Mercurial > repos > iuc > mothur_count_seqs
view count.seqs.xml @ 1:ecbd9ed733e6 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 16:55:24 -0400 |
parents | b6f7f17203ad |
children | 0cd054e2876d |
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<tool profile="16.07" id="mothur_count_seqs" name="Count.seqs" version="@WRAPPER_VERSION@.0"> <description>(aka make.table) counts the number of sequences represented by the representative</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 "$name" name.dat && #if $grouping.use == "yes": ln -s "$grouping.group" grouping.group.dat && #end if echo 'count.seqs( name=name.dat, #if $grouping.use == "yes": group=grouping.group.dat, #if $grouping.groups: groups=${ str($grouping.groups).replace(",","-") }, #end if #end if large=$large )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> <conditional name="grouping"> <param name="use" type="select" label="Use a Group file to include counts for groups"> <option value="no" selected="true">no</option> <option value="yes">yes</option> </param> <when value="yes"> <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/> <param name="groups" type="select" label="groups - Groups to display" multiple="true"> <help>All groups displayed if none are selected.</help> <options> <filter type="data_meta" ref="group" key="groups"/> </options> </param> </when> <when value="no"/> </conditional> <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="seq_count" format="mothur.count_table" from_work_dir="name*.count_table" label="${tool.name} on ${on_string}: count_table"/> </outputs> <tests> <test><!-- test default params --> <param name="name" value="amazon.names"/> <output name="seq_count" file="amazon.count_table" ftype="mothur.count_table"/> <expand macro="logfile-test"/> </test> <test><!-- test with group file --> <param name="name" value="amazon.names"/> <param name="use" value="yes"/> <param name="group" value="amazon.groups"/> <output name="seq_count" file="amazon_withgroups.count_table" ftype="mothur.count_table"/> <expand macro="logfile-test"/> </test> <test> <!-- test with group file and subset of groups --> <param name="name" value="amazon.names"/> <param name="use" value="yes"/> <param name="group" value="amazon.groups" ftype="mothur.groups"/> <param name="groups" value="pasture"/> <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/> <expand macro="logfile-test"/> </test> <test> <!-- test with group file and multiple groups --> <param name="name" value="amazon.names"/> <param name="use" value="yes"/> <param name="group" value="amazon.groups" ftype="mothur.groups"/> <param name="groups" value="pasture,forest"/> <output name="seq_count" md5="b18c03aee561cd24a36b00ad9b22255a" ftype="mothur.count_table"/> <expand macro="logfile-test"/> </test> </tests> <help> <![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The count.seqs_ command counts the number of sequences represented by the representative sequence in a name_ file and generates a count_table_. If a group_ file is given, it will also provide the group count breakdown. .. _name: https://www.mothur.org/wiki/Name_file .. _group: https://www.mothur.org/wiki/Group_file .. _count.seqs: https://www.mothur.org/wiki/Count.seqs .. _count_table: https://www.mothur.org/wiki/Count_File v.1.21.0: Updated to Mothur 1.33 ]]> </help> <expand macro="citations"/> </tool>