Mercurial > repos > iuc > mothur_get_mimarkspackage

comparison get.mimarkspackage.xml @ 3:437a9a9a9c00 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 09:58:19 -0500
parents 793a04ad1837
children e7708e0ba8a0
comparison
equal deleted inserted replaced
2:3446d8f41bb4 3:437a9a9a9c00
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 "$input.infile" input.infile.dat && 13 ln -s '$input.infile' input.infile.dat &&
14 14
15 echo 'get.mimarkspackage( 15 echo 'get.mimarkspackage(
16 #if $input.filetype == "group": 16 #if $input.filetype == "group":
17 group=input.infile.dat, 17 group=input.infile.dat,
18 #elif $input.filetype == "oligos": 18 #elif $input.filetype == "oligos":
19 oligos=input.infile.dat, 19 oligos=input.infile.dat,
20 #end if 20 #end if
21 package=$package, 21 package=$package,
22 requiredonly=$requiredonly 22 requiredonly=$requiredonly
23 )' 23 )'
24 | sed 's/ //g' ## mothur trips over whitespace 24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur 25 | mothur
26 | tee mothur.out.log 26 | tee mothur.out.log
27 ]]></command> 27 ]]></command>
28 <inputs> 28 <inputs>
29 <conditional name="input"> 29 <conditional name="input">
30 <param name="filetype" type="select" label="input type"> 30 <param name="filetype" type="select" label="input type">
31 <option value="group">group file</option> 31 <option value="group">group file</option>
74 <param name="requiredonly" value="true"/> 74 <param name="requiredonly" value="true"/>
75 <output name="package_out" md5="975cd41eb9a97725795c582dc7e903a3" ftype="tabular"/> 75 <output name="package_out" md5="975cd41eb9a97725795c582dc7e903a3" ftype="tabular"/>
76 <expand macro="logfile-test"/> 76 <expand macro="logfile-test"/>
77 </test> 77 </test>
78 </tests> 78 </tests>
79 <help> 79 <help><![CDATA[
80 <![CDATA[
81 80
82 @MOTHUR_OVERVIEW@ 81 @MOTHUR_OVERVIEW@
83 82
84 **Command Documentation** 83 **Command Documentation**
85 84
86 The get.mimarkspackage_ command creates a mimarks package form with your groups. 85 The get.mimarkspackage_ command creates a mimarks package form with your groups.
87 86
88 .. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage 87 .. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage
89 88
90 ]]> 89 ]]></help>
91 </help>
92 <citations> 90 <citations>
93 <citation type="doi">10.1128/AEM.01541-09</citation> 91 <citation type="doi">10.1128/AEM.01541-09</citation>
94 </citations> 92 </citations>
95 </tool> 93 </tool>