Mercurial > repos > iuc > mothur_dist_seqs
view dist.seqs.xml @ 1:efc735bcc806 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 16:51:56 -0400 |
parents | d103727775eb |
children | 189b742d2434 |
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<tool profile="16.07" id="mothur_dist_seqs" name="Dist.seqs" version="@WRAPPER_VERSION@.0"> <description>calculate uncorrected pairwise distances between aligned 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 && echo 'dist.seqs( fasta=fasta.dat, #if $calc: calc=$calc, #end if countends=$countends, #if $cutoff: cutoff=$cutoff, #end if #if $output: output=$output, #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="mothur.align,fasta" label="fasta - Alignment Fasta"/> <param name="calc" type="select" label="calc - Calc Method - Gap Penality"> <option value="" selected="true">use default</option> <option value="onegap">onegap - counts a string of gaps as a single gap</option> <option value="nogaps">nogaps - ignores gaps</option> <option value="eachgap ">eachgap - penalize each gap</option> </param> <param name="countends" type="boolean" checked="true" truevalue="true" falsevalue="false" label="countends - Penalize terminal gaps"/> <param name="cutoff" type="float" value="" min="0.0" optional="true" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Do not save any distances larger than this, a common value would be 0.10"/> <param name="output" type="select" label="output - Distance Matrix Output Format" help=""> <option value="" selected="true">Default Column-Formatted Matrix</option> <option value="lt">Phylip formatted Lower Triangle Matrix</option> <option value="square">Phylip formatted Square Matrix</option> </param> </inputs> <outputs> <expand macro="logfile-output"/> <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist"> <change_format> <when input="output" value="lt" format="mothur.lower.dist"/> <when input="output" value="square" format="mothur.square.dist"/> </change_format> </data> </outputs> <tests> <test><!-- test with default params --> <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/> <output name="out_dist" md5="2c4817bb8657b4df2dcb1f2a019f505e" ftype="mothur.pair.dist"/> <expand macro="logfile-test"/> </test> <test><!-- test with all params custom --> <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/> <param name="calc" value="nogaps"/> <param name="countends" value="false"/> <param name="cutoff" value="0.3"/> <param name="output" value="lt"/> <output name="out_dist" md5="8a5ccf1ad8f1c344cf4d3e2c97d4cdc6" ftype="mothur.lower.dist"/> <expand macro="logfile-test"/> </test> </tests> <help> <![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The dist.seqs_ command will calculate uncorrected pairwise distances between aligned sequences. The command will generate a column-formatted_distance_matrix_ that is compatible with the column option in the read.dist command. The command is also able to generate a phylip-formatted_distance_matrix_. There are several options for how to handle gap comparisons and terminal gaps. .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _dist.seqs: https://www.mothur.org/wiki/Dist.seqs v.1.20.0: Updated to Mothur 1.33 ]]> </help> <expand macro="citations"/> </tool>