diff dimet_differential_multigroup_analysis.xml @ 2:b581ea4908ae draft

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

--- a/dimet_differential_multigroup_analysis.xml	Tue Jan 23 14:58:10 2024 +0000
+++ b/dimet_differential_multigroup_analysis.xml	Thu Feb 15 12:55:12 2024 +0000
@@ -11,10 +11,9 @@
     <command detect_errors="exit_code"><![CDATA[
     @INIT_CONFIG@
     @INIT_DIFF_MULTIGROUP_ANALYSIS@
-    @INIT_STAT_TEST@
     @INIT_DATATYPES@
     @INIT_GROUPS@
-    @INIT_CONDITIONS@
+    @INIT_PLOT_CONDITIONS@
     @INIT_TIMEPOINTS@
     @INIT_MULTIGROUP_COMPARISONS@
     HYDRA_FULL_ERROR=1 python -m dimet
@@ -36,16 +35,14 @@
             datatypes:${datatypes_avail}
         }'
         '++analysis.method.datatypes=${datatypes_avail}'
-        '++analysis.method.qualityDistanceOverSpan='${qualityDistanceOverSpan}''
         '++analysis.timepoints=${timepoints}'
         '++analysis.conditions=${comparisons}'
         '++analysis.dataset.label='
-        '++analysis.statistical_test=${statistical_test}'
         '++analysis.method.correction_method=${correction_method}'
         '++analysis.method.impute_values=${impute_values}'
         '++analysis.dataset.subfolder='
         '++analysis.method.grouping=${groups}'
-        '++analysis.dataset.conditions=${conds}'
+        '++analysis.dataset.conditions=${conditions}'
          #if $metadata_path:
              '++analysis.dataset.metadata=metadata'
          #end if
@@ -69,12 +66,11 @@
     @REMOVE_CONFIG@
     ]]></command>
     <inputs>
-        <expand macro="input_parameters_diff_analysis"/>
-        <expand macro="conditions_multigroup"/>
+        <expand macro="input_parameters_multi_diff_analysis"/>
+        <expand macro="plot_factor_list"/>
         <expand macro="timepoint_multigroup"/>
         <expand macro="compartments"/>
         <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."/>
     </inputs>
 
     <outputs>
@@ -87,10 +83,16 @@
             <param name="data_input_selector" value="abundance" />
             <param name="abundance_file" ftype="tabular" value="rawAbundances3.csv"/>
             <param name="metadata_path" ftype="tabular" value="example3_metadata.csv"/>
-            <param name="stat_test" value="Tt"/>
             <param name="correction_method" value="bonferroni"/>
-            <param name="qualityDistanceOverSpan" value="-0.3"/>
-            <param name="conditions" value="Control,Cond1,Cond2"/>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="Control"/>
+            </repeat>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="Cond1"/>
+            </repeat>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="Cond2"/>
+            </repeat>
             <param name="timepoint" value="T0h,T2h"/>
             <param name="compartments" value="cell"/>
 
@@ -104,7 +106,7 @@
 
     **Input data files**
 
-This tool computes the Kruskall Wallis test over 3 or more groups,
+This tool computes the Kruskal-Wallis test over 3 or more groups,
 to evaluate if at least one group is significantly different to the other groups (H0: median of all of the groups is equal). For illustration see the section **Metadata File Information** which contains three conditions: Control, Core_mass and Edge_tissue, across one single time point, thus 3 groups (number-of-groups-in-my-data = number-of-conditions x number-of-timepoints)).
 
 This tool requires (at max.) 5 tab-delimited .csv files as inputs. There are two types of files:
@@ -247,11 +249,15 @@
 
 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>