diff phyloseq_plot_bar.xml @ 6:8a9c340debc8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit a5ae2f86b2955290a4c81ab234f02cc51020f970

--- a/phyloseq_plot_bar.xml	Tue Feb 04 14:39:08 2025 +0000
+++ b/phyloseq_plot_bar.xml	Thu Mar 13 09:49:02 2025 +0000
@@ -10,45 +10,46 @@
 --input '$input'
 --x '$x'
 --fill '$fill'
---facet '${facet}'
+--facet '$facet'
+--topX '$topX'
+'$keepOthers'
+'$keepNonAssigned'
+'$normalize'
+'$normalize_x'
+'$nolines'
+--width '$width'
+--height '$height'
+--device '$device'
 --output '$output'
---topX '${topX}'
---keepOthers '${keepOthers}'
---keepNonAssigned '${keepNonAssigned}'
---normalize '${normalize}'
---width '${width}'
---height '${height}'
---device '${device}'
---nolines '${nolines}'
   ]]></command>
   <inputs>
     <expand macro="phyloseq_input"/>
-    <param name="x" type="text" optional="true" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum). If not specified, the Samples are taken." />
-    <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)." />
+    <param name="x" type="text" optional="true" label="X-axis variable" help="Variable for the x-axis (Metadata columns). If not specified, the Samples are taken." />
+    <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Species). Use 'ASV' as argument to show each OTU/ASV." />
     <param name="facet" type="text" optional="true" label="Facet by variable" help="Variable to facet the chart by (e.g., SampleType)." />
     <param name="topX" value="10" type="integer" optional="true" label="Top X" help="Only show the ranks with the top X abundance." />
-    <param name="keepOthers" type="boolean" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." />
-    <param name="keepNonAssigned" type="boolean" label="Keep Non Assigned" help="Keep OTUs that are not assigned at this rank and label as 'Not Assigned'." />
-    <param name="normalize" type="boolean" label="Normalize" help="Normalize abundances to sum to 100%. Normalization is performed before Top X selection." />
+    <param name="keepOthers" type="boolean" truevalue="--keepOthers" falsevalue="" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." />
+    <param name="keepNonAssigned" type="boolean" truevalue="--keepNonAssigned" falsevalue="" label="Keep 'Not Assigned'" help="Keep OTUs that are not assigned at this rank and label as 'Not Assigned'." />
+    <param name="normalize" type="boolean" truevalue="--normalize" falsevalue="" label="Normalize" help="Normalize abundances to sum to 100%. Normalization is performed before Top X selection." />
+    <param name="normalize_x" type="boolean" truevalue="--normalize_x" falsevalue="" label="Normalize x" help="Normalize abundances of the x group to sum to 100%. Normalization is performed before Top X selection. Ignores facetting!" />
+    <param name="nolines" type="boolean" truevalue="--nolines" falsevalue="" label="Remove Separation Lines" help="Do not add OTU separation lines in the bars." />
     <param name="width" type="float" value="10" optional="true" label="Plot Width" help="Width of the output plot in inches." />
     <param name="height" type="float" value="8" optional="true" label="Plot Height" help="Height of the output plot in inches." />
-    <param name="device" type="select" value="pdf" label="Output Device" help="Device to use for the output file. Options include pdf, png, and others.">
+    <param name="device" type="select" value="pdf" label="Output Device" help="File format to use for the output file. ">
       <option value="pdf">PDF</option>
       <option value="png">PNG</option>
-      <option value="jpeg">JPEG</option>
+      <option value="jpg">JEG</option>
       <option value="tiff">TIFF</option>
     </param>
-    <param name="nolines" type="boolean" label="Remove Separation Lines" help="Do not add separation lines between bars in the chart." />
   </inputs>
   <outputs>
     <data name="output" format="pdf" label="Bar Chart (${device})">
       <change_format>
-        <when format="pdf" value="pdf"/>
-        <when format="png" value="png"/>
-        <when format="jpeg" value="jpeg"/>
-        <when format="tiff" value="tiff"/>
+        <when input="device" format="pdf" value="pdf"/>
+        <when input="device" format="png" value="png"/>
+        <when input="device" format="jpg" value="jpg"/>
+        <when input="device" format="tiff" value="tiff"/>
       </change_format>
-
     </data>
   </outputs>
 
@@ -58,13 +59,8 @@
       <param name="input" value="output.phyloseq" ftype="phyloseq"/>
       <param name="x" value="Property"/>
       <param name="fill" value="Phylum"/>
-      <param name="device" value="pdf"/>
-      <output name="output" ftype="pdf">
-        <assert_contents>
-          <has_text text="%PDF"/>
-          <has_text text="%%EOF"/>
-        </assert_contents>
-      </output>
+      <param name="device" value="png"/>
+      <output name="output" file="expected_output_01.png" ftype="png" compare="image_diff"/>
     </test>
 
     <!-- Test 2: TopX filtering and normalization -->
@@ -72,34 +68,31 @@
       <param name="input" value="output.phyloseq" ftype="phyloseq"/>
       <param name="x" value="Property"/>
       <param name="fill" value="Genus"/>
-      <param name="facet" value="SampleType"/>
+      <param name="facet" value="Number"/>
       <param name="topX" value="10"/>
       <param name="normalize" value="true"/>
-      <output name="output" ftype="pdf">
-        <assert_contents>
-          <has_text text="%PDF"/>
-          <has_text text="%%EOF"/>
-        </assert_contents>
-      </output>
+      <param name="device" value="png"/>
+      <output name="output" file="expected_output_02.png" ftype="png" compare="image_diff"/>
     </test>
 
-    <!-- Test 3: without OTU lines, Others and non assigned -->
-      <test>
+
+    <!-- Test 3: without OTU lines, Others and non assigned --> 
+    <test>
       <param name="input" value="output.phyloseq" ftype="phyloseq"/>
       <param name="x" value="Sample"/>
       <param name="fill" value="Genus"/>
       <param name="facet" value=""/>
       <param name="topX" value="10"/>
       <param name="normalize" value="false"/>
-      <param name="keepOthers" value="false"/>
+      <param name="keepOthers" value="true"/>
       <param name="keepNonAssigned" value="false"/>
       <param name="nolines" value="true"/>
-      <param name="device" value="pdf"/>
-      <output name="output" file="expected_output.pdf" ftype="pdf" compare="sim_size"/>
+      <param name="device" value="png"/>
+      <output name="output" file="expected_output_03.png" ftype="png" compare="image_diff"/>
     </test>
 
-    <!-- Test 4: with normalization, Others and non assigned -->
-      <test>
+    <!-- Test 4: with normalization, Others and non assigned --> 
+    <test>
       <param name="input" value="output.phyloseq" ftype="phyloseq"/>
       <param name="x" value="Sample"/>
       <param name="fill" value="Genus"/>
@@ -109,32 +102,95 @@
       <param name="keepOthers" value="true"/>
       <param name="keepNonAssigned" value="true"/>
       <param name="nolines" value="false"/>
-      <param name="device" value="pdf"/>
-      <output name="output" file="expected_output_normalize.pdf" ftype="pdf" compare="sim_size"/>
+      <param name="device" value="png"/>
+      <output name="output" file="expected_output_04.png" ftype="png" compare="image_diff"/>
     </test>
+
+    <!-- Test 5: with normalization, Others and non assigned, normalization x --> 
+    <test>
+      <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+      <param name="x" value="Property"/>
+      <param name="fill" value="Genus"/>
+      <param name="facet" value=""/>
+      <param name="topX" value="10"/>
+      <param name="normalize" value="true"/>
+      <param name="keepOthers" value="true"/>
+      <param name="keepNonAssigned" value="true"/>
+      <param name="normalize_x" value="true"/>
+      <param name="nolines" value="false"/>
+      <param name="device" value="png"/>
+      <output name="output" file="expected_output_05.png" ftype="png" compare="image_diff"/>
+    </test>
+
+    <!-- Test 6: Minimal -->
+    <test>
+      <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+      <param name="device" value="png"/>
+      <output name="output" file="expected_output_06.png" ftype="png" compare="image_diff"/>
+    </test>
+
   </tests>
 
-  <help>
-    **Description**
+<help>
+<![CDATA[
+**Description**
+
+This tool generates bar charts from a phyloseq object using the 'plot_bar' function in R.
+It allows filtering, normalization, and customization of plots for visualizing microbial community composition.
+
+**Inputs**
+
+- **Input**: A phyloseq object in RDS format.
+
+- **X-axis variable**: The variable to use for the x-axis (Metadata columns).
+
+- **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Species).
 
-    This tool generates bar charts from a phyloseq object using the `plot_bar` function.
+- **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
+
+- **Top X**: Display only the top X most abundant taxa.
+
+- **Keep 'Others'**: Group non-top taxa as 'Others'.
+
+- **Keep 'Not Assigned'**: Retain unassigned taxa labeled as 'Not Assigned'.
 
-    **Inputs**
+- **Normalize**: Normalize abundances to sum to 100%.
+
+- **Remove Separation Lines**: Do not add OTU separation lines in the bars.
+
+- **Width and Height**: Dimensions of the plot in inches (default: 10x8).
+
+- **Device**: Output format (e.g., pdf, png, jpg, tiff).
 
-    - **Input**: A phyloseq object in RDS format.
-    - **X-axis variable**: The variable to use for the x-axis (e.g., Sample, Phylum).
-    - **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Order).
-    - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
-    - **Width and Height**: Dimensions of the plot in inches (default: 10x8).
-    - **Device**: Output format (e.g., pdf, png, jpeg, tiff).
+**Outputs**
+
+- A file containing the bar chart in the specified format.
+
+**Usage Notes**
+
+Ensure that the input file is a valid phyloseq object in RDS format.
+
+**Examples**
+
+- *Basic Bar Plot with Others and Not Assigned and with separation lines*
 
-    **Outputs**
+  .. image:: $PATH_TO_IMAGES/standard_plot.png  
+     :width: 515  
+     :height: 395  
 
-    - A file containing the bar chart in the specified format.
+- *Faceted Plot*
 
-    **Usage Notes**
+  .. image:: $PATH_TO_IMAGES/facet_plot.png  
+     :width: 515  
+     :height: 395  
+
+- *ASV as fill input and removed separation lines*
 
-    Ensure that the input file is a valid phyloseq object in RDS format.
-  </help>
+  .. image:: $PATH_TO_IMAGES/asv_fill_plot.png  
+     :width: 515  
+     :height: 395  
+]]>
+</help>
+
   <expand macro="citations"/>
 </tool>