Mercurial > repos > iuc > mothur_summary_qual
view summary.qual.xml @ 9:86a40294e149 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author | iuc |
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date | Thu, 21 Jan 2021 23:43:36 +0000 |
parents | a40036faabe8 |
children | 7afd2d352e05 |
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<tool profile="16.07" id="mothur_summary_qual" name="Summary.qual" version="@WRAPPER_VERSION@.0"> <description>Summarize the quality scores</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 '$qfile' qfile.dat && ln -s '$name' name.dat && ln -s '$count' count.dat && echo 'summary.qual( qfile=qfile.dat #if $name: ,name=name.dat #end if #if $count: ,count=count.dat #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/> <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/> <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="out_summary" format="mothur.summary" from_work_dir="qfile*.summary" label="${tool.name} on ${on_string}: summary"/> </outputs> <tests> <test> <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/> <output name="out_summary" md5="04de7c9d0f3889d5e121db9d9070c935"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information. .. _summary.qual: https://www.mothur.org/wiki/Summary.qual ]]></help> <expand macro="citations"/> </tool>