diff dimet_differential_analysis.xml @ 2:e45e03a99d56 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f

--- a/dimet_differential_analysis.xml	Tue Jan 23 14:59:08 2024 +0000
+++ b/dimet_differential_analysis.xml	Thu Feb 15 12:53:06 2024 +0000
@@ -13,7 +13,7 @@
     @INIT_DIFF_ANALYSIS@
     @INIT_STAT_TEST@
     @INIT_GROUPS@
-    @INIT_COMPARISONS@
+    @INIT_DIFF_ANALYSIS_COMPARISONS@
     HYDRA_FULL_ERROR=1 python -m dimet
         -cp '$__new_file_path__/config'
         '++hydra.run.dir=differential_analysis'
@@ -43,7 +43,7 @@
          '++analysis.method.impute_values=${impute_values}'
          '++analysis.statistical_test=${statistical_test}'
          '++analysis.dataset.subfolder='
-         '++analysis.dataset.conditions=${conds}'
+         '++analysis.dataset.conditions=${conditions}'
          #if $metadata_path:
              '++analysis.dataset.metadata=metadata'
          #end if
@@ -68,7 +68,7 @@
     ]]></command>
     <inputs>
         <expand macro="input_parameters_diff_analysis"/>
-        <expand macro="conditions"/>
+        <expand macro="factor_list"/>
         <expand macro="timepoint"/>
         <expand macro="correction_method"/>
         <param name="qualityDistanceOverSpan" type="float" min="-1.0" max="-0.1" value="-0.3" label="quality Distance Over Span" help="Default value is -0.3."/>
@@ -85,9 +85,15 @@
             <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/>
             <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
             <param name="correction_method" value="bonferroni"/>
+            <param name="statistical_test_type" value="parametric"/>
             <param name="stat_test" value="Tt"/>
             <param name="qualityDistanceOverSpan" value="-0.3"/>
-            <param name="conditions" value='Control,L-Cycloserine'/>
+            <repeat name="factor_list">
+                <param name="condition" value="Control"/>
+            </repeat>
+            <repeat name="factor_list">
+                <param name="condition" value="L-Cycloserine"/>
+            </repeat>
             <param name="timepoint" value='T0,T2h'/>
              <output_collection name="report" type="list" count="4">
                 <element file="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv"  name="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>
@@ -283,12 +289,17 @@
 
 There exist hints on use that will guide you, next to the parameters.
 
+For more information about the implemented statistical tests, please visit:  https://github.com/cbib/DIMet/wiki/2-Statistical-tests
+
+The output files are explained in https://github.com/cbib/DIMet/wiki/3-Output
+
+
 
 **Available data for testing**
 
-You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent
+You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
 files for you are located in the subfolders inside the data folder).
-You can also use the minimal data examples from https://zenodo.org/record/8380706
+You can also use the minimal data examples from https://zenodo.org/record/10579891
 
  ]]>
     </help>