Mercurial > repos > iuc > mothur_make_group
diff make.group.xml @ 2:4f91a75ac701 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 22:09:11 -0400 |
parents | 992d380f24ea |
children | 63a75db03ecc |
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--- a/make.group.xml Tue Sep 05 17:02:41 2017 -0400 +++ b/make.group.xml Tue Mar 20 22:09:11 2018 -0400 @@ -7,35 +7,34 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - #set fastas = '' - #set groups = '' - #set count = 0 +#set fastas = '' +#set groups = '' +#set count = 0 - #if $method.how == 'collection': - #for $i in $method.fasta_collection: - ln -s '$i' fasta_${i.element_identifier}.dat && - #set fastas+='fasta_'+$i.element_identifier+'.dat-' - #set groups+=$i.element_identifier+'-' - #end for - #else - #for $i in $method.inputs: - ln -s '$i.fasta' fasta_${count}.dat && - #set fastas+='fasta_'+str($count)+'.dat-' - #set groups+=str($i.group)+'-' - #set count+=1 - #end for - #end if +#if $method.how == 'collection': + #for $i in $method.fasta_collection: + ln -s '$i' fasta_${i.element_identifier}.dat && + #set fastas+='fasta_'+$i.element_identifier+'.dat-' + #set groups+=$i.element_identifier+'-' + #end for +#else + #for $i in $method.inputs: + ln -s '$i.fasta' fasta_${count}.dat && + #set fastas+='fasta_'+str($count)+'.dat-' + #set groups+=str($i.group)+'-' + #set count+=1 + #end for +#end if - echo 'make.group( - fasta=${ str($fastas).rstrip('-') }, - groups=${ str($groups).rstrip('-') } - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log - +echo 'make.group( + fasta=${ str($fastas).rstrip('-') }, + groups=${ str($groups).rstrip('-') } +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="method"> @@ -53,6 +52,7 @@ </repeat> </when> </conditional> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -70,6 +70,7 @@ <param name="group" value="testgroup2"/> </repeat> <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> <!-- test auto-creation from collection --> @@ -81,11 +82,11 @@ </collection> </param> <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/> - <expand macro="logfile-test"/> + <param name="savelog" value="true"/> + <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -96,7 +97,6 @@ .. _group: https://www.mothur.org/wiki/Group_file .. _make.group: https://www.mothur.org/wiki/Make.group -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>