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comparison make_eml.xml @ 1:9d56f6480194 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 5f7298d572c63d2c43f7dc0c4d9edcaecaa5ccb7
author ecology
date Fri, 17 Nov 2023 17:07:36 +0000
parents 9cbac7a9b1a3
children 8a697f446051
comparison
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0:9cbac7a9b1a3 1:9d56f6480194
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.3.1">r-base</requirement> 4 <requirement type="package" version="4.3.1">r-base</requirement>
5 <requirement type="package" version="3.5.5">r-emlassemblyline</requirement> 5 <requirement type="package" version="3.5.5">r-emlassemblyline</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8
8 mkdir output_template && 9 mkdir output_template &&
9 #for $input in $templates 10 #for $input in $templates
10 ln -s '$input' 'output_template/${input.element_identifier}.txt'; 11 ln -s '$input' 'output_template/${input.element_identifier}';
11 #end for 12 #end for
13
14 #set $table = ""
15 mkdir data_files &&
16 #for $indata in $inputdata
17 ln -s '$indata' 'data_files/${indata.element_identifier}';
18 #set $table += $indata.element_identifier + " ";
19 #end for
20
21 #set $other = ""
22 #for $data_other in $dataother
23 ln -s '$data_other' 'data_files/${data_other.element_identifier}';
24 #set $other += $data_other.element_identifier + " ";
25 #end for
26
27 #set $quotetable =""
28 #for $q in $table_quote
29 #set $quotetable += $q.quote + ",";
30 #end for
31
12 Rscript 32 Rscript
13 '$__tool_directory__/make_eml.R' 2> err.txt 33 '$__tool_directory__/make_eml.R' 2> err.txt
14 'title' 34 '$title'
35 '$temporal_coverage.start'
36 '$temporal_coverage.end'
37 '$table'
38 '$other'
39 '$destable'
40 '$desother'
41 '$quotetable'
42 '$table_url'
43 '$other_url'
44
15 ]]></command> 45 ]]></command>
16 <inputs> 46 <inputs>
17 <param name="templates" type="data_collection" collection_type="list" format="tabular" label="Upload all EAL templates" help= "Input a data collection." /> 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." />
18 <param name="title" type="text" label="Title for your dataset." /> 48 <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"/>
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"/>
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" >
52 <param name="quote" type="select" label="What's the quotes of your data table ?" optional="true">
53 <option value="quote">Quote</option>
54 <option value="apostrophe">Apostrophe</option>
55 <option value="none">None</option>
56 </param>
57 </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"/>
59 </section>
60 <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"/>
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"/>
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"/>
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>
19 </inputs> 70 </inputs>
20 <outputs> 71 <outputs>
21 <data name="metadataout" from_work_dir="eml.xml" format="xml" label="EML"/> 72 <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"/> 73 <data name="error" from_work_dir="err.txt" format="txt" label="Warning message"/>
23 </outputs> 74 </outputs>
24 <tests> 75 <tests>
25 <test expect_num_outputs="2"> 76 <test expect_num_outputs="2">
26 <param name="templates"> 77 <param name="templates">
27 <collection type="list"> 78 <collection type="list">
28 <element name="annotations" value="annotations.txt"/> 79 <element name="annotations.txt" value="annotations.txt"/>
29 <element name="keywords" value="keywords.txt" /> 80 <element name="keywords.txt" value="keywords.txt" />
30 <element name="attributes_data_blary_al" value="attributes_data_blary_al.txt"/> 81 <element name="attributes_data_blary_al.txt" value="attributes_data_blary_al.txt"/>
31 <element name="catvars_data_blary_al" value="catvars_data_blary_al.txt"/> 82 <element name="catvars_data_blary_al.txt" value="catvars_data_blary_al.txt"/>
32 <element name="geographic_coverage" value="geographic_coverage.txt" /> 83 <element name="geographic_coverage.txt" value="geographic_coverage.txt" />
33 <element name="personnel" value="personnel.txt" /> 84 <element name="personnel.txt" value="personnel.txt" />
34 </collection> 85 </collection>
35 </param> 86 </param>
36 <output name="metadataout" > 87 <output name="metadataout" >
37 <assert_contents> 88 <assert_contents>
38 <is_valid_xml /> 89 <is_valid_xml />
42 </test> 93 </test>
43 </tests> 94 </tests>
44 <help><![CDATA[ 95 <help><![CDATA[
45 .. class:: warningmark 96 .. class:: warningmark
46 97
47 '''TIP''' This tool accept as inputs only Galaxy collections containing EAL templates. 98 '''TIP''' This tool accept as inputs only Galaxy collections containing EAL templates in tabular format.
48 99
49 **What it does?** 100 **What it does?**
50 -------------------- 101 --------------------
51 102
52 This tool produce EML metadata from EAL templates. 103 This tool produce EML metadata from EAL templates.
59 110
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 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
61 on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates. 112 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*. 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*.
63 114
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
64 .. class:: infomark 127 .. class:: infomark
65 128
66 Templates can be directly edited in Galaxy (view **eml2eal** tool for more information.) 129 Templates can be directly edited in Galaxy (view **eml2eal** tool for more information.)
67 130
68 131