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comparison align.check.xml @ 0:9d91e7974012 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:36:43 -0400
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children 814a34469480
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-1:000000000000 0:9d91e7974012
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat &&
14 ln -s "$name" name.dat &&
15 ln -s "$count" count.dat &&
16 ln -s "$map" map.dat &&
17
18 echo 'align.check(
19 fasta=fasta.dat,
20 #if $name:
21 name=name.dat,
22 #end if
23 #if $count:
24 count=count.dat,
25 #end if
26 map=map.dat
27 )'
28 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur
30 | tee mothur.out.log
31 ]]></command>
32 <inputs>
33 <param name="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/>
34 <conditional name="ss">
35 <param name="source" label="Select Secondary Structure Map from" type="select">
36 <option value="cached">Cached Secondary Structure Maps</option>
37 <option value="history">Your History</option>
38 </param>
39 <when value="cached">
40 <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions">
41 <options from_data_table="mothur_map">
42 </options>
43 </param>
44 </when>
45 <when value="history">
46 <param name="map" format="mothur.map" type="data" label="Secondary Structure Map"/>
47 </when>
48 </conditional>
49 <param name="count" type="data" format="mothur.count_table" label="count_table file" optional="true" help="You can also provide a name file associated with your fasta file"/>
50 <param name="name" type="data" format="mothur.names" label="names file" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence"/>
51 </inputs>
52 <outputs>
53 <expand macro="logfile-output"/>
54 <data name="out_file" format="mothur.align.check" from_work_dir="fasta.align.check" label="${tool.name} on ${on_string}: align.check"/>
55 </outputs>
56 <tests>
57 <test><!-- test with defaults -->
58 <param name="fasta" value="amazon.align_head_short"/>
59 <param name="source" value="history"/>
60 <param name="map" value="silva.ss.map.head"/>
61 <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/>
62 <expand macro="logfile-test"/>
63 </test>
64 <test><!-- test with names file -->
65 <param name="fasta" value="amazon.align_head_short"/>
66 <param name="source" value="history"/>
67 <param name="map" value="silva.ss.map.head"/>
68 <param name="name" value="amazon.align_head.names"/>
69 <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/>
70 <expand macro="logfile-test"/>
71 </test>
72 </tests>
73 <help>
74 <![CDATA[
75
76 @MOTHUR_OVERVIEW@
77
78 **Command Documentation**
79
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.
81
82 .. _secondary_structure_map: https://www.mothur.org/wiki/Secondary_structure_map
83 .. _align.check: https://www.mothur.org/wiki/Align.check
84 ]]>
85 </help>
86 <expand macro="citations"/>
87 </tool>