Mercurial > repos > biomonika > linkyx

annotate LINKYX_reformat_trinity_header.xml @ 13:ef5c8ed727b0

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
toolshed12
author biomonika <biomonika@psu.edu>
date Wed, 10 Sep 2014 10:49:56 -0400
parents e6866610a434
children 2cbcdfd5d489
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
1 <tool id="reformat_trinity_header" name="reformat_trinity_header">
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
2 <description>Reformat Trinity header</description>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
3 <requirements>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
4 <requirement type="set_environment">LINKYX_PATH</requirement>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
5 <requirement type="set_environment">SAMTOOLS</requirement>
13
ef5c8ed727b0 toolshed12
biomonika <biomonika@psu.edu>
parents: 10
diff changeset
6 <requirement type="set_environment">PERL_PATH</requirement>
9
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
7 <requirement type="package" version="0.1.19">samtools</requirement>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
8 </requirements>
10
e6866610a434 toolshed9
biomonika <biomonika@psu.edu>
parents: 9
diff changeset
9 <command interpreter="bash">LINKYX_reformat_trinity_header.sh $output $input1</command>
9
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
10 <inputs>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
11 <param format="fasta" name="input1" type="data" label="Trinity.fasta"/>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
12 </inputs>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
13 <outputs>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
14 <data format="fasta" name="output" />
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
15 </outputs>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
16
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
17 <tests>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
18 <test>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
19 <output name="out_file1" file="Trinity.fasta"/>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
20 </test>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
21 </tests>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
22
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
23 <help>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
24 Reformat Trinity header, keep only part until first space.
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
25 </help>
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
26
695d28139f3e toolshed8
biomonika <biomonika@psu.edu>
parents:
diff changeset
27 </tool>