Mercurial > repos > iuc > mothur_get_seqs
diff get.seqs.xml @ 2:5acd4d7339b9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 21:55:58 -0400 |
parents | bfd467665e6c |
children | c8b640a7aea1 |
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--- a/get.seqs.xml Tue Sep 05 16:53:01 2017 -0400 +++ b/get.seqs.xml Tue Mar 20 21:55:58 2018 -0400 @@ -7,54 +7,54 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$accnos" accnos.dat && - ln -s "$fasta_in" fasta_in.dat && - ln -s "$fastq_in" fastq_in.dat && - ln -s "$count_in" count_in.dat && - ln -s "$qfile_in" qfile_in.dat && - ln -s "$name_in" name_in.dat && - ln -s "$group_in" group_in.dat && - ln -s "$alignreport_in" alignreport_in.dat && - ln -s "$list_in" list_in.dat && - ln -s "$taxonomy_in" taxonomy_in.dat && +## create symlinks to input datasets +ln -s '$accnos' accnos.dat && +ln -s '$fasta_in' fasta_in.dat && +ln -s '$fastq_in' fastq_in.dat && +ln -s '$count_in' count_in.dat && +ln -s '$qfile_in' qfile_in.dat && +ln -s '$name_in' name_in.dat && +ln -s '$group_in' group_in.dat && +ln -s '$alignreport_in' alignreport_in.dat && +ln -s '$list_in' list_in.dat && +ln -s '$taxonomy_in' taxonomy_in.dat && - echo 'get.seqs( - accnos=accnos.dat, - #if $fasta_in: - fasta=fasta_in.dat, - #end if - #if $fastq_in: - fastq=fastq_in.dat, - #end if - #if $count_in: - count=count_in.dat, - #end if - #if $qfile_in: - qfile=qfile_in.dat, - #end if - #if $name_in: - name=name_in.dat, - #end if - #if $group_in: - group=group_in.dat, - #end if - #if $alignreport_in: - alignreport=alignreport_in.dat, - #end if - #if $list_in: - list=list_in.dat, - #end if - #if $taxonomy_in: - taxonomy=taxonomy_in.dat, - #end if - dups=$dups - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'get.seqs( + accnos=accnos.dat, + #if $fasta_in: + fasta=fasta_in.dat, + #end if + #if $fastq_in: + fastq=fastq_in.dat, + #end if + #if $count_in: + count=count_in.dat, + #end if + #if $qfile_in: + qfile=qfile_in.dat, + #end if + #if $name_in: + name=name_in.dat, + #end if + #if $group_in: + group=group_in.dat, + #end if + #if $alignreport_in: + alignreport=alignreport_in.dat, + #end if + #if $list_in: + list=list_in.dat, + #end if + #if $taxonomy_in: + taxonomy=taxonomy_in.dat, + #end if + dups=$dups +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/> @@ -68,6 +68,7 @@ <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> <param name="dups" type="boolean" truevalue="dups" falsevalue="false" checked="true" label="dups - Apply to duplicates"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -105,12 +106,14 @@ <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> <param name="dups" value=""/> <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> - <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/> + <output name="fastq_out" md5="81d026f969e15b8c8701f8dc5f3a6904"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> @@ -120,18 +123,19 @@ <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> <param name="dups" value="false"/> <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/> - <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/> + <output name="fastq_out" md5="81d026f969e15b8c8701f8dc5f3a6904"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> <param name="accnos" value="amazon.bad.accnos"/> <param name="count_in" value="amazon.count_table"/> <output name="count_out" md5="6892dd99850ce9e9f8f15e77b28f57e2"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -148,7 +152,7 @@ .. _get.seqs: https://www.mothur.org/wiki/Get.seqs v.1.27.0 : Updated to Mothur 1.33, added count and fastq params -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>