changeset 0:918940a0944c draft

initial upload of isoplot.xml

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isoplot.xml	Mon Jun 28 11:48:58 2021 +0000
@@ -0,0 +1,134 @@
+<tool id='isoplot' name='Isoplot: Generate plots from isocor output' version='0.1.0'>
+    <requirements>
+        <requirement type='package' version='1.3.0'>isoplot</requirement>
+    </requirements>
+    <command><![CDATA[
+         isoplot '$datafile' 'galaxy' '$format' --value '$value' --template '$template_file'
+#if $SP.generate_barplot:
+    -bp
+#end if
+#if $SP.generate_meanplot:
+    -mb
+#end if
+#if $SP.generate_heatmap:
+    -hm
+#end if
+#if $SP.generate_clustermap:
+    -cm
+#end if
+#if $IP.generate_barplot:
+    -IB
+#end i
+#if $IP.generate_meanplot:
+    -IM
+#end if
+#if $IP.generate_heatmap:
+    -HM
+#end if
+#if $stack:
+    -s
+#end if
+#if $verbosity:
+    -v
+#end if
+#if $annotation:
+    -a
+#end if
+-g -z '$output2' > $output1 2> '$output3'
+    ]]></command>
+    <inputs>
+        <param name='datafile' type='data' format='csv, tsv' multiple='true' label='Upload data file' />
+        <param name='template_file' type='data' format='csv, xlsx' multiple='true' label='Template file' 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' name='generate_barplot' label='Flag to generate barplots' argument='-bp'
+                   optional='true'/>
+            <param type='boolean' name='generate_meanplot' label='Flag to generate meaned barplots' argument='-mb'
+                   optional='true'/>
+            <!--<param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots'
+                   argument='-sa' optional='true'/>/-->
+            <param type='boolean' name='generate_heatmap' label='Flag to generate heatmap' argument='-hm'
+                   optional='true'/>
+            <param type='boolean' name='generate_clustermap' label='Flag to generate clustermap' argument='-cm'
+                   optional='true'/>
+        </section>
+        <section name='IP' title='Select interactive plots to generate'>
+            <param type='boolean' name='generate_barplot' label='Flag to generate barplots' argument='-IB'
+                   optional='true'/>
+            <param type='boolean' name='generate_meanplot' label='Flag to generate meaned barplots' argument='-IM'
+                   optional='true'/>
+           <!-- <param type='boolean' name='generate_areaplot' label='Flag to generate stacked area plots' argument='-IS'
+                   optional='true'/>-->
+            <param type='boolean' name='generate_heatmap' label='Flag to generate heatmap' argument='-HM'
+                   optional='true'/>
+        </section>
+        <param type='boolean' name='stack' label='Flag to unstack bars in barplots' argument='-s' optional='true'/>
+        <param type='boolean' name='verbosity' label='Flag to get debug information' argument='-v' optional='true'/>
+        <param type='boolean' name='annotation' label='Flag to add annotations on the maps' argument='-a'
+               optional='true'/>
+    </inputs>
+    <outputs>
+        <data name='output1' format='csv' label='Formatted data used for plotting' />
+        <data name='output2' format='zip' label='Resulting plots' />
+        <data name='output3' format='txt' label='Run Info' />
+    </outputs>
+    <help><![CDATA[
+
+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_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>
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