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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d139641e5afb8c75b8aded37bdbd7aecae0fb83
author ecology
date Wed, 13 Sep 2023 19:56:16 +0000
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children 9d56f6480194
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-1:000000000000 0:9cbac7a9b1a3
1 <tool id="makeeml" name="Make EML" version="0.1.0+galaxy0">
2 <description> Create EML from EAL templates</description>
3 <requirements>
4 <requirement type="package" version="4.3.1">r-base</requirement>
5 <requirement type="package" version="3.5.5">r-emlassemblyline</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir output_template &&
9 #for $input in $templates
10 ln -s '$input' 'output_template/${input.element_identifier}.txt';
11 #end for
12 Rscript
13 '$__tool_directory__/make_eml.R' 2> err.txt
14 'title'
15 ]]></command>
16 <inputs>
17 <param name="templates" type="data_collection" collection_type="list" format="tabular" label="Upload all EAL templates" help= "Input a data collection." />
18 <param name="title" type="text" label="Title for your dataset." />
19 </inputs>
20 <outputs>
21 <data name="metadataout" from_work_dir="eml.xml" format="xml" label="EML"/>
22 <data name="error" from_work_dir="err.txt" format="txt" label="Warning message"/>
23 </outputs>
24 <tests>
25 <test expect_num_outputs="2">
26 <param name="templates">
27 <collection type="list">
28 <element name="annotations" value="annotations.txt"/>
29 <element name="keywords" value="keywords.txt" />
30 <element name="attributes_data_blary_al" value="attributes_data_blary_al.txt"/>
31 <element name="catvars_data_blary_al" value="catvars_data_blary_al.txt"/>
32 <element name="geographic_coverage" value="geographic_coverage.txt" />
33 <element name="personnel" value="personnel.txt" />
34 </collection>
35 </param>
36 <output name="metadataout" >
37 <assert_contents>
38 <is_valid_xml />
39 <xml_element path="./dataset"/>
40 </assert_contents>
41 </output>
42 </test>
43 </tests>
44 <help><![CDATA[
45 .. class:: warningmark
46
47 '''TIP''' This tool accept as inputs only Galaxy collections containing EAL templates.
48
49 **What it does?**
50 --------------------
51
52 This tool produce EML metadata from EAL templates.
53 This tool can be used in the continuation of the eml2eal tool.
54
55 **How to use it?**
56 --------------------
57 To use this tool, you can select, in your history a data collection with EAL templates made by the eml2eal tool.
58 You can also select your own templates that you have to integrate into a Galaxy collection.
59
60 To do so you can select the **Upload file** tool, select the *Collection* tab, upload all your templates, click on the *Start* button to integrate the files to Galaxy and then click
61 on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates.
62 You also can upload your files to Galaxy, select them in the history by clicking the *Select items* button, click on the newly appeared box on the right and select *Build dataset list*.
63
64 .. class:: infomark
65
66 Templates can be directly edited in Galaxy (view **eml2eal** tool for more information.)
67
68
69 You then have to select your collection in the upload box of the tool and click **Execute** to get your EML metadata.
70 ]]></help>
71 </tool>