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comparison TEiso/GFFToBed_Wrapper.xml @ 1:15d6811e6bf5 draft

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author urgi-team
date Tue, 24 May 2016 08:59:28 -0400
parents 3d22562b4489
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0:3d22562b4489 1:15d6811e6bf5
1 <tool id="GFFToBed" name="GFFToBed" version="1.0"> 1 <tool id="GFFToBed" name="GFFToBed" version="1.0">
2 <description>GFFToBed can convert a result GTF file of Cufflinks into a bed file.</description> 2 <description>GFFToBed can convert a result GTF file into a bed file.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0">TEiso_Tools</requirement> 4 <requirement type="package" version="1.0">TEiso_Tools</requirement>
5 </requirements> 5 </requirements>
6 <version_command> 6 <version_command>
7 GFFToBed.py --version 7 GFFToBed.py --version
8 </version_command> 8 </version_command>
9 <command interpreter="python"> 9 <command interpreter="python">
10 GFFToBedWrapper_Wrapper.py -i $inputFile -o $outputFile 10 GFFToBed_Wrapper.py -i $inputFile -o $outputFile
11 </command> 11 </command>
12 <inputs> 12 <inputs>
13 <param name="inputFile" type="data" format="gff" label="indicate a transcript GTF file of cufflinks."/> 13 <param name="inputFile" type="data" format="gff" label="indicate a transcript GTF file of cufflinks."/>
14 </inputs> 14 </inputs>
15 <outputs> 15 <outputs>
16 <data name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/> 16 <data name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
17 </outputs> 17 </outputs>
18 <help><![CDATA[ 18 <help><![CDATA[
19
20 **GFFToBed_wrapper converts a result GTF file of Cufflinks into a bed file.**
21 19
20
21 **GFFToBed_wrapper converts a result GTF file into a bed file.**
22 22
23 **what it does :** 23 **what it does :**
24 24
25 converts a result GTF file of Cufflinks into a bed file. 25 converts a result GFF3 file into a bed file
26 26
27 It can take: Chromosome, Start, End, ID, Target, strand 27 it can take: Chromosome, Start, End, ID, Target, strand.
28 28
29 ----- 29 -----
30 30
31 **input format :** 31 **example :**
32 32
33 .. class:: infomark 33 a GFF3 file of the Transposable elements as input file: ::
34 34
35 2L DmelCaf1_2_2_REPET_TEs match 47519 52563 0.0 + . ID=ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11;Target=RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050;Identity=99.8 35 2L DmelCaf1_2_2_REPET_TEs match 47519 52563 0.0 + . ID=ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11;Target=RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050;Identity=99.8
36 36 2L DmelCaf1_2_2_REPET_TEs match 16205 16490 0.0 + . ID=ms2_dmel_chr2L_RXX-LARD_DmelCaf1_2_2-L-B578-Map1;Target=RXX-LARD_DmelCaf1_2_2-L-B578-Map1 2551 2828;Identity=97.5
37 2R DmelCaf1_2_2_REPET_TEs match 24134 24428 0.0 - . ID=ms4350_dmel_chr2R_RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1;Target=RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1 2894 3273
37 38
38 ----- 39 -----
39 40
40 **output format :** 41 output format: ::
41 42
42 2L 47519 52563 ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050 + 43 2L 47519 52563 ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050 +
43 44 2L 16205 16490 ms2_dmel_chr2L_RXX-LARD_DmelCaf1_2_2-L-B578-Map1 RXX-LARD_DmelCaf1_2_2-L-B578-Map1 2551 2828 +
44 ----- 45 2R 24134 24428 ms4350_dmel_chr2R_RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1 RXX-LARD-chim_DmelCaf1_2_2-L-B414-Map1 2894 3273 -
45 46
46 47
47 -----
48
49 **reference :**
50 48
51 ]]> 49 ]]>
52 </help> 50 </help>
53 </tool> 51 </tool>