Mercurial > repos > iuc > mothur_make_shared

comparison make.shared.xml @ 4:5faa13c51864 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 09:31:17 -0500
parents 35e4be39c33d
children 0b282bb8843b
comparison
equal deleted inserted replaced
3:d933285fab3c 4:5faa13c51864
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>
104 <element name="0.22" md5="592b4fb84412de47be18e64ef26b7a80" ftype="mothur.shared"/> 104 <element name="0.22" md5="592b4fb84412de47be18e64ef26b7a80" ftype="mothur.shared"/>
105 </output_collection> 105 </output_collection>
106 <expand macro="logfile-test"/> 106 <expand macro="logfile-test"/>
107 </test> 107 </test>
108 </tests> 108 </tests>
109 <help> 109 <help><![CDATA[
110 <![CDATA[
111 110
112 @MOTHUR_OVERVIEW@ 111 @MOTHUR_OVERVIEW@
113 112
114 **Command Documentation** 113 **Command Documentation**
115 114
119 .. _list: https://www.mothur.org/wiki/List_file 118 .. _list: https://www.mothur.org/wiki/List_file
120 .. _group: https://www.mothur.org/wiki/Group_file 119 .. _group: https://www.mothur.org/wiki/Group_file
121 .. _shared: https://www.mothur.org/wiki/Shared_file 120 .. _shared: https://www.mothur.org/wiki/Shared_file
122 .. _rabund: https://www.mothur.org/wiki/Rabund_file 121 .. _rabund: https://www.mothur.org/wiki/Rabund_file
123 .. _make.shared: https://www.mothur.org/wiki/Make.shared 122 .. _make.shared: https://www.mothur.org/wiki/Make.shared
124 ]]> 123
125 </help> 124 ]]></help>
126 <expand macro="citations"/> 125 <expand macro="citations"/>
127 </tool> 126 </tool>