comparison degap.seqs.xml @ 2:f643cbd3a967 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:56:13 -0400
parents 7cd72305d496
children
comparison
equal deleted inserted replaced
1:bd09ab148632 2:f643cbd3a967
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 'degap.seqs( 15 echo 'degap.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" label="fasta - Dataset"/> 23 <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/>
24 <expand macro="param-savelog"/>
24 </inputs> 25 </inputs>
25 <outputs> 26 <outputs>
26 <expand macro="logfile-output"/> 27 <expand macro="logfile-output"/>
27 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.ng.fasta" label="${tool.name} on ${on_string}: fasta"/> 28 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.ng.fasta" label="${tool.name} on ${on_string}: fasta"/>
28 </outputs> 29 </outputs>
29 <tests> 30 <tests>
30 <test> 31 <test>
31 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> 32 <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.ng.fasta"/> 33 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta"/>
34 <param name="savelog" value="true"/>
33 <expand macro="logfile-test"/> 35 <expand macro="logfile-test"/>
34 </test> 36 </test>
35 </tests> 37 </tests>
36 <help> 38 <help>
37 <![CDATA[ 39 <![CDATA[