Mercurial > repos > iuc > mothur_make_shared

comparison make.shared.xml @ 3:4ad0836d0ade draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:57:06 -0400
parents c4b6d7acffbf
children
comparison
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2:83dabeeadb55 3:4ad0836d0ade
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 "$intype.otu" intype_otu.dat && 13 ln -s '$intype.otu' intype_otu.dat &&
14 #if $intype.infile == "otulist": 14 #if $intype.infile == "otulist":
15 ln -s "$intype.group" intype_group.dat && 15 ln -s '$intype.group' intype_group.dat &&
16 #end if
17
18 echo 'make.shared(
19 #if $intype.infile == "biom":
20 biom=intype_otu.dat
21 #else
22 #if $intype.group.is_of_type("mothur.groups"):
23 group=intype_group.dat,
24 #elif $intype.group.is_of_type("mothur.count_table"):
25 count=intype_group.dat,
16 #end if 26 #end if
27 #if $intype.label:
28 label=${ str($intype.label).replace(",","-") },
29 #end if
30 #if $intype.groups:
31 groups=${ str($intype.groups).replace(",","-") },
32 #end if
33 list=intype_otu.dat
34 #end if
35 )'
36 | sed 's/ //g' ## mothur trips over whitespace
37 | mothur
38 | tee mothur.out.log &&
17 39
18 echo 'make.shared( 40 ## move output files to correct destination
19 #if $intype.infile == "biom": 41 mv mothur.*.logfile "$logfile" &&
20 biom=intype_otu.dat 42 #if $intype.infile == 'otulist' and $intype.groups:
21 #else 43 mv intype_otu*.groups "$groupout"
22 #if $intype.group.is_of_type("mothur.groups"): 44 #else
23 group=intype_group.dat, 45 mv intype_otu*.shared "$shared"
24 #elif $intype.group.is_of_type("mothur.count_table"): 46 #end if
25 count=intype_group.dat,
26 #end if
27 #if $intype.label:
28 label=${ str($intype.label).replace(",","-") },
29 #end if
30 #if $intype.groups:
31 groups=${ str($intype.groups).replace(",","-") },
32 #end if
33 list=intype_otu.dat
34 #end if
35 )'
36 | sed 's/ //g' ## mothur trips over whitespace
37 | mothur
38 | tee mothur.out.log &&
39
40 ## move output files to correct destination
41 mv mothur.*.logfile "$logfile" &&
42 #if $intype.infile == 'otulist' and $intype.groups:
43 mv intype_otu*.groups "$groupout"
44 #else
45 mv intype_otu*.shared "$shared"
46 #end if
47 ]]></command> 47 ]]></command>
48 <inputs> 48 <inputs>
49 <conditional name="intype"> 49 <conditional name="intype">
50 <param name="infile" type="select" label="Select input type" help=""> 50 <param name="infile" type="select" label="Select input type" help="">
51 <option value="otulist">OTU list</option> 51 <option value="otulist">OTU list</option>
65 </when> 65 </when>
66 <when value="biom"> 66 <when value="biom">
67 <param name="otu" type="data" format="biom1" label="Biom 1.0 file"/> 67 <param name="otu" type="data" format="biom1" label="Biom 1.0 file"/>
68 </when> 68 </when>
69 </conditional> 69 </conditional>
70 <expand macro="param-savelog"/>
70 </inputs> 71 </inputs>
71 <outputs> 72 <outputs>
72 <expand macro="logfile-output"/> 73 <expand macro="logfile-output"/>
73 <data name="shared" format="mothur.shared" from_work_dir="intype_otu*.shared" label="${tool.name} on ${on_string}: shared"/> 74 <data name="shared" format="mothur.shared" from_work_dir="intype_otu*.shared" label="${tool.name} on ${on_string}: shared"/>
74 <data name="groupout" format="mothur.groups" from_work_dir="intype_otu*.groups" label="${tool.name} on ${on_string}: groups"> 75 <data name="groupout" format="mothur.groups" from_work_dir="intype_otu*.groups" label="${tool.name} on ${on_string}: groups">
82 <tests> 83 <tests>
83 <test><!-- test with biom file --> 84 <test><!-- test with biom file -->
84 <param name="infile" value="biom"/> 85 <param name="infile" value="biom"/>
85 <param name="otu" value="example.biom"/> 86 <param name="otu" value="example.biom"/>
86 <output name="shared" md5="e44d5ca4e4a5dbc68e8219c5690aa156" ftype="mothur.shared"/> 87 <output name="shared" md5="e44d5ca4e4a5dbc68e8219c5690aa156" ftype="mothur.shared"/>
88 <param name="savelog" value="true"/>
87 <expand macro="logfile-test"/> 89 <expand macro="logfile-test"/>
88 </test> 90 </test>
89 <test><!-- test with otu and group file--> 91 <test><!-- test with otu and group file-->
90 <param name="infile" value="otulist"/> 92 <param name="infile" value="otulist"/>
91 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 93 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
92 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 94 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
93 <output name="shared" file="amazon.an.shared" ftype="mothur.shared"/> 95 <output name="shared" file="amazon.an.shared" ftype="mothur.shared"/>
96 <param name="savelog" value="true"/>
94 <expand macro="logfile-test"/> 97 <expand macro="logfile-test"/>
95 </test> 98 </test>
96 <test><!-- test with label and group select--> 99 <test><!-- test with label and group select-->
97 <param name="infile" value="otulist"/> 100 <param name="infile" value="otulist"/>
98 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 101 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
101 <param name="groups" value="forest,pasture"/> 104 <param name="groups" value="forest,pasture"/>
102 <output name="groupout" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> 105 <output name="groupout" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
103 <output_collection name="labelshares" count="3"> 106 <output_collection name="labelshares" count="3">
104 <element name="0.22" md5="592b4fb84412de47be18e64ef26b7a80" ftype="mothur.shared"/> 107 <element name="0.22" md5="592b4fb84412de47be18e64ef26b7a80" ftype="mothur.shared"/>
105 </output_collection> 108 </output_collection>
109 <param name="savelog" value="true"/>
106 <expand macro="logfile-test"/> 110 <expand macro="logfile-test"/>
107 </test> 111 </test>
108 </tests> 112 </tests>
109 <help> 113 <help><![CDATA[
110 <![CDATA[
111 114
112 @MOTHUR_OVERVIEW@ 115 @MOTHUR_OVERVIEW@
113 116
114 **Command Documentation** 117 **Command Documentation**
115 118
119 .. _list: https://www.mothur.org/wiki/List_file 122 .. _list: https://www.mothur.org/wiki/List_file
120 .. _group: https://www.mothur.org/wiki/Group_file 123 .. _group: https://www.mothur.org/wiki/Group_file
121 .. _shared: https://www.mothur.org/wiki/Shared_file 124 .. _shared: https://www.mothur.org/wiki/Shared_file
122 .. _rabund: https://www.mothur.org/wiki/Rabund_file 125 .. _rabund: https://www.mothur.org/wiki/Rabund_file
123 .. _make.shared: https://www.mothur.org/wiki/Make.shared 126 .. _make.shared: https://www.mothur.org/wiki/Make.shared
124 ]]> 127
125 </help> 128 ]]></help>
126 <expand macro="citations"/> 129 <expand macro="citations"/>
127 </tool> 130 </tool>