $fasta".fai"
|
|
|
11
|
|
0
|
12 flaimapper
|
|
|
13 -v
|
|
|
14 -f $output_format
|
|
|
15 -o $output
|
|
|
16 -m $mask
|
|
|
17 -r $fasta
|
|
|
18 #for $alignment in $alignments
|
|
|
19 $alignment
|
|
|
20 #end for
|
|
|
21 </command>
|
|
|
22
|
|
3
|
23 <version_command>flaimapper --version</version_command>
|
|
|
24
|
|
0
|
25 <inputs>
|
|
|
26 <param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
|
|
|
27
|
|
|
28 <param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" />
|
|
|
29
|
|
2
|
30 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
|
|
|
31
|
|
|
32 <param name="output_format" type="select" label="Output format">
|
|
0
|
33 <option value="1">Tabular (1 fragment per column)</option>
|
|
|
34 <option value="2">Tabular (1 precursor per column)</option>
|
|
|
35 <option value="3">GenBank</option>
|
|
|
36 <!-- option value="gtf">GTF/GFF</option -->
|
|
|
37 </param>
|
|
|
38 </inputs>
|
|
|
39
|
|
|
40 <outputs>
|
|
|
41 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
|
|
|
42 </outputs>
|
|
|
43
|
|
|
44 <help>
|
|
|
45 FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data
|
|
|
46
|
|
|
47 doi:10.1093/bioinformatics/btu696
|
|
|
48 </help>
|
|
|
49 </tool> |
