diff entities_template.xml @ 0:5bfceb4ef59b draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/entities_template.xml	Sat Dec 23 20:40:51 2023 +0000
@@ -0,0 +1,66 @@
+<tool id="entities_template" name="Make entities templates for raster, vector and other entities files" version="0.1.1+galaxy0" profile="22.05">
+    <description>for EML metadata creation</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 += $indata.element_identifier + " ";
+    #end for
+    
+    Rscript 
+         '$__tool_directory__/entities_templates.R'
+         '$table'
+         
+    ]]></command>
+    <inputs>
+         <param name="templates" type="data_collection"  collection_type="list" label="Upload EAL attributes templates (with if exist catvars and custom units files)" help= "Input a data collection" />
+         <param name="inputdata" type="data_collection"  collection_type="list"  label="Upload all data files wich are raster and/or vector and/or other entities files" help= "Input a data collection."/>
+    </inputs>
+    <outputs>
+       <data name="output" from_work_dir="output_template/entities.txt" format="txt" label="entities.txt"/>
+    </outputs>
+    <tests>
+        <test>
+           <param name="templates">
+              <collection type="list">
+                 <element name="attributes_data_7.txt" value="attributes_data_7.txt" />
+                 <element name="catvars_data_7.txt" value="catvars_data_7.txt" />
+                 <element name="custom_units.txt" value="custom_units.txt" />
+              </collection>
+           </param>
+           <param name="inputdata">
+              <collection type="list">
+                 <element name="data_7.GeoJSON" value="data_7.GeoJSON" />
+              </collection>
+           </param>          
+           <output name="output" value="entities.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    
+**What it does?**
+--------------------
+
+This tool is used to produce EAL templates call entities for raster, vector and other entities files used to build EML metadata. It produces the following eal files: 
+
+- entities.txt (it describe some variables)
+
+After that, this file can be edited to add information about your data and then be used in the make eml tool to produce EML metadata.   
+
+**How to use it?**
+--------------------
+To use this tool, you need to select, in your history a data collection with all your EAL attributes templates (with if exist catvars and custom units files). 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*.
+You need also to input all your data files Upload all data files wich are raster and/or vector and/or other entities files.
+    ]]></help>
+</tool>
+