diff gaiac_boxplot/gaiac_boxplot.xml @ 0:0763bb545f98 draft

planemo upload for repository https://github.com/jaidevjoshi83/gaiac.git commit c29a769ed165f313a6410925be24f776652a9663-dirty

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+++ b/gaiac_boxplot/gaiac_boxplot.xml	Thu May 15 14:44:13 2025 +0000
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+<tool id="gaiac_box_plot" name="GAIAC Box Plot" version="0.1.0" python_template_version="3.10" >
+  <description>Generates box plots for numerical data columns in a dataset</description>
+  <requirements>
+    <requirement type="package" version="2.2.3">pandas</requirement>
+    <requirement type="package" version="3.10.0">matplotlib</requirement>
+    <requirement type="package" version="0.13.2">seaborn</requirement>
+  </requirements>
+
+  <stdio>
+    <exit_code range="1" level="fatal" />
+  </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/boxplot.py' --infile '$infile' -C '$clm_list_y' -H  '$fig_height' -W '$fig_width' -T '$plottitile' -O 'out.png' --ylab '$clm_lab_y' --xlab '$clm_lab_x'
+
+            #if $Sel_x_tick_labels.Plot == 'advance'
+                --custom_xtick_name  '$Sel_x_tick_labels.label'
+            #end if          
+    ]]></command>
+
+  <inputs> 
+    <param name="infile" type="data" format="tabular" label="Input file" />
+    <param name="plottitile" type="text" value="Box Plot" label="Plot title" />
+    <param name="fig_height" type="text" value="3" label="Figure Height" />
+    <param name="fig_width" type="text" value="5" label="Figure Width" />
+    <param name="clm_lab_y" type="text" value="" size="30" label="Label for y axis"/>
+    <param name="clm_lab_x" type="text" value="" size="30" label="Label for x axis"/>
+    <param name="clm_list_y" label="Select columns for y axis" type="data_column" data_ref="infile" numerical="True" multiple="true" use_header_names="true">
+        <validator type="no_options" message="Please select atleast one column."/>
+    </param>
+   
+    <conditional name='Sel_x_tick_labels' >
+      <param name="Plot" type="select" label="label for legend" argument="" help="Data plotting method">
+        <option value="advance" > Advance option for custom labels for X tick labels</option>
+        <option value="default" selected="true"> Default labels</option>
+      </param>
+
+      <when value="advance">
+          <param name="label" type="text" value="" label="label for X tick as text" help="A list that gives custom labels for legends as comma seperated text"/>
+      </when>
+
+      <when value="default">
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name='output1' format='png' label="Output" from_work_dir="out.png" ></data>
+  </outputs>
+  
+  <tests>
+   <test>
+    <!-- Input file and plot parameters -->
+    <param name="infile" value="test.tsv"/>
+    <param name="plottitile" value="Box Plot"/>
+    <param name="fig_height" value="5"/>
+    <param name="fig_width" value="7"/>
+    <param name="clm_lab_y" value="Values"/>
+    <param name="clm_lab_x" value="Categories"/>
+    <!-- Select the column for the Y axis -->
+    <param name="clm_list_y" value="1"/>
+    <!-- Use default for custom X tick labels -->
+    <param name="Sel_x_tick_labels|Plot" value="default"/>
+    <!-- Output file -->
+    <output name="output1" file="out.png" />
+   </test>
+  </tests>
+
+  <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+This tool generates boxplot for the selected columns (parameters) from the dataset 
+
+-----
+
+**Inputs**
+    Boxplot    
+       * **--infile** Input files
+       * **--column_list_y** List of columns 
+       * **--custom_xtick_name**  xtick label
+       * **--output** Output file
+       * **--title**  Figure title 
+       * **--height**  Figure height
+       * **--width** Figure width
+       * **--ylab** Y labels
+       * **--xlab** X labels 
+       
+-----
+
+
+**Outputs**
+    * Returns png file with the boxplot]]></help>
+
+<citations>
+  <citation type="bibtex">
+
+
+    @article{dubey2022,
+   title={AirPiuG-Galaxy software platform based open-source GUI tools for data collection and analysis from low cost air pollution sensors},
+   author={Dubey, R and Joshi, J and Patra, A and Blankenberg, D},
+   journal={GitHub repository},
+   url = {https://github.com/ravishdubey/OPCN3API},
+   year={2022},
+   publisher={GitHub}
+   }
+
+  </citation>
+
+</citations>
+</tool>
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