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comparison flaimapper.xml @ 8:c5df479c423b draft

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author yhoogstrate
date Thu, 19 Mar 2015 10:17:46 -0400
parents b0b15ff831bf
children 138748e037e4
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7:548e7c482077 8:c5df479c423b
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="flaimapper" name="FlaiMapper" version="1.1.0"> 2 <tool id="flaimapper" name="FlaiMapper" version="1.1.2.a">
3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description> 3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.1.0">flaimapper</requirement>
6 <requirement type="package" version="0.7.7">pysam</requirement> 5 <requirement type="package" version="0.7.7">pysam</requirement>
6 <requirement type="package" version="0.8.1">pysam</requirement>
7 <requirement type="package" version="1.1.2">flaimapper</requirement>
7 </requirements> 8 </requirements>
9
10 <version_command>flaimapper --version</version_command>
11
8 <command> 12 <command>
9 ##rm $mask".tbi"
10 ##rm $fasta".fai"
11
12 flaimapper 13 flaimapper
13 -v 14 -v
14 -f $output_format 15 -f $output_format
15 -o $output 16 -o $output
16 -m $mask 17 -m $mask
17 -r $fasta 18 -r $fasta
18 #for $alignment in $alignments 19
19 $alignment 20 #for $alignment in $alignments
20 #end for 21 $alignment
22 #end for
21 </command> 23 </command>
22
23 <version_command>flaimapper --version</version_command>
24 24
25 <inputs> 25 <inputs>
26 <param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" /> 26 <param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
27 27
28 <param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" /> 28 <param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" />
29 29
30 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> 30 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
31 31
32 <param name="output_format" type="select" label="Output format"> 32 <param name="output_format" type="select" label="Output format">
33 <option value="1">Tabular (1 fragment per column)</option> 33 <option value="1">Tabular (1 fragment per column)</option>
34 <option value="2">Tabular (1 precursor per column)</option> 34 <option value="2">Tabular (1 precursor per column)</option>
35 <option value="3">GenBank</option> 35 <option value="3">GenBank</option>
36 <!-- option value="gtf">GTF/GFF</option --> 36 <!-- option value="gtf">GTF/GFF</option -->
37 </param> 37 </param>
38 </inputs> 38 </inputs>
39 39
40 <outputs> 40 <outputs>
41 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> 41 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
42 </outputs> 42 </outputs>
43 43
44 <help> 44 <help>
45 You must have 'easy_install' installed.
46
45 FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data 47 FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data
46 48
47 doi:10.1093/bioinformatics/btu696 49 doi:10.1093/bioinformatics/btu696
48 </help> 50 </help>
49 </tool> 51 </tool>