Mercurial > repos > iuc > mothur_remove_dists
view remove.dists.xml @ 1:0ec8be51451b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author | iuc |
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date | Tue, 05 Sep 2017 17:03:44 -0400 |
parents | 741303a463c8 |
children | 0df1987fb914 |
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<tool profile="16.07" id="mothur_remove_dists" name="Remove.dists" version="@WRAPPER_VERSION@.0"> <description>Removes distances from a phylip or column file</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 "$accnos" accnos.dat && ln -s "$input.dist" input_dist.dat && echo 'remove.dists( accnos=accnos.dat, #if $input.source == "phylip": phylip=input_dist.dat #else column=input_dist.dat #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <conditional name="input"> <param name="source" type="select" label="Select input format"> <option value="column">Pairwise Column Distance Matrix</option> <option value="phylip">Phylip Distance Matrix</option> </param> <when value="column"> <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> </when> <when value="phylip"> <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> </when> </conditional> <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="pick_dist" format_source="dist" from_work_dir="input_dist*.pick.dat" label="${tool.name} on ${on_string}: pick.dist"/> </outputs> <tests> <test> <param name="source" value="phylip"/> <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/> <output name="pick_dist" md5="ec444ddb897d21864a245e8645fcda33" ftype="mothur.square.dist"/> <expand macro="logfile-test"/> </test> </tests> <help> <![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The remove.dists_ removes distances from a phylip or column file related to groups or sequences listed in an accnos file. .. _remove.dists: https://www.mothur.org/wiki/Remove.dists ]]> </help> <expand macro="citations"/> </tool>