Mercurial > repos > iuc > mothur_get_mimarkspackage
comparison get.mimarkspackage.xml @ 2:74a93a1ec22c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 22:25:46 -0400 |
parents | ad446a792958 |
children | 6c54b38dd0da |
comparison
equal
deleted
inserted
replaced
1:dfbe7c1d0c5e | 2:74a93a1ec22c |
---|---|
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=$requiredonly |
23 )' | 23 )' |
24 | sed 's/ //g' ## mothur trips over whitespace | 24 | sed 's/ //g' ## mothur trips over whitespace |
25 | mothur | 25 | mothur |
26 | tee mothur.out.log | 26 | tee mothur.out.log |
27 ]]></command> | 27 ]]></command> |
28 <inputs> | 28 <inputs> |
29 <conditional name="input"> | 29 <conditional name="input"> |
30 <param name="filetype" type="select" label="input type"> | 30 <param name="filetype" type="select" label="input type"> |
31 <option value="group">group file</option> | 31 <option value="group">group file</option> |
53 <option value="soil">soil</option> | 53 <option value="soil">soil</option> |
54 <option value="wastewater">wastewater</option> | 54 <option value="wastewater">wastewater</option> |
55 <option value="waterc">waterc</option> | 55 <option value="waterc">waterc</option> |
56 </param> | 56 </param> |
57 <param name="requiredonly" type="boolean" truevalue="true" falsevalue="false" checked="false" label="requiredonly - used to indicate you only want the required mimarks fields printed. Default=false"/> | 57 <param name="requiredonly" type="boolean" truevalue="true" falsevalue="false" checked="false" label="requiredonly - used to indicate you only want the required mimarks fields printed. Default=false"/> |
58 <expand macro="param-savelog"/> | |
58 </inputs> | 59 </inputs> |
59 <outputs> | 60 <outputs> |
60 <expand macro="logfile-output"/> | 61 <expand macro="logfile-output"/> |
61 <data name="package_out" format="tabular" from_work_dir="input.infile*.tsv" label="${tool.name} on ${on_string}: mimarks package"/> | 62 <data name="package_out" format="tabular" from_work_dir="input.infile*.tsv" label="${tool.name} on ${on_string}: mimarks package"/> |
62 </outputs> | 63 </outputs> |
63 <tests> | 64 <tests> |
64 <test><!-- test with group file --> | 65 <test><!-- test with group file --> |
65 <param name="filetype" value="group"/> | 66 <param name="filetype" value="group"/> |
66 <param name="infile" value="amazon.groups" ftype="mothur.groups"/> | 67 <param name="infile" value="amazon.groups" ftype="mothur.groups"/> |
67 <output name="package_out" md5="8e97dbe732b257494b796d23a3688d5a" ftype="tabular"/> | 68 <output name="package_out" md5="8e97dbe732b257494b796d23a3688d5a" ftype="tabular"/> |
69 <param name="savelog" value="true"/> | |
68 <expand macro="logfile-test"/> | 70 <expand macro="logfile-test"/> |
69 </test> | 71 </test> |
70 <test><!-- test with oligos --> | 72 <test><!-- test with oligos --> |
71 <param name="filetype" value="oligos"/> | 73 <param name="filetype" value="oligos"/> |
72 <param name="infile" value="GQY1XT001.oligos" ftype="mothur.oligos"/> | 74 <param name="infile" value="GQY1XT001.oligos" ftype="mothur.oligos"/> |
73 <param name="package" value="human_associated"/> | 75 <param name="package" value="human_associated"/> |
74 <param name="requiredonly" value="true"/> | 76 <param name="requiredonly" value="true"/> |
75 <output name="package_out" md5="975cd41eb9a97725795c582dc7e903a3" ftype="tabular"/> | 77 <output name="package_out" md5="975cd41eb9a97725795c582dc7e903a3" ftype="tabular"/> |
78 <param name="savelog" value="true"/> | |
76 <expand macro="logfile-test"/> | 79 <expand macro="logfile-test"/> |
77 </test> | 80 </test> |
78 </tests> | 81 </tests> |
79 <help> | 82 <help><![CDATA[ |
80 <![CDATA[ | |
81 | 83 |
82 @MOTHUR_OVERVIEW@ | 84 @MOTHUR_OVERVIEW@ |
83 | 85 |
84 **Command Documentation** | 86 **Command Documentation** |
85 | 87 |
86 The get.mimarkspackage_ command creates a mimarks package form with your groups. | 88 The get.mimarkspackage_ command creates a mimarks package form with your groups. |
87 | 89 |
88 .. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage | 90 .. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage |
89 | 91 |
90 ]]> | 92 ]]></help> |
91 </help> | |
92 <citations> | 93 <citations> |
93 <citation type="doi">10.1128/AEM.01541-09</citation> | 94 <citation type="doi">10.1128/AEM.01541-09</citation> |
94 </citations> | 95 </citations> |
95 </tool> | 96 </tool> |