diff dimet_enrichment_plot.xml @ 2:2de209fb390b draft

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

--- a/dimet_enrichment_plot.xml	Tue Jan 23 14:55:42 2024 +0000
+++ b/dimet_enrichment_plot.xml	Thu Feb 15 12:52:26 2024 +0000
@@ -11,7 +11,7 @@
     <command detect_errors="exit_code"><![CDATA[
     @INIT_CONFIG@
     @INIT_ENRICHMENT_PLOT@
-    @INIT_CONDITIONS@
+    @INIT_PLOT_CONDITIONS@
     @INIT_TIMEPOINTS@
     @INIT_ENRICHMENT_METABOLITES@
     HYDRA_FULL_ERROR=1 python -m dimet
@@ -29,7 +29,7 @@
                 _target_: dimet.method.MeanEnrichmentLinePlotConfig,
                 label: mean_enrichment_line_plot,
                 name: "Generate mean enrichment line plots",
-                palette_condition: muted,
+                palette_condition: ${output_options.palette},
                 palette_metabolite: auto_multi_color,
                 xaxis_title: ${output_options.xaxis_title},
                 alpha: ${output_options.alpha},
@@ -45,7 +45,7 @@
         '++analysis.dataset.label='
         '++analysis.timepoints=${timepoints}'
         '++analysis.dataset.subfolder='
-        '++analysis.dataset.conditions=${conds}'
+        '++analysis.dataset.conditions=${conditions}'
 
         #if $metadata_path:
              '++analysis.dataset.metadata=metadata'
@@ -57,7 +57,7 @@
     ]]></command>
     <inputs>
         <expand macro="input_parameters_enrichment"/>
-        <expand macro="conditions"/>
+        <expand macro="plot_factor_list"/>
         <expand macro="timepoint"/>
         <expand macro="compartments_enrichment"/>
         <expand macro="enrichment_metabolites_list"/>
@@ -66,6 +66,7 @@
                 <option value="pdf">Pdf</option>
                 <option value="svg">Svg</option>
             </param>
+            <expand macro="palette"/>
             <param name="color_lines_by" type="select" value="condition" display="radio" label="Select color for lines" help="Please enter at max 1 format">
                 <option value="condition">Condition</option>
                 <option value="metabolite">Metabolite</option>
@@ -97,7 +98,12 @@
         <test>
             <param name="me_or_frac_contrib_file" ftype="tabular" value="FracContribution_C.csv"/>
             <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
-            <param name="conditions" value='Control,L-Cycloserine'/>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="Control"/>
+            </repeat>
+            <repeat name="plot_factor_list">
+                <param name="condition" value="L-Cycloserine"/>
+            </repeat>
             <param name="timepoint" value='T0,T2h'/>
             <param name="compartments" value='cell,med'/>
             <param name="metabolites_list" value="Fumaric_acid,Glycine,L-Proline"/>
@@ -229,9 +235,9 @@
 
 **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>