Mercurial > repos > iuc > mothur_reverse_seqs
diff reverse.seqs.xml @ 2:503898f17f42 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 21:55:28 -0400 |
parents | a8a1a7c5ab14 |
children |
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--- a/reverse.seqs.xml Tue Sep 05 17:17:59 2017 -0400 +++ b/reverse.seqs.xml Tue Mar 20 21:55:28 2018 -0400 @@ -7,20 +7,21 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$fasta" fasta.dat && +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && - echo 'reverse.seqs( - fasta=fasta.dat - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'reverse.seqs( + fasta=fasta.dat +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -30,11 +31,11 @@ <test> <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -43,7 +44,7 @@ The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta. .. _reverse.seqs: https://www.mothur.org/wiki/Reverse.seqs -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>