Mercurial > repos > ecology > makeeml
comparison make_eml.xml @ 4:59349973537f draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32
author | ecology |
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date | Sat, 23 Dec 2023 20:41:10 +0000 |
parents | 8a697f446051 |
children | 4cf24a95c4ff |
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3:642e31c435c9 | 4:59349973537f |
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1 <tool id="makeeml" name="Make EML" version="0.1.0+galaxy0" profile="22.05"> | 1 <tool id="makeeml" name="Make EML" version="0.1.1+galaxy1" profile="22.05"> |
2 <description> Create EML from EAL templates</description> | 2 <description> Create EML from EAL templates</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="4.3.1">r-base</requirement> | 4 <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container> |
5 <requirement type="package" version="3.5.5">r-emlassemblyline</requirement> | |
6 </requirements> | 5 </requirements> |
7 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
8 | 7 |
9 mkdir output_template && | 8 mkdir output_template && |
10 #for $input in $templates | 9 #for $input in $templates |
16 #for $indata in $inputdata | 15 #for $indata in $inputdata |
17 ln -s '$indata' 'data_files/${indata.element_identifier}'; | 16 ln -s '$indata' 'data_files/${indata.element_identifier}'; |
18 #set $table += $indata.element_identifier + " "; | 17 #set $table += $indata.element_identifier + " "; |
19 #end for | 18 #end for |
20 | 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 | |
21 #set $other = "" | 32 #set $other = "" |
22 #for $data_other in $dataother | 33 #for $data_other in $dataother |
23 ln -s '$data_other' 'data_files/${data_other.element_identifier}'; | 34 ln -s '$data_other' 'data_files/${data_other.element_identifier}'; |
24 #set $other += $data_other.element_identifier + " "; | 35 #set $other += $data_other.element_identifier + " "; |
25 #end for | 36 #end for |
27 #set $quotetable ="" | 38 #set $quotetable ="" |
28 #for $q in $table_quote | 39 #for $q in $table_quote |
29 #set $quotetable += $q.quote + ","; | 40 #set $quotetable += $q.quote + ","; |
30 #end for | 41 #end for |
31 | 42 |
43 | |
32 Rscript | 44 Rscript |
33 '$__tool_directory__/make_eml.R' 2> err.txt | 45 '$__tool_directory__/make_eml.R' 2> err.txt |
34 '$title' | 46 '$title' |
35 '$temporal_coverage.start' | 47 '$temporal_coverage.start' |
36 '$temporal_coverage.end' | 48 '$temporal_coverage.end' |
37 '$table' | 49 '$table' |
50 '$raster' | |
51 '$vector' | |
38 '$other' | 52 '$other' |
39 '$destable' | 53 '$destable' |
54 '$desraster' | |
55 '$desvector' | |
40 '$desother' | 56 '$desother' |
41 '$quotetable' | 57 '$quotetable' |
42 '$table_url' | 58 '$table_url' |
43 '$other_url' | 59 '$other_url' |
60 '$raster_url' | |
61 '$vector_url' | |
44 | 62 |
45 ]]></command> | 63 ]]></command> |
46 <inputs> | 64 <inputs> |
47 <param name="templates" type="data_collection" collection_type="list" format="tabular" label="Upload all EAL templates" help= "Input a data collection with only tabular files." /> | 65 <param name="templates" type="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> | |
48 <section name="data_table" title="Do you have data table ? " > | 71 <section name="data_table" title="Do you have data table ? " > |
49 <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"/> | 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"/> |
50 <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"/> | 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"/> |
51 <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" > | 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" > |
52 <param name="quote" type="select" label="What's the quotes of your data table ?" optional="true"> | 75 <param name="quote" type="select" label="What's the quotes of your data table ?" optional="true"> |
55 <option value="none">None</option> | 78 <option value="none">None</option> |
56 </param> | 79 </param> |
57 </repeat> | 80 </repeat> |
58 <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"/> | 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"/> |
59 </section> | 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> | |
60 <section name="data_other" title="Do you have other data entity ? " > | 93 <section name="data_other" title="Do you have other data entity ? " > |
61 <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"/> | 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"/> |
62 <param name="desother" type="text" label="Give a short description of your data file. If there are multiple data files please separate your descriptions with a comma (,) in the same order of your data input" 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"/> |
63 <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"/> | 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"/> |
64 </section> | |
