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comparison get.mimarkspackage.xml @ 0:ad446a792958 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 05:59:44 -0400
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children 74a93a1ec22c
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1 <tool profile="16.07" id="mothur_get_mimarkspackage" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0">
2 <description>creates a mimarks package form with your groups</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 "$input.infile" input.infile.dat &&
14
15 echo 'get.mimarkspackage(
16 #if $input.filetype == "group":
17 group=input.infile.dat,
18 #elif $input.filetype == "oligos":
19 oligos=input.infile.dat,
20 #end if
21 package=$package,
22 requiredonly=$requiredonly
23 )'
24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur
26 | tee mothur.out.log
27 ]]></command>
28 <inputs>
29 <conditional name="input">
30 <param name="filetype" type="select" label="input type">
31 <option value="group">group file</option>
32 <option value="oligos" selected="true">oligos file</option>
33 </param>
34 <when value="group">
35 <param name="infile" type="data" format="mothur.groups" label="group file"/>
36 </when>
37 <when value="oligos">
38 <param name="infile" type="data" format="mothur.oligos" label="oligos"/>
39 </when>
40 </conditional>
41 <param name="package" type="select" label="package - select the mimarks package you would like to use">
42 <option value="air">air</option>
43 <option value="host_associated">host_associated</option>
44 <option value="human_associated">human_associated</option>
45 <option value="human_gut">human_gut</option>
46 <option value="human_oral">human_oral</option>
47 <option value="human_skin">human_skin</option>
48 <option value="human_vaginal">human_vaginal</option>
49 <option value="microbial">microbial</option>
50 <option value="miscellaneous" selected="true">miscellaneous</option>
51 <option value="plant_associated">plant_associated</option>
52 <option value="sediment">sediment</option>
53 <option value="soil">soil</option>
54 <option value="wastewater">wastewater</option>
55 <option value="waterc">waterc</option>
56 </param>
57 <param name="requiredonly" type="boolean" truevalue="true" falsevalue="false" checked="false" label="requiredonly - used to indicate you only want the required mimarks fields printed. Default=false"/>
58 </inputs>
59 <outputs>
60 <expand macro="logfile-output"/>
61 <data name="package_out" format="tabular" from_work_dir="input.infile*.tsv" label="${tool.name} on ${on_string}: mimarks package"/>
62 </outputs>
63 <tests>
64 <test><!-- test with group file -->
65 <param name="filetype" value="group"/>
66 <param name="infile" value="amazon.groups" ftype="mothur.groups"/>
67 <output name="package_out" md5="8e97dbe732b257494b796d23a3688d5a" ftype="tabular"/>
68 <expand macro="logfile-test"/>
69 </test>
70 <test><!-- test with oligos -->
71 <param name="filetype" value="oligos"/>
72 <param name="infile" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
73 <param name="package" value="human_associated"/>
74 <param name="requiredonly" value="true"/>
75 <output name="package_out" md5="975cd41eb9a97725795c582dc7e903a3" ftype="tabular"/>
76 <expand macro="logfile-test"/>
77 </test>
78 </tests>
79 <help>
80 <![CDATA[
81
82 @MOTHUR_OVERVIEW@
83
84 **Command Documentation**
85
86 The get.mimarkspackage_ command creates a mimarks package form with your groups.
87
88 .. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage
89
90 ]]>
91 </help>
92 <citations>
93 <citation type="doi">10.1128/AEM.01541-09</citation>
94 </citations>
95 </tool>