Mercurial > repos > jjohnson > mothur_toolsuite

comparison mothur/tools/mothur/align.check.xml @ 2:e990ac8a0f58

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:39:06 -0400
parents fcc0778f6987
children 49058b1f8d3f
comparison
equal deleted inserted replaced
1:fcc0778f6987 2:e990ac8a0f58
1 <tool id="mothur_align_check" name="Align.check" version="1.16.0"> 1 <tool id="mothur_align_check" name="Align.check" version="1.19.0">
2 <description>Calculate the number of potentially misaligned bases</description> 2 <description>Calculate the number of potentially misaligned bases</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='align.check' 5 --cmd='align.check'
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align\.check$:'$out_file 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align\.check$:'$out_file
7 --outputdir='$logfile.extra_files_path' 7 --outputdir='$logfile.extra_files_path'
8 --fasta=$fasta 8 --fasta=$fasta
9 --map=$map 9 --map=$ss.map
10 </command> 10 </command>
11 <inputs> 11 <inputs>
12 <param name="fasta" type="data" format="align" label="fasta - Sequences"/> 12 <param name="fasta" type="data" format="align" label="fasta - Aligned Sequences"/>
13 <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions"> 13 <conditional name="ss">
14 <options from_file="mothur_map.loc"> 14 <param name="source" label="Select Secondary Structure Map from" type="select">
15 <column name="name" index="0" /> 15 <option value="cached">Cached Secondary Structure Maps</option>
16 <column name="value" index="1" /> 16 <option value="history">Your History</option>
17 </options> 17 </param>
18 </param> 18 <when value="cached">
19 <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions">
20 <options from_file="mothur_map.loc">
21 <column name="name" index="0" />
22 <column name="value" index="1" />
23 </options>
24 </param>
25 </when>
26 <when value="history">
27 <param name="map" format="map" type="data" label="Secondary Structure Map" />
28 </when>
29 </conditional>
19 </inputs> 30 </inputs>
20 <outputs> 31 <outputs>
21 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> 32 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
22 <data format="align.check" name="out_file" label="${tool.name} on ${on_string}: align.check"/> 33 <data format="align.check" name="out_file" label="${tool.name} on ${on_string}: align.check"/>
23 </outputs> 34 </outputs>
35 46
36 .. _Mothur: http://www.mothur.org/wiki/Main_Page 47 .. _Mothur: http://www.mothur.org/wiki/Main_Page
37 48
38 **Command Documenation** 49 **Command Documenation**
39 50
40 The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment. 51 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.
41 52
53 .. _secondary_structure_map: http://www.mothur.org/wiki/Secondary_structure_map
42 .. _align.check: http://www.mothur.org/wiki/Align.check 54 .. _align.check: http://www.mothur.org/wiki/Align.check
43 55
44 </help> 56 </help>
45 </tool> 57 </tool>