Mercurial > repos > iuc > mothur_trim_seqs
diff trim.seqs.xml @ 2:baa3df51e2b7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 21:56:31 -0400 |
parents | 143f949a5def |
children |
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--- a/trim.seqs.xml Tue Sep 05 17:02:03 2017 -0400 +++ b/trim.seqs.xml Tue Mar 20 21:56:31 2018 -0400 @@ -7,64 +7,65 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$fasta" fasta.dat && - ln -s "$names" names.dat && - ln -s "$count" count.dat && - #if $oligo.add == "yes": - ln -s "$oligo.oligos" oligo.oligos.dat && - #end if - #if $qual.add2 == "yes": - ln -s "$qual.qfile" qual.qfile.dat && - #end if +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && +ln -s '$names' names.dat && +ln -s '$count' count.dat && +#if $oligo.add == "yes": + ln -s '$oligo.oligos' oligo.oligos.dat && +#end if +#if $qual.add2 == "yes": + ln -s '$qual.qfile' qual.qfile.dat && +#end if - echo 'trim.seqs( - fasta=fasta.dat, - minlength=$minlength, - maxlength=$maxlength, - maxambig=$maxambig, - maxhomop=$maxhomop, - keepfirst=$keepfirst, - removelast=$removelast, - #if $oligo.add == "yes": - oligos=oligo.oligos.dat, - bdiffs=$oligo.bdiffs, - pdiffs=$oligo.pdiffs, - tdiffs=$oligo.tdiffs, - ldiffs=$oligo.ldiffs, - sdiffs=$oligo.sdiffs, - keepforward=$oligo.keepforward, - allfiles=$oligo.allfiles, - #end if - #if $qual.add2 == "yes": - qfile=qual.qfile.dat, - qaverage=$qual.qaverage, - qthreshold=$qual.qthreshold, - qwindowaverage=$qual.qwindowaverage, - qwindowsize=$qual.qwindowsize, - rollaverage=$qual.rollaverage, - qstepsize=$qual.qstepsize, - qtrim=$qual.qtrim, - #end if - flip=$flip, - #if $names: - name=names.dat, - #end if - logtransform=$logtransform, - checkorient=$checkorient, - #if $count: - count=count.dat, - #end if - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log - ## prevent these two files from being gathered into collection - && mv fasta.trim.fasta fasta.trim - && mv fasta.scrap.fasta fasta.scrap +echo 'trim.seqs( + fasta=fasta.dat, + minlength=$minlength, + maxlength=$maxlength, + maxambig=$maxambig, + maxhomop=$maxhomop, + keepfirst=$keepfirst, + removelast=$removelast, + #if $oligo.add == "yes": + oligos=oligo.oligos.dat, + bdiffs=$oligo.bdiffs, + pdiffs=$oligo.pdiffs, + tdiffs=$oligo.tdiffs, + ldiffs=$oligo.ldiffs, + sdiffs=$oligo.sdiffs, + keepforward=$oligo.keepforward, + allfiles=$oligo.allfiles, + #end if + #if $qual.add2 == "yes": + qfile=qual.qfile.dat, + qaverage=$qual.qaverage, + qthreshold=$qual.qthreshold, + qwindowaverage=$qual.qwindowaverage, + qwindowsize=$qual.qwindowsize, + rollaverage=$qual.rollaverage, + qstepsize=$qual.qstepsize, + qtrim=$qual.qtrim, + #end if + flip=$flip, + #if $names: + name=names.dat, + #end if + logtransform=$logtransform, + checkorient=$checkorient, + #if $count: + count=count.dat, + #end if + processors='\${GALAXY_SLOTS:-8}' +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log + +## prevent these two files from being gathered into collection +&& mv fasta.trim.fasta fasta.trim +&& mv fasta.scrap.fasta fasta.scrap ]]></command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/> @@ -113,6 +114,7 @@ <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. If you run trim.seqs with an oligos file that contains group labels, trim.seqs will create a new *.trim.count_table with the group information included. "/> <param name="logtransform" type="boolean" truevalue="true" falsevalue="false" checked="false" label="logtransform" help="allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform."/> <param name="checkorient" type="boolean" truevalue="true" falsevalue="false" checked="false" label="checkorient - search the reverse complement?" help="If you are running the trim.seqs command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment. "/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -157,6 +159,7 @@ <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/> <output name="trim_names" md5="1b8c6c47052bb69524ef56ebb764fb8f" ftype="mothur.names"/> <output name="scrap_names" md5="80f9252837e4b189f06ec00469b88e85" ftype="mothur.names"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with count table --> @@ -167,6 +170,7 @@ <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/> <output name="trim_count" md5="836b4d72a8cda3741ef435741783b384" ftype="mothur.count_table"/> <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with oligos --> @@ -178,6 +182,7 @@ <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/> <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/> <output name="groups_file" md5="198957282c234e825414e175d926046a" ftype="mothur.groups"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with oligos and allfiles parameter --> @@ -195,6 +200,7 @@ <output_collection name="fasta_allfiles" count="9"> <element name="F003D144" md5="025ff271ac24ecb898863d7fcbfabf10" ftype="fasta"/> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with qfile--> @@ -206,11 +212,11 @@ <output name="scrap_fasta" md5="a4d3ef3d91b4c0146ec84bb7aad3987c" ftype="fasta"/> <output name="trim_qual" md5="3d4e2d3c7dd43b90660ab9c923d9eab1" ftype="qual454"/> <output name="scrap_qual" md5="22931236d082c2b77811bbf912c1f4b1" ftype="qual454"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -220,7 +226,6 @@ .. _trim.seqs: https://www.mothur.org/wiki/Trim.seqs -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>