Mercurial > repos > iuc > mothur_dist_seqs
diff dist.seqs.xml @ 1:699ed9de9edf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 18:09:02 -0400 |
| parents | 2b4254acee00 |
| children | 2211f97b6d1b |
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--- a/dist.seqs.xml Fri Jun 24 16:29:54 2016 -0400 +++ b/dist.seqs.xml Thu May 18 18:09:02 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 && @@ -25,9 +28,10 @@ )' | sed 's/ //g' ## mothur trips over whitespace | mothur + | tee mothur.out.log ]]></command> <inputs> - <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> + <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> @@ -72,13 +76,13 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**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: http://www.mothur.org/wiki/Column-formatted_distance_matrix -.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix -.. _dist.seqs: http://www.mothur.org/wiki/Dist.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 +.. _dist.seqs: https://www.mothur.org/wiki/Dist.seqs v.1.20.0: Updated to Mothur 1.33