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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
author ecology
date Tue, 10 Sep 2024 12:50:00 +0000
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-1:000000000000 0:26ebf553b435
1 <tool id="makeeml" name="Make EML" version="0.1.1+galaxy1" profile="22.05">
2 <description> Create EML from EAL templates</description>
3 <requirements>
4 <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7
8 mkdir output_template &&
9 #for $input in $templates
10 ln -s '$input' 'output_template/${input.element_identifier}';
11 #end for
12
13 #set $table = ""
14 mkdir data_files &&
15 #for $indata in $inputdata
16 ln -s '$indata' 'data_files/${indata.element_identifier}';
17 #set $table += $indata.element_identifier + " ";
18 #end for
19
20 #set $raster = ""
21 #for $data_raster in $dataraster
22 ln -s '$data_raster' 'data_files/${data_raster.element_identifier}';
23 #set $raster += $data_raster.element_identifier + " ";
24 #end for
25
26 #set $vector = ""
27 #for $data_vector in $datavector
28 ln -s '$data_vector' 'data_files/${data_vector.element_identifier}';
29 #set $vector += $data_vector.element_identifier + " ";
30 #end for
31
32 #set $other = ""
33 #for $data_other in $dataother
34 ln -s '$data_other' 'data_files/${data_other.element_identifier}';
35 #set $other += $data_other.element_identifier + " ";
36 #end for
37
38 #set $quotetable =""
39 #for $q in $table_quote
40 #set $quotetable += $q.quote + ",";
41 #end for
42
43
44 Rscript
45 '$__tool_directory__/make_eml.R' 2> err.txt
46 '$title'
47 '$temporal_coverage.start'
48 '$temporal_coverage.end'
49 '$table'
50 '$raster'
51 '$vector'
52 '$other'
53 '$destable'
54 '$desraster'
55 '$desvector'
56 '$desother'
57 '$quotetable'
58 '$table_url'
59 '$other_url'
60 '$raster_url'
61 '$vector_url'
62
63 ]]></command>
64 <inputs>
65 <param name="templates" type="data" format="data" multiple="True" label="Upload all EAL templates" help="You can upload dataset collection or upload templates one by one (especially if there are multiple format)."/>
66 <param name="title" type="text" label="Title for your dataset." />
67 <section name="temporal_coverage" title="Temporal coverage" expanded="true">
68 <param name="start" type="text" label="Beginning date of the dataset in the format YYYY-MM-DD" optional="false"/>
69 <param name="end" type="text" label="Ending date of the dataset in the format YYYY-MM-DD" optional="false"/>
70 </section>
71 <section name="data_table" title="Do you have data table ? " >
72 <param name="inputdata" type="data_collection" collection_type="list" label="Upload all data files wich are data table" help= "Input a data collection." optional = "true"/>
73 <param name="destable" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/>
74 <repeat name="table_quote" title="What's the quotes of your data table ? Repeat this parameter as many time as the number of data tables you've input and in the same order" >
75 <param name="quote" type="select" label="What's the quotes of your data table ?" optional="true">
76 <option value="quote">Quote</option>
77 <option value="apostrophe">Apostrophe</option>
78 <option value="none">None</option>
79 </param>
80 </repeat>
81 <param name="table_url" type="text" label="Give the publicly accessible URL from which your data table can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/>
82 </section>
83 <section name="data_raster" title="Do you have raster data ? " >
84 <param name="dataraster" type="data_collection" collection_type="list" label="Upload all data files wich are spatial raster" help= "Input a data collection." optional = "true"/>
85 <param name="desraster" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/>
86 <param name="raster_url" type="text" label="Give the publicly accessible URL from which your raster data entity can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/>
87 </section>
88 <section name="data_vector" title="Do you have vector data ? " >
89 <param name="datavector" type="data_collection" collection_type="list" label="Upload all data files wich are spatial vector" help= "Input a data collection." optional = "true"/>
90 <param name="desvector" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/>
91 <param name="vector_url" type="text" label="Give the publicly accessible URL from which your vector data entity can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/>
92 </section>
93 <section name="data_other" title="Do you have other data entity ? " >
94 <param name="dataother" type="data_collection" collection_type="list" label="Upload all data files wich are other entity" help= "Input a data collection." optional = "true"/>
95 <param name="desother" type="text" label="Give a short description of your data file. If there is multiple data files please separate your descriptions with a comma (,) in the same order of your data input" optional = "true"/>
96 <param name="other_url" type="text" label="Give the publicly accessible URL from which your other data entity can be downloaded. If more than one, data files please separate your URLs with a comma (,) in the same order of your data input. If wanting to include URLs for some but not all then use a - for those that don't have a URL." optional = "true"/>
97 </section>
98 </inputs>
99 <outputs>
100 <data name="metadataout" from_work_dir="eml.xml" format="xml" label="EML"/>
101 <data name="error" from_work_dir="err.txt" format="txt" label="Warning message"/>
102 </outputs>
103 <tests>
104 <test expect_num_outputs="2">
105 <param name="templates" value="annotations.txt,keywords.txt,attributes_data_blary_al.txt,catvars_data_blary_al.txt,geographic_coverage.tabular,personnel.txt" >
106 </param>
107 <output name="metadataout" >
108 <assert_contents>
109 <is_valid_xml />
110 <xml_element path="./dataset"/>
111 </assert_contents>
112 </output>
113 </test>
114 </tests>
115 <help><![CDATA[
116
117
118 **What it does?**
119 --------------------
120
121 This tool produce EML metadata from EAL templates.
122 This tool can be used in the continuation of the eml2eal tool.
123
124 **How to use it?**
125 --------------------
126 To use this tool, you can select, in your history a data collection with EAL templates or select templates one by one.
127
128 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
129 on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates.
130 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*.
131
132 .. class:: infomark
133
134 Templates can be directly edited in Galaxy (view **eml2eal** tool for more information.)
135
136
137
138 ]]></help>
139 <citations>
140 <citation type="bibtex">@Manual{,
141 title = {EMLassemblyline: A tool kit for building EML metadata workflows},
142 author = {Colin Smith},
143 year = {2022},
144 note = {https://github.com/EDIorg/EMLassemblyline,
145 https://ediorg.github.io/EMLassemblyline/},
146 }</citation>
147 </citations>
148 </tool>