--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_eml.xml	Tue Sep 10 12:50:00 2024 +0000
@@ -0,0 +1,148 @@
+<tool id="makeeml" name="Make EML" version="0.1.1+galaxy1" profile="22.05">
+    <description> Create EML from EAL templates</description>
+    <requirements>
+        <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    
+    mkdir output_template &&
+    #for $input in $templates
+        ln -s '$input' 'output_template/${input.element_identifier}';
+    #end for
+   
+    #set $table = ""
+    mkdir data_files && 
+    #for $indata in $inputdata
+        ln -s '$indata' 'data_files/${indata.element_identifier}';
+        #set $table += $indata.element_identifier + " ";
+    #end for
+    
+    #set $raster = ""
+    #for $data_raster in $dataraster
+        ln -s '$data_raster' 'data_files/${data_raster.element_identifier}';
+        #set $raster += $data_raster.element_identifier + " ";
+    #end for
+    
+    #set $vector = ""
+    #for $data_vector in $datavector
+        ln -s '$data_vector' 'data_files/${data_vector.element_identifier}';
+        #set $vector += $data_vector.element_identifier + " ";
+    #end for
+    
+    #set $other = ""
+    #for $data_other in $dataother
+        ln -s '$data_other' 'data_files/${data_other.element_identifier}';
+        #set $other += $data_other.element_identifier + " ";
+    #end for
+  
+    #set $quotetable ="" 
+    #for $q in $table_quote 
+       #set $quotetable += $q.quote + ",";
+    #end for 
+
+    
+    Rscript 
+     '$__tool_directory__/make_eml.R' 2> err.txt
+     '$title'
+     '$temporal_coverage.start'
+     '$temporal_coverage.end'
+     '$table'
+     '$raster'
+     '$vector'
+     '$other'
+     '$destable'
+     '$desraster'
+     '$desvector'
+     '$desother'
+     '$quotetable'
+     '$table_url'
+     '$other_url'
+     '$raster_url'
+     '$vector_url'
+		
+    ]]></command>
+    <inputs>
+        <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)."/>
+        <param name="title" type="text" label="Title for your dataset." />
+      <section name="temporal_coverage" title="Temporal coverage" expanded="true">
+	<param name="start" type="text" label="Beginning date of the dataset in the format YYYY-MM-DD" optional="false"/>
+	<param name="end" type="text" label="Ending date of the dataset in the format YYYY-MM-DD" optional="false"/>
+      </section>
+      <section name="data_table" title="Do you have data table ? " >
+        <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"/>
+        <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"/>
+        <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" >
+                <param name="quote" type="select" label="What's the quotes of your data table ?" optional="true">
+                 <option value="quote">Quote</option>
+                 <option value="apostrophe">Apostrophe</option>
+                 <option value="none">None</option>
+                </param>
+        </repeat>
+        <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"/>
+      </section>
+      <section name="data_raster" title="Do you have raster data ? " >
+        <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"/>
+        <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"/>
+        <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"/>
+      </section>
+      <section name="data_vector" title="Do you have vector data ? " >
+        <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"/>
+        <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"/>
+        <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"/>
+      </section>
+      <section name="data_other" title="Do you have other data entity ? " >
+        <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"/>
+        <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"/>
+        <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"/>
+      </section>
+    </inputs>
+    <outputs>
+		 <data name="metadataout" from_work_dir="eml.xml" format="xml" label="EML"/>
+		 <data name="error" from_work_dir="err.txt" format="txt" label="Warning message"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2"> 
+            <param name="templates" value="annotations.txt,keywords.txt,attributes_data_blary_al.txt,catvars_data_blary_al.txt,geographic_coverage.tabular,personnel.txt" >
+            </param>
+            <output name="metadataout" >
+                <assert_contents>
+                    <is_valid_xml />
+                    <xml_element path="./dataset"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+<help><![CDATA[
+
+
+**What it does?**
+--------------------
+
+This tool produce EML metadata from EAL templates.
+This tool can be used in the continuation of the eml2eal tool.
+
+**How to use it?**
+--------------------
+To use this tool, you can select, in your history a data collection with EAL templates or select templates one by one.
+
+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
+on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates.
+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*.
+
+ .. class:: infomark 
+ 
+ Templates can be directly edited in Galaxy (view **eml2eal** tool for more information.)
+ 
+
+
+]]></help>
+<citations>
+       <citation type="bibtex">@Manual{,
+       title = {EMLassemblyline: A tool kit for building EML metadata workflows},
+       author = {Colin Smith},
+       year = {2022},
+       note = {https://github.com/EDIorg/EMLassemblyline,
+       https://ediorg.github.io/EMLassemblyline/},
+       }</citation>
+    </citations>
+</tool>