changeset 5:78f776370dfb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8

--- a/dimet_differential_analysis.xml	Wed Mar 27 16:49:35 2024 +0000
+++ b/dimet_differential_analysis.xml	Tue May 21 13:44:23 2024 +0000
@@ -267,11 +267,11 @@
 
 You can precise how you want your analysis to be executed, with the parameters:
 
-- **conditions**: the conditions present in your data, specifying in first place your CONTROL condition (this ordering is crucial to make the comparisons in a coherent sense).
+- **conditions**: the conditions present in your data, to perform the pairwise comparison.
 
 - **comparisons** : the pairs of [condition, timepoint] groups to compare
 
-- **datatypes** : the measures type(s) that you want to run
+- **datatypes** : the measures type(s) that you want to run (see above in Input data files section)
 
 - **statistical_test** : choose, by type of measure, the specific statistical test to be applied.
 

--- a/macros.xml	Wed Mar 27 16:49:35 2024 +0000
+++ b/macros.xml	Tue May 21 13:44:23 2024 +0000
@@ -1,7 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.2.4</token>
-    <token name="@VERSION_SUFFIX@">1</token>
-    <token name="@EXECUTABLE@">pca</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
@@ -490,7 +489,7 @@
                     </valid>
                 </sanitizer>
             </param>
-            <repeat name="factor_list" title="Conditions" default="2" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). You have to load a metadata file prior to have access to condition list">
+            <repeat name="factor_list" title="Conditions" default="2" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the last specified condition is the reference). You have to load a metadata file prior to have access to condition list">
                 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
                     <options from_dataset="metadata_path">
                         <column name="condition" index="1"/>
@@ -552,7 +551,7 @@
         </repeat>
     </xml>
     <xml name="factor_list">
-        <repeat name="factor_list" title="Conditions" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). You have to load a metadata file prior to have access to condition list">
+        <repeat name="factor_list" title="Conditions" min="2" max="2" help="Specify conditions to be taken into account from metadata file (for each comparison, the last specified condition is the reference). You have to load a metadata file prior to have access to condition list">
             <param name="condition" label="Condition" type="select" optional="false" multiple="false">
                 <options from_dataset="metadata_path">
                     <column name="condition" index="1"/>
@@ -615,6 +614,11 @@
     #if $abundance_file:
         ln -s '$abundance_file' data/abundance.csv &&
     #end if
+    #set $axisx = "condition"
+    #if str( $output_options.bar_color ) == "condition":
+        #set $axisx = "timepoint"
+    #end if
+
     ]]></token>
     <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[