Mercurial > repos > iuc > mothur_mimarks_attributes

comparison mimarks.attributes.xml @ 2:371a522fc3a1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:57:39 -0400
parents 1a45cc9dc7ee
children 247d1bacbefe
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1:9e6590ddc54e 2:371a522fc3a1
1 <tool profile="16.07" id="mothur_mimarks_attributes" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0"> 1 <tool profile="16.07" id="mothur_mimarks_attributes" name="Mimarks.attributes" version="@WRAPPER_VERSION@.0">
2 <description>Reads bioSample Attributes xml and generates source for get.mimarkspackage command</description> 2 <description>Reads bioSample Attributes xml and generates source for get.mimarkspackage command</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
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 "$biosample_in" biosample_in.dat && 13 ln -s '$biosample_in' biosample_in.dat &&
14 14
15 echo 'mimarks.attributes( 15 echo 'mimarks.attributes(
16 xml=biosample_in.dat 16 xml=biosample_in.dat
17 )' 17 )'
18 | sed 's/ //g' ## mothur trips over whitespace 18 | sed 's/ //g' ## mothur trips over whitespace
19 | mothur 19 | mothur
20 | tee mothur.out.log 20 | tee mothur.out.log
21 ]]></command> 21 ]]></command>
22 <inputs> 22 <inputs>
23 <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/> 23 <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/>
24 <!-- TODO: add package type options (currently none described in documentation apart from default) 24 <!-- TODO: add package type options (currently none described in documentation apart from default)
25 <param name="package" type="select" label="package - select the mimarks package you would like to use"> 25 <param name="package" type="select" label="package - select the mimarks package you would like to use">
26 <option value="MIMARKS.survey" selected="true">MIMARKS.survey</option> 26 <option value="MIMARKS.survey" selected="true">MIMARKS.survey</option>
27 </param>--> 27 </param>-->
28 <expand macro="param-savelog"/>
28 </inputs> 29 </inputs>
29 <outputs> 30 <outputs>
30 <expand macro="logfile-output"/> 31 <expand macro="logfile-output"/>
31 <data name="source_out" format="txt" from_work_dir="biosample_in*.source" label="${tool.name} on ${on_string}: source"/> 32 <data name="source_out" format="txt" from_work_dir="biosample_in*.source" label="${tool.name} on ${on_string}: source"/>
32 </outputs> 33 </outputs>
33 <tests> 34 <tests>
34 <test> 35 <test>
35 <param name="biosample_in" value="biosample.xml" ftype="xml"/> 36 <param name="biosample_in" value="biosample.xml" ftype="xml"/>
36 <output name="source_out" md5="682288477dd8866465ba475bd0825517" ftype="txt"/> 37 <output name="source_out" md5="682288477dd8866465ba475bd0825517" ftype="txt"/>
38 <param name="savelog" value="true"/>
37 <expand macro="logfile-test"/> 39 <expand macro="logfile-test"/>
38 </test> 40 </test>
39 </tests> 41 </tests>
40 <help> 42 <help><![CDATA[
41 <![CDATA[
42 43
43 @MOTHUR_OVERVIEW@ 44 @MOTHUR_OVERVIEW@
44 45
45 **Command Documentation** 46 **Command Documentation**
46 47
47 The mimarks.attributes_ Reads bioSample Attributes xml and generates source for make.sra command. 48 The mimarks.attributes_ command reads `BioSample Attributes`_ xml and generates source for get.mimarkspackage_ command.
48 49
49 ]]> 50 .. _mimarks.attributes: https://www.mothur.org/w/index.php?search=mimarks.attributes
50 </help> 51 .. _BioSample Attributes: https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/
52 .. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage
53
54 ]]></help>
51 <citations> 55 <citations>
52 <citation type="doi">10.1128/AEM.01541-09</citation> 56 <citation type="doi">10.1128/AEM.01541-09</citation>
53 </citations> 57 </citations>
54 </tool> 58 </tool>