65 <param name="title" type="text" label="Title for your dataset." /> | |
66 <section name="temporal_coverage" title="Temporal coverage" > | |
67 <param name="start" type="text" label="Beginning date of the dataset in the format YYYY-MM-DD" /> | |
68 <param name="end" type="text" label="Ending date of the dataset in the format YYYY-MM-DD" /> | |
69 </section> | 97 </section> |
70 </inputs> | 98 </inputs> |
71 <outputs> | 99 <outputs> |
72 <data name="metadataout" from_work_dir="eml.xml" format="xml" label="EML"/> | 100 <data name="metadataout" from_work_dir="eml.xml" format="xml" label="EML"/> |
73 <data name="error" from_work_dir="err.txt" format="txt" label="Warning message"/> | 101 <data name="error" from_work_dir="err.txt" format="txt" label="Warning message"/> |
74 </outputs> | 102 </outputs> |
75 <tests> | 103 <tests> |
76 <test expect_num_outputs="2"> | 104 <test expect_num_outputs="2"> |
77 <param name="templates"> | 105 <param name="templates" value="annotations.txt,keywords.txt,attributes_data_blary_al.txt,catvars_data_blary_al.txt,geographic_coverage.tabular,personnel.txt" > |
78 <collection type="list"> | |
79 <element name="annotations.txt" value="annotations.txt"/> | |
80 <element name="keywords.txt" value="keywords.txt" /> | |
81 <element name="attributes_data_blary_al.txt" value="attributes_data_blary_al.txt"/> | |
82 <element name="catvars_data_blary_al.txt" value="catvars_data_blary_al.txt"/> | |
83 <element name="geographic_coverage.txt" value="geographic_coverage.txt" /> | |
84 <element name="personnel.txt" value="personnel.txt" /> | |
85 </collection> | |
86 </param> | 106 </param> |
87 <output name="metadataout" > | 107 <output name="metadataout" > |
88 <assert_contents> | 108 <assert_contents> |
89 <is_valid_xml /> | 109 <is_valid_xml /> |
90 <xml_element path="./dataset"/> | 110 <xml_element path="./dataset"/> |
91 </assert_contents> | 111 </assert_contents> |
92 </output> | 112 </output> |
93 </test> | 113 </test> |
94 </tests> | 114 </tests> |
95 <help><![CDATA[ | 115 <help><![CDATA[ |
96 .. class:: warningmark | |
97 | 116 |
98 '''TIP''' This tool accept as inputs only Galaxy collections containing EAL templates in tabular format. | |
99 | 117 |
100 **What it does?** | 118 **What it does?** |
101 -------------------- | 119 -------------------- |
102 | 120 |
103 This tool produce EML metadata from EAL templates. | 121 This tool produce EML metadata from EAL templates. |
104 This tool can be used in the continuation of the eml2eal tool. | 122 This tool can be used in the continuation of the eml2eal tool. |
105 | 123 |
106 **How to use it?** | 124 **How to use it?** |
107 -------------------- | 125 -------------------- |
108 To use this tool, you can select, in your history a data collection with EAL templates made by the eml2eal tool. | 126 To use this tool, you can select, in your history a data collection with EAL templates or select templates one by one. |
109 You can also select your own templates that you have to integrate into a Galaxy collection. | |
110 | 127 |
111 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 | 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 |
112 on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates. | 129 on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates. |
113 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*. | 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*. |
114 | |
115 **Recommended optional input:** | |
116 | |
117 Data files : If you have data files you can input them to give more information in your metadata file. There are two parameters to do to so. The first is "Do you have data table ?" that provide you to import a collection with all your data table. The second is "Do you have other data entity ?" is for all your data file that not data table. | |
118 | |
119 Description : You can add a short description of each data files you input. If there are multiple data files, please separate your descriptions with a comma (,) in the same order of your data input | |
120 | |
121 Quote : If you have import data table files, you can specify if there are quotes and what type of quote is it. Repeat this parameter as many times as the number of data tables you've input and in the same order | |
122 | |
123 Title : You can give a title for your dataset. | |
124 | |
125 Temporal coverage : You can specify the temporal coverage of your data. | |
126 | 131 |
127 .. class:: infomark | 132 .. class:: infomark |
128 | 133 |
129 Templates can be directly edited in Galaxy (view **eml2eal** tool for more information.) | 134 Templates can be directly edited in Galaxy (view **eml2eal** tool for more information.) |
130 | 135 |
131 | 136 |
132 You then have to select your collection in the upload box of the tool and click **Execute** to get your EML metadata. | 137 |
133 ]]></help> | 138 ]]></help> |
134 </tool> | 139 </tool> |