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comparison flaimapper-gtf-from-fasta.xml @ 4:8faba9df2791 draft

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author yhoogstrate
date Fri, 31 Jul 2015 05:30:55 -0400
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3:efd29213e8e5 4:8faba9df2791
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.2.1.w1"> 2 <tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.2.1.w2">
3 <description>Extract GTF file from FASTA file (as FlaiMapper reference).</description> 3 <description>Extract GTF file from FASTA file (as FlaiMapper reference).</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.2.1">flaimapper</requirement> 5 <requirement type="package" version="1.2.1">flaimapper</requirement>
6 </requirements> 6 </requirements>
7 7
8 <stdio> 8 <stdio>
9 <regex 9 <regex
10 match="[fai_load] build FASTA index." 10 match="[fai_load] build FASTA index."
11 source="stderr" 11 source="stderr"
12 level="log" 12 level="log"
13 description="The FASTA file is being indexed." /> 13 description="The FASTA file is being indexed." />
14 </stdio> 14 </stdio>
15 15
16 <version_command>flaimapper --version</version_command> 16 <version_command>flaimapper --version</version_command>
17 17
18 <command> 18 <command><![CDATA[
19 gtf-from-fasta 19 gtf-from-fasta -o $output $fasta
20 -o $output 20 ]]></command>
21 $fasta 21
22 </command> 22 <inputs>
23 23 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="This is the FASTA file that fits the used reference genome (e.g. hg19 or a ncRNA database)." />
24 <inputs> 24 </inputs>
25 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> 25
26 </inputs> 26 <outputs>
27 27 <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" />
28 <outputs> 28 </outputs>
29 <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" /> 29
30 </outputs> 30 <tests>
31 31 <test>
32 <tests> 32 <param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" />
33 <test> 33
34 <param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" /> 34 <output name="output" file="test3/reference.gtf" />
35 35 </test>
36 <output name="output" file="test3/reference.gtf" /> 36 </tests>
37 </test> 37
38 </tests> 38 <help><![CDATA[
39
40 <help>
41 FlaiMapper wrapper for Galaxy 39 FlaiMapper wrapper for Galaxy
42 ============================= 40 =============================
43 41
44 https://github.com/yhoogstrate/flaimapper 42 https://github.com/yhoogstrate/flaimapper
45 http://www.ncbi.nlm.nih.gov/pubmed/25338717 43 http://www.ncbi.nlm.nih.gov/pubmed/25338717
98 ----------- 96 -----------
99 97
100 * Repository-Maintainer: Youri Hoogstrate 98 * Repository-Maintainer: Youri Hoogstrate
101 * Repository-Developers: Youri Hoogstrate 99 * Repository-Developers: Youri Hoogstrate
102 100
103 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools 101 * Repository-Development: https://github.com/ErasmusMC-Bioinformatics/galaxy-tools
104 102
105 The tool wrapper has been written by Youri Hoogstrate from the Erasmus 103 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
106 Medical Center (Rotterdam, Netherlands). 104 Medical Center (Rotterdam, Netherlands).
107 105
108 </help> 106 ]]></help>
109 107
110 <citations> 108 <citations>
111 <citation type="doi">10.1093/bioinformatics/btu696</citation> 109 <citation type="doi">10.1093/bioinformatics/btu696</citation>
112 </citations> 110 </citations>
113 </tool> 111 </tool>