diff getDensityPlots_text.xml @ 1:754d511df1a3 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowtext_scatterplot commit 2944aa6b74efcdb8d5cbf31abf27b352dcad9ac9"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getDensityPlots_text.xml	Tue Jul 14 09:40:13 2020 -0400
@@ -0,0 +1,83 @@
+<tool id="gen_density_plots_txt" name="Generate scatter plots" version="1.1+galaxy0" profile="18.01">
+  <description>for any given markers in a txt-converted FCS file</description>
+  <requirements>
+    <requirement type="package" version="3.3.2">r-ggplot2</requirement>
+    <requirement type="package" version="2.23_17">r-kernsmooth</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:9" level="fatal" />
+    <exit_code range="10" level="fatal" description="Please provide a comma separated list of channels to plot" />
+    <exit_code range="11" level="fatal" description="Please provide numeric values for the list of channels to plot" />
+    <exit_code range="12" level="fatal" description="Please provide more than one channel to plot" />
+    <exit_code range="13:" level="fatal"/>
+  </stdio>
+  <command><![CDATA[
+      Rscript $__tool_directory__/getDensityPlots_text.R '${input}' '${channels}' '${output}' '${outformat}'
+  ]]>
+  </command>
+  <inputs>
+    <param format="flowtext" name="input" type="data" label="txt-converted FCS file"/>
+    <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot FSC vs SSC if the channels are found."/>
+    <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load.">
+      <option value="PNG">PNG</option>
+      <option value="PDF">PDF</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="png" name="output" label="Scatter Plots of ${channels} from ${input.name} in ${outformat}">
+      <change_format>
+        <when input="outformat" value="PDF" format="pdf" />
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="input.flowtext"/>
+      <param name="channels" value="i.e.:1,3,4"/>
+      <param name="outformat" value="PDF"/>
+      <output name="output" file="graph.pdf" compare="sim_size" delta="2000000"/>
+    </test>
+    <test>
+      <param name="input" value="input.flowtext"/>
+      <param name="channels" value="1,3,5"/>
+      <param name="outformat" value="PNG"/>
+      <output name="output" file="graph2.png" compare="sim_size" delta="1000000"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool allows generation of density scatter plots using ggplot2.
+
+-----
+
+**Input files**
+
+This tool takes txt-converted FCS files as input.
+
+**Output files**
+
+This tool generates a scatter plot for each marker combination in a single png file. A pdf file can optionally be generated.
+
+class:: warningmark
+
+PDF are larger files that may take some time to load. It might be faster to