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comparison align.check.xml @ 0:5fce559c4ffa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 17:29:43 -0400
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-1:000000000000 0:5fce559c4ffa
1 <tool profile="16.07" id="mothur_align_check" name="Align.check" version="@WRAPPER_VERSION@.0">
2 <description>Calculate the number of potentially misaligned bases</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$fasta" fasta.dat &&
11 ln -s "$name" name.dat &&
12 ln -s "$count" count.dat &&
13 ln -s "$map" map.dat &&
14
15 echo 'align.check(
16 fasta=fasta.dat,
17 #if $name:
18 name=name.dat,
19 #end if
20 #if $count:
21 count=count.dat,
22 #end if
23 map=map.dat
24 )'
25 | sed 's/ //g' ## mothur trips over whitespace
26 | mothur
27 ]]></command>
28 <inputs>
29 <param name="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/>
30 <conditional name="ss">
31 <param name="source" label="Select Secondary Structure Map from" type="select">
32 <option value="cached">Cached Secondary Structure Maps</option>
33 <option value="history">Your History</option>
34 </param>
35 <when value="cached">
36 <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions">
37 <options from_data_table="mothur_map">
38 </options>
39 </param>
40 </when>
41 <when value="history">
42 <param name="map" format="mothur.map" type="data" label="Secondary Structure Map"/>
43 </when>
44 </conditional>
45 <param name="count" type="data" format="mothur.count_table" label="count_table file" optional="true" help="You can also provide a name file associated with your fasta file"/>
46 <param name="name" type="data" format="mothur.names" label="names file" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence"/>
47 </inputs>
48 <outputs>
49 <expand macro="logfile-output"/>
50 <data name="out_file" format="mothur.align.check" from_work_dir="fasta.align.check" label="${tool.name} on ${on_string}: align.check"/>
51 </outputs>
52 <tests>
53 <test><!-- test with defaults -->
54 <param name="fasta" value="amazon.align_head_short"/>
55 <param name="source" value="history"/>
56 <param name="map" value="silva.ss.map.head"/>
57 <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/>
58 <expand macro="logfile-test"/>
59 </test>
60 <test><!-- test with names file -->
61 <param name="fasta" value="amazon.align_head_short"/>
62 <param name="source" value="history"/>
63 <param name="map" value="silva.ss.map.head"/>
64 <param name="name" value="amazon.align_head.names"/>
65 <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/>
66 <expand macro="logfile-test"/>
67 </test>
68 </tests>
69 <help>
70 <![CDATA[
71
72 @MOTHUR_OVERVIEW@
73
74 **Command Documenation**
75
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.
77
78 .. _secondary_structure_map: http://www.mothur.org/wiki/Secondary_structure_map
79 .. _align.check: http://www.mothur.org/wiki/Align.check
80 ]]>
81 </help>
82 <expand macro="citations"/>
83 </tool>