Mercurial > repos > iuc > mothur_pairwise_seqs
diff pairwise.seqs.xml @ 1:4f382764768a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 18:26:27 -0400 |
| parents | 4e1ecccf9ab0 |
| children | cc74f42d74a2 |
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--- a/pairwise.seqs.xml Fri Jun 24 16:43:30 2016 -0400 +++ b/pairwise.seqs.xml Thu May 18 18:26:27 2017 -0400 @@ -4,8 +4,11 @@ <import>macros.xml</import> </macros> <expand macro="requirements"/> + <expand macro="stdio"/> <expand macro="version_command"/> - <command detect_errors="aggressive"><![CDATA[ + <command><![CDATA[ + @SHELL_OPTIONS@ + ## create symlinks to input datasets ln -s "$fasta" fasta.dat && @@ -32,6 +35,7 @@ )' | sed 's/ //g' ## mothur trips over whitespace | mothur + | tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> @@ -50,7 +54,7 @@ <param name="cutoff" type="float" value="0.0" min="0" 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"/> <conditional name="scoring"> <param name="setby" type="select" label="Scoring match, mismatch, gapopen, and gapextend" help=""> - <option value="default" selecte="true">Use default settings</option> + <option value="default" selected="true">Use default settings</option> <option value="user">Manually set scoring values</option> </param> <when value="default"/> @@ -109,15 +113,15 @@ @MOTHUR_OVERVIEW@ -.. _Mothur: http://www.mothur.org/wiki/Main_Page +.. _Mothur: https://www.mothur.org/wiki/Main_Page -**Command Documenation** +**Command Documentation** The pairwise.seqs_ command will calculate uncorrected pairwise distances between sequencesi as a column-formatted_distance_matrix_ or phylip-formatted_distance_matrix_. -.. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix -.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix -.. _pairwise.seqs: http://www.mothur.org/wiki/Pairwise.seqs +.. _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 +.. _pairwise.seqs: https://www.mothur.org/wiki/Pairwise.seqs ]]> </help>