Mercurial > repos > iuc > mothur_reverse_seqs

comparison reverse.seqs.xml @ 3:8b91c609f0c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:24:53 -0500
parents 24279ccecac5
children 876bc0ef523d
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2:6e7521b64024 3:8b91c609f0c0
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 14
15 echo 'reverse.seqs( 15 echo 'reverse.seqs(
16 fasta=fasta.dat 16 fasta=fasta.dat
17 )' 17 )'
18 | sed 's/ //g' ## mothur trips over whitespace 18 | sed 's/ //g' ## mothur trips over whitespace
19 | mothur 19 | mothur
20 | tee mothur.out.log 20 | tee mothur.out.log
21 ]]></command> 21 ]]></command>
22 <inputs> 22 <inputs>
23 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/> 23 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/>
24 </inputs> 24 </inputs>
25 <outputs> 25 <outputs>
31 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> 31 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
32 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head"/> 32 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head"/>
33 <expand macro="logfile-test"/> 33 <expand macro="logfile-test"/>
34 </test> 34 </test>
35 </tests> 35 </tests>
36 <help> 36 <help><![CDATA[
37 <![CDATA[
38 37
39 @MOTHUR_OVERVIEW@ 38 @MOTHUR_OVERVIEW@
40 39
41 **Command Documentation** 40 **Command Documentation**
42 41
43 The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta. 42 The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta.
44 43
45 .. _reverse.seqs: https://www.mothur.org/wiki/Reverse.seqs 44 .. _reverse.seqs: https://www.mothur.org/wiki/Reverse.seqs
46 ]]> 45
47 </help> 46 ]]></help>
48 <expand macro="citations"/> 47 <expand macro="citations"/>
49 </tool> 48 </tool>