Mercurial > repos > iuc > mothur_align_check
diff align.check.xml @ 1:cf25efc1895b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 18:10:31 -0400 |
| parents | 5fce559c4ffa |
| children | 2fc7aad419ff |
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--- a/align.check.xml Fri Jun 24 17:29:43 2016 -0400 +++ b/align.check.xml Thu May 18 18:10:31 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 "$fasta" fasta.dat && ln -s "$name" name.dat && @@ -24,6 +27,7 @@ )' | sed 's/ //g' ## mothur trips over whitespace | mothur + | tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/> @@ -71,12 +75,12 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**Command Documentation** The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment using a secondary_structure_map_. If you are familiar with the editor window in ARB, this is the same as counting the number of ~, #, -, and = signs. -.. _secondary_structure_map: http://www.mothur.org/wiki/Secondary_structure_map -.. _align.check: http://www.mothur.org/wiki/Align.check +.. _secondary_structure_map: https://www.mothur.org/wiki/Secondary_structure_map +.. _align.check: https://www.mothur.org/wiki/Align.check ]]> </help> <expand macro="citations"/>