diff PAMPA_GLM_SP.xml @ 2:6c14021f678e draft

"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"

--- a/PAMPA_GLM_SP.xml	Mon Jul 27 09:55:27 2020 -0400
+++ b/PAMPA_GLM_SP.xml	Sun Nov 22 18:40:40 2020 +0000
@@ -15,15 +15,20 @@
          'species.code'
          #if $settings.advanced=='advanced' 
              $settings.distrib
-             'FALSE'
+             $settings.rdata
          #else
              'None'
-             'FALSE'
+             'false'
          #end if
          'unitSp'
          '$__tool_directory__/FunctPAMPAGalaxy.r' 
          '$output_summary'
          '$output_recap'
+         #if $settings.advanced=='advanced'
+             #if $settings.rdata=='true'
+                 '$output_GLM'
+             #end if
+         #end if
     ]]>
     </command>
     <inputs>
@@ -34,18 +39,19 @@
         </conditional>
     </inputs>
     <outputs>
-
         <data name="output_summary" from_work_dir="GLMSummary.tabular" format="tabular" label="GLM - Results from your population analysis on ${on_string}"/>
         <expand macro="pampa_output_GLM"/>
     </outputs>
     <tests>
-        <test> 
+        <test expect_num_outputs="4"> 
             <param name="input_metric" value="Presence_absence_table_sansszcl_cropped.tabular"/>
             <param name="input_unitobs" value="Unitobs.tabular"/>
             <param name="varint" value="4"/>
             <param name="varrep" value="year,site,habitat"/>
             <param name="varrand" value="site"/>
-            <param name="advanced" value="simple"/>
+            <param name="advanced" value="advanced"/>
+            <param name="distrib" value="None"/>
+            <param name="rdata" value="true"/>
             <output name="output_summary">
                 <assert_contents> 
                     <has_n_lines n="4"/>
@@ -53,14 +59,31 @@
             </output>
             <output name="output_recap">  
                 <assert_contents> 
-                    <has_n_lines n="607"/>
+                    <has_n_lines n="606"/>
                 </assert_contents> 
             </output>     
             <output name="output_rate">
                 <assert_contents> 
-                    <has_n_lines n="46"/>
+                    <has_n_lines n="45"/>
                 </assert_contents> 
             </output>
+            <output_collection name="output_GLM"  type="list" count="3">
+                <element name="GLM_Abalstel" ftype="Rdata">
+                    <assert_contents> 
+                        <has_size value="199219" delta="10000"/>
+                    </assert_contents> 
+                </element>
+                <element name="GLM_Hemifasc" ftype="Rdata">
+                    <assert_contents> 
+                        <has_size value="202264" delta="10000"/>
+                    </assert_contents> 
+                </element>
+                <element name="GLM_Zebrscop" ftype="Rdata">
+                    <assert_contents> 
+                        <has_size value="207311" delta="10000"/>
+                    </assert_contents> 
+                </element>
+            </output_collection>
         </test>
     </tests>
     <edam_topics>
@@ -126,6 +149,8 @@
 |              ...               |      ...     |   ...   |   ...  |     ...    | ... |       
 +--------------------------------+--------------+---------+--------+------------+-----+ 
 
+The site may represent the same entity as the location or represent an aggregation of several locations.
+
 |
 
 **Output**