Mercurial > repos > iuc > dimet_abundance_plot

changeset 5:279ce0d93d53 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
author iuc
date Tue, 21 May 2024 13:45:48 +0000
parents 5e379358c023
children db1e58e44a5c
files dimet_abundance_plot.xml macros.xml
diffstat 2 files changed, 16 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/dimet_abundance_plot.xml	Wed Mar 27 16:52:31 2024 +0000
+++ b/dimet_abundance_plot.xml	Tue May 21 13:45:48 2024 +0000
@@ -29,8 +29,8 @@
                 _target_: dimet.method.AbundancePlotConfig,
                 label: abundance_plot,
                 name: "Generate abundance plots",
-                barcolor: timepoint,
-                axisx: condition,
+                barcolor: '${output_options.bar_color}',
+                axisx: ${axisx},
                 axisx_labeltilt: '${output_options.axisx_labeltilt}',
                 height_each_subfig: '${output_options.height_each_subfig}',
                 palette:${output_options.palette},
@@ -66,6 +66,10 @@
                 <option value="pdf">Pdf</option>
                 <option value="svg">Svg</option>
             </param>
+            <param name="bar_color" type="select" value="timepoint" display="radio" label="Select output figure barcolor" help="Please enter at max 1 format">
+                    <option value="timepoint">timepoint</option>
+                    <option value="condition">condition</option>
+            </param>
             <param name="axisx_labeltilt" type="integer" min="0" max="180" value="70" label="X axis label tilt"
                    help="Default value is 70."/>
             <param name="width_each_subfig" type="float" min="1.0" max="15.0" value="3.0" label="width of subfig plots"
@@ -76,7 +80,6 @@
                    help="Default value is false."/>
             <param name="do_stripplot" type="boolean" value="false" label="add strip plot on abundance bar"
                    help="Default value is false."/>
-
         </section>
     </inputs>
     <outputs>
@@ -96,6 +99,8 @@
             <param name="metabolites_list" value="Fru1P"/>
             <section name="output_options">
                 <param name="axisx_labeltilt" value="70"/>
+                <param name="bar_color" value="timepoint"/>
+                <param name="axisx" value="condition"/>
                 <param name="palette" value="pastel"/>
                 <param name="width_each_subfig" value="3.0"/>
                 <param name="height_each_subfig" value="5.5"/>
--- a/macros.xml	Wed Mar 27 16:52:31 2024 +0000
+++ b/macros.xml	Tue May 21 13:45:48 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[