Mercurial > repos > iuc > mothur_summary_seqs
view summary.seqs.xml @ 5:411ddfefe041 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author | iuc |
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date | Fri, 03 Aug 2018 14:25:55 -0400 |
parents | d68125f75fc2 |
children | 600c14c6dcc5 |
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<tool profile="16.07" id="mothur_summary_seqs" name="Summary.seqs" version="@WRAPPER_VERSION@.0"> <description>Summarize the quality of sequences</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @SHELL_OPTIONS@ ## create symlinks to input datasets ln -s '$fasta' fasta.dat && ln -s '$name' name.dat && ln -s '$count' count.dat && echo 'summary.seqs( fasta=fasta.dat, #if $name: name=name.dat, #end if #if $count: count=count.dat, #end if processors='\${GALAXY_SLOTS:-8}' )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Dataset"/> <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/> <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="out_summary" format="mothur.summary" from_work_dir="fasta*.summary" label="${tool.name} on ${on_string}: summary"/> </outputs> <tests> <test> <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> <output name="out_summary" file="Mock_S280_L001_R1_001_small.trim.contigs.summary" ftype="mothur.summary"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test names input --> <param name="fasta" value="amazon.unique.fasta"/> <param name="name" value="amazon.names"/> <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test count input --> <param name="fasta" value="amazon.unique.fasta"/> <param name="count" value="amazon.count_table"/> <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. .. _summary.seqs: https://www.mothur.org/wiki/Summary.seqs ]]></help> <expand macro="citations"/> </tool>