Mercurial > repos > yhoogstrate > flaimapper

comparison flaimapper-gtf-from-fasta.xml @ 24:bd695d4cb7c4 draft

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author yhoogstrate
date Sun, 29 Mar 2015 02:43:11 -0400
parents e0c0fc569303
children 19d1402611ef
comparison
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23:e0c0fc569303 24:bd695d4cb7c4
10 10
11 <command> 11 <command>
12 gtf-from-fasta 12 gtf-from-fasta
13 -o $output 13 -o $output
14 $fasta 14 $fasta
15 2> stderr.txt ;
16
17 grep -v '[fai_load] build FASTA index.' stderr.txt >&amp2 ;
18 </command> 15 </command>
16
17 <stdio>
18 <regex
19 match="[fai_load] build FASTA index."
20 source="stderr"
21 level="log"
22 description="The FASTA file is being indexed." />
23 </stdio>
19 24
20 <inputs> 25 <inputs>
21 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> 26 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
22 </inputs> 27 </inputs>
23 28
24 <outputs> 29 <outputs>
25 <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" /> 30 <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" />
26 </outputs> 31 </outputs>
32
33 <tests>
34 <test>
35 <param name="fasta" value="ncrnadb09.fa" />
36
37 <param name="output" value="ncrnadb09.gtf" />
38 </test>
39 </tests>
27 40
28 <help> 41 <help>
29 FlaiMapper wrapper for Galaxy 42 FlaiMapper wrapper for Galaxy
30 ============================= 43 =============================
31 44