Mercurial > repos > iuc > mothur_align_check

comparison align.check.xml @ 3:2fc7aad419ff draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:29:22 -0500
parents cf25efc1895b
children 4e7411b1aa3d
comparison
equal deleted inserted replaced
2:bd3e7fe37de6 3:2fc7aad419ff
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 ln -s "$name" name.dat && 14 ln -s '$name' name.dat &&
15 ln -s "$count" count.dat && 15 ln -s '$count' count.dat &&
16 ln -s "$map" map.dat && 16 ln -s '$map' map.dat &&
17 17
18 echo 'align.check( 18 echo 'align.check(
19 fasta=fasta.dat, 19 fasta=fasta.dat,
20 #if $name: 20 #if $name:
21 name=name.dat, 21 name=name.dat,
22 #end if 22 #end if
23 #if $count: 23 #if $count:
24 count=count.dat, 24 count=count.dat,
25 #end if 25 #end if
26 map=map.dat 26 map=map.dat
27 )' 27 )'
28 | sed 's/ //g' ## mothur trips over whitespace 28 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur 29 | mothur
30 | tee mothur.out.log 30 | tee mothur.out.log
31 && cat fasta.align.check
31 ]]></command> 32 ]]></command>
32 <inputs> 33 <inputs>
33 <param name="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/> 34 <param argument="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/>
34 <conditional name="ss"> 35 <conditional name="ss">
35 <param name="source" label="Select Secondary Structure Map from" type="select"> 36 <param name="source" label="Select Secondary Structure Map from" type="select">
36 <option value="cached">Cached Secondary Structure Maps</option> 37 <option value="cached">Cached Secondary Structure Maps</option>
37 <option value="history">Your History</option> 38 <option value="history">Your History</option>
39 </param>
40 <when value="cached">
41 <param argument="map" type="select" label="Secondary structure map">
42 <options from_data_table="mothur_map"/>
38 </param> 43 </param>
39 <when value="cached"> 44 </when>
40 <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions"> 45 <when value="history">
41 <options from_data_table="mothur_map"> 46 <param argument="map" format="mothur.map" type="data" label="Secondary Structure Map"/>
42 </options> 47 </when>
43 </param> 48 </conditional>
44 </when> 49 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count_table file"
45 <when value="history"> 50 help="You can also provide a name file associated with your fasta file"/>
46 <param name="map" format="mothur.map" type="data" label="Secondary Structure Map"/> 51 <param argument="name" type="data" format="mothur.names" optional="true" label="names file"
47 </when> 52 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"/>
48 </conditional> 53 </inputs>
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> 54 <outputs>
53 <expand macro="logfile-output"/> 55 <expand macro="logfile-output"/>
54 <data name="out_file" format="mothur.align.check" from_work_dir="fasta.align.check" label="${tool.name} on ${on_string}: align.check"/> 56 <data name="align.check" format="mothur.align.check" from_work_dir="fasta.align.check" label="${tool.name} on ${on_string}: align.check"/>
55 </outputs> 57 </outputs>
56 <tests> 58 <tests>
57 <test><!-- test with defaults --> 59 <test><!-- test with defaults -->
58 <param name="fasta" value="amazon.align_head_short"/> 60 <param name="fasta" value="amazon.align_head_short"/>
59 <param name="source" value="history"/> 61 <param name="source" value="history"/>
60 <param name="map" value="silva.ss.map.head"/> 62 <param name="map" value="silva.ss.map.head"/>
61 <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/> 63 <output name="align.check" ftype="mothur.align.check">
64 <assert_contents>
65 <expand macro="test-aligncheck-format"/>
66 <has_text text="U68589"/>
67 </assert_contents>
68 </output>
62 <expand macro="logfile-test"/> 69 <expand macro="logfile-test"/>
63 </test> 70 </test>
64 <test><!-- test with names file --> 71 <test><!-- test with names file -->
65 <param name="fasta" value="amazon.align_head_short"/> 72 <param name="fasta" value="amazon.align_head_short"/>
66 <param name="source" value="history"/> 73 <param name="source" value="history"/>
67 <param name="map" value="silva.ss.map.head"/> 74 <param name="map" value="silva.ss.map.head"/>
68 <param name="name" value="amazon.align_head.names"/> 75 <param name="name" value="amazon.align_head.names"/>
69 <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/> 76 <output name="align.check" ftype="mothur.align.check">
77 <assert_contents>
78 <expand macro="test-aligncheck-format"/>
79 <has_text text="U68589"/>
80 </assert_contents>
81 </output>
70 <expand macro="logfile-test"/> 82 <expand macro="logfile-test"/>
71 </test> 83 </test>
72 </tests> 84 </tests>
73 <help> 85 <help><![CDATA[
74 <![CDATA[
75 86
76 @MOTHUR_OVERVIEW@ 87 @MOTHUR_OVERVIEW@
77 88
78 **Command Documentation** 89 **Command Documentation**
79 90
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. 91 The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence
92 alignment using a secondary_structure_map_. If you are familiar with the editor window in ARB, this is the same as
93 counting the number of ~, #, -, and = signs.
81 94
82 .. _secondary_structure_map: https://www.mothur.org/wiki/Secondary_structure_map 95 .. _secondary_structure_map: https://www.mothur.org/wiki/Secondary_structure_map
83 .. _align.check: https://www.mothur.org/wiki/Align.check 96 .. _align.check: https://www.mothur.org/wiki/Align.check
84 ]]> 97
85 </help> 98 ]]></help>
86 <expand macro="citations"/> 99 <expand macro="citations"/>
87 </tool> 100 </tool>