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comparison align.check.xml @ 1:cf25efc1895b draft

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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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0:5fce559c4ffa 1:cf25efc1895b
2 <description>Calculate the number of potentially misaligned bases</description> 2 <description>Calculate the number of potentially misaligned bases</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$fasta" fasta.dat && 13 ln -s "$fasta" fasta.dat &&
11 ln -s "$name" name.dat && 14 ln -s "$name" name.dat &&
12 ln -s "$count" count.dat && 15 ln -s "$count" count.dat &&
13 ln -s "$map" map.dat && 16 ln -s "$map" map.dat &&
22 #end if 25 #end if
23 map=map.dat 26 map=map.dat
24 )' 27 )'
25 | sed 's/ //g' ## mothur trips over whitespace 28 | sed 's/ //g' ## mothur trips over whitespace
26 | mothur 29 | mothur
30 | tee mothur.out.log
27 ]]></command> 31 ]]></command>
28 <inputs> 32 <inputs>
29 <param name="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/> 33 <param name="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/>
30 <conditional name="ss"> 34 <conditional name="ss">
31 <param name="source" label="Select Secondary Structure Map from" type="select"> 35 <param name="source" label="Select Secondary Structure Map from" type="select">
69 <help> 73 <help>
70 <![CDATA[ 74 <![CDATA[
71 75
72 @MOTHUR_OVERVIEW@ 76 @MOTHUR_OVERVIEW@
73 77
74 **Command Documenation** 78 **Command Documentation**
75 79
76 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. 80 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.
77 81
78 .. _secondary_structure_map: http://www.mothur.org/wiki/Secondary_structure_map 82 .. _secondary_structure_map: https://www.mothur.org/wiki/Secondary_structure_map
79 .. _align.check: http://www.mothur.org/wiki/Align.check 83 .. _align.check: https://www.mothur.org/wiki/Align.check
80 ]]> 84 ]]>
81 </help> 85 </help>
82 <expand macro="citations"/> 86 <expand macro="citations"/>
83 </tool> 87 </tool>