diff isoplot.xml @ 0:8b54f922377a draft

"planemo upload for repository https://github.com/llegregam/Isoplot/tree/main commit 091a7a9b697ca1638cdc3fc13003f0cb4430e06e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isoplot.xml	Fri Sep 03 08:01:12 2021 +0000
@@ -0,0 +1,138 @@
+<tool id='isoplot' name='Isoplot: Generate plots from isocor output' version='1.3.0+galaxy0' profile='20.01'>
+    <requirements>
+        <requirement type='package' version='1.3.0'>isoplot</requirement>
+    </requirements>
+    <command><![CDATA[
+         isoplot '$datafile' 'galaxy' '$format' --value '$value' --template '$template_file' $SP.barplot $SP.meaned_barplot 
+         $SP.static_heatmap $SP.static_clustermap $IP.interactive_barplot $IP.interactive_meanplot $IP.interactive_heatmap
+#if $unstack:
+    -s
+#end if
+#if $verbosity:
+    -v
+#end if
+#if $annotation:
+    -a
+#end if
+-g -z '$plots_output' > $data_output 2> '$log_output'
+    ]]></command>
+    <inputs>
+        <param name='datafile' type='data' format='csv, tabular' multiple='true' label='Upload data that has been corrected by Isocor (.tsv format)' />
+        <param name='template_file' type='data' format='csv, xlsx' multiple='true' label='Upload template file containing plot metadata (.xlsx format)' argument='--template'/>
+        <!--param name='run_name' type='text' label='Run name' /-->
+        <param name='format' type='select' label='Plot format'>
+            <option value='pdf'>pdf</option>
+            <option value='jpeg'>jpeg</option>
+            <option value='png'>png</option>
+            <option value='svg'>svg</option>
+            <option value='html'>html</option>
+        </param>
+        <param name='value' type='select' label='Data to plot' >
+            <option value='corrected_area'>Corrected Area</option>
+            <option value='isotopologue_fraction'>Isotopologue Fraction</option>
+            <option value='mean_enrichment'>Mean Enrichment</option>
+        </param>
+        <section name='SP' title='Select static plots to generate'>
+            <param type='boolean' argument='--barplot' label='Flag to generate barplots' truevalue='-bp' falsevalue=''/>
+            <param type='boolean' argument='--meaned_barplot' label='Flag to generate meaned barplots' truevalue='-mb' falsevalue=''/>
+            <!--<param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots'
+                   argument='-sa' optional='true'/>/-->
+            <param type='boolean' argument='--static_heatmap' label='Flag to generate heatmap' truevalue='-hm' falsevalue=''/>
+            <param type='boolean' argument='--static_clustermap' label='Flag to generate clustermap' truevalue='-cm' falsevalue=''/>
+        </section>
+        <section name='IP' title='Select interactive plots to generate'>
+            <param type='boolean' argument='--interactive_barplot' label='Flag to generate barplots' truevalue='-IB' falsevalue=''/>
+            <param type='boolean' argument='--interactive_meanplot' label='Flag to generate meaned barplots' truevalue='-IM' falsevalue=''/>
+           <!-- <param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots' argument='-IS'
+                   optional='true'/>-->
+            <param type='boolean' argument='--interactive_heatmap' label='Flag to generate heatmap' truevalue='-HM' falsevalue=''/>
+        </section>
+        <param type='boolean' name='unstack' label='Flag to unstack bars in barplots' truevalue='-s' falsevalue=''/>
+        <param type='boolean' name='verbosity' label='Flag to get debug information' truevalue='-v' falsevalue=''/>
+        <param type='boolean' name='annotation' label='Flag to add annotations on the maps' truevalue='-a' falsevalue=''/>
+    </inputs>
+    
+    <outputs>
+        <data name='data_output' format='csv' label='Formatted data used for plotting' />
+        <data name='plots_output' format='zip' label='Resulting plots' />
+        <data name='log_output' format='txt' label='Run Info' />
+    </outputs>
+    
+    <tests>
+        <test>
+    	  <param name='datafile' value='input_data.csv' />
+    	  <param name='template_file' value='input_template.xlsx'/>
+    	  <param name='format' value='pdf' />
+    	  <param name='value' value='isotopologue_fraction' />
+    	  <section name='SP' >
+    	   <param name='barplot' value='true' />
+    	  </section>
+    	  <section name='IP' >
+    	   <param name='interactive_barplot' value='true' />
+    	  </section>
+          <output name='data_output' file='data_out.csv'/>
+          <output name='plots_output'>
+            <assert_contents>
+                <has_size value='2852573' delta='1000' />
+            </assert_contents>
+            </output>
+    	  <output name='log_output'>
+            <assert_contents>
+                <has_text text='- isoplot_log.main.cli_process - INFO - Plots created. Run is terminated' />
+            </assert_contents>
+          </output>
+        </test>
+    </tests>  
+    
+    <help><![CDATA[
+
+.. class:: warningmark
+
+ We strongly encourage you to read the `documentation <https://isoplot.readthedocs.io/en/latest/>`_ before using Isoplot.
+
+Isoplot2: Plotting isotopic labelling MS data
+=============================================
+
+**Positional arguments:**
+
+  input_path		Path to datafile
+  run_name              Name of the current run
+  format                Format of generated file
+
+**optional arguments:**
+  -h, --help            show this help message and exit
+  --value		Choices: "corrected_area", "isotopologue_fraction", "mean_enrichment". Select values to plot. This option can be given multiple times
+
+  -m METABOLITE         Metabolite(s) to plot. For all, type in 'all'                        
+  -c CONDITION          Condition(s) to plot. For all, type in 'all'
+  -t TIME               Time(s) to plot. For all, type in 'all'
+  -tp, --template TEMPLATE_PATH     Path to template file
+
+  -sa, --stacked_areaplot  Create static stacked areaplot
+  -bp, --barplot           Create static barplot
+  -mb, --meaned_barplot    Create static barplot with meaned replicates
+
+  -IB, --interactive_barplot		Create interactive stacked barplot
+  -IM, --interactive_stacked_meanplot		Create interactive stacked barplot with meaned replicates
+  -IS, --interactive_areaplot		Create interactive stacked areaplot
+  -hm, --static_heatmap		Create a static heatmap using mean enrichment data
+  -cm, --static_clustermap		Create a static heatmap with clustering using mean enrichment data
+  -HM, --interactive_heatmap		Create interactive heatmap using mean enrichment data
+
+  -s, --stack           Add option if barplots should be unstacked
+  -v, --verbose         Turns logger to debug mode
+  -a, --annot           Add option if annotations should be added on maps
+
+    ]]></help>
+    <citations>
+        <citation type='bibtex'>
+    @misc{githubisoplot,
+      author = {Le Gregam, Loic},
+      year = {2021},
+      title = {isoplot},
+      publisher = {GitHub},
+      journal = {GitHub repository},
+      url = {https://github.com/llegregam},
+    }</citation>
+        </citations>
+    </tool>