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comparison get.mimarkspackage.xml @ 0:066b8aaf5a9a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:32:41 -0400
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-1:000000000000 0:066b8aaf5a9a
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="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$input.infile" input.infile.dat &&
11
12 echo 'get.mimarkspackage(
13 #if $input.filetype == "group":
14 group=input.infile.dat,
15 #elif $input.filetype == "oligos":
16 oligos=input.infile.dat,
17 #else:
18 file=input.infile.dat,
19 #end if
20 package=$package,
21 requiredonly=$requiredonly
22 )'
23 | sed 's/ //g' ## mothur trips over whitespace
24 | mothur
25 ]]></command>
26 <inputs>
27 <conditional name="input">
28 <param name="filetype" type="select" label="input type">
29 <option value="group">group file</option>
30 <option value="oligos" selected="true">oligos file</option>
31 <option value="file">other file (e.g. output from mimarks.attributes)</option>
32 </param>
33 <when value="group">
34 <param name="infile" type="data" format="mothur.groups" label="group file"/>
35 </when>
36 <when value="oligos">
37 <param name="infile" type="data" format="mothur.oligos" label="oligos"/>
38 </when>
39 <when value="file">
40 <param name="infile" type="data" format="txt" label="file"/>
41 </when>
42 </conditional>
43 <param name="package" type="select" label="package - select the mimarks package you would like to use">
44 <option value="air">air</option>
45 <option value="host_associated">host_associated</option>
46 <option value="human_associated">human_associated</option>
47 <option value="human_gut">human_gut</option>
48 <option value="human_oral">human_oral</option>
49 <option value="human_skin">human_skin</option>
50 <option value="human_vaginal">human_vaginal</option>
51 <option value="microbial">microbial</option>
52 <option value="miscellaneous" selected="true">miscellaneous</option>
53 <option value="plant_associated">plant_associated</option>
54 <option value="sediment">sediment</option>
55 <option value="soil">soil</option>
56 <option value="wastewater">wastewater</option>
57 <option value="waterc">waterc</option>
58 </param>
59 <param name="requiredonly" type="boolean" truevalue="true" falsevalue="false" checked="false" label="requiredonly - used to indicate you only want the required mimarks fields printed. Default=false"/>
60 </inputs>
61 <outputs>
62 <expand macro="logfile-output"/>
63 <data name="package_out" format="tabular" from_work_dir="input.infile*.tsv" label="${tool.name} on ${on_string}: mimarks package"/>
64 </outputs>
65 <tests>
66 <test><!-- test with group file -->
67 <param name="filetype" value="group"/>
68 <param name="infile" value="amazon.groups" ftype="mothur.groups"/>
69 <output name="package_out" md5="8e97dbe732b257494b796d23a3688d5a" ftype="tabular"/>
70 <expand macro="logfile-test"/>
71 </test>
72 <test><!-- test with oligos -->
73 <param name="filetype" value="oligos"/>
74 <param name="infile" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
75 <param name="package" value="human_associated"/>
76 <param name="requiredonly" value="true"/>
77 <output name="package_out" md5="975cd41eb9a97725795c582dc7e903a3" ftype="tabular"/>
78 <expand macro="logfile-test"/>
79 </test>
80 <test><!-- test with other file (output from mimarks.attributes)-->
81 <param name="filetype" value="file"/>
82 <param name="infile" value="biosample.source" ftype="txt"/>
83 <output name="package_out" file="biosample.tsv" ftype="tabular"/>
84 <expand macro="logfile-test"/>
85 </test>
86 </tests>
87 <help>
88 <![CDATA[
89
90 @MOTHUR_OVERVIEW@
91
92 **Command Documenation**
93
94 The get.mimarkspackage_ command creates a mimarks package form with your groups.
95
96 .. _get.mimarkspackage: http://www.mothur.org/wiki/Get.mimarkspackage
97
98 ]]>
99 </help>
100 <citations>
101 <citation type="doi">10.1128/AEM.01541-09</citation>
102 </citations>
103 </tool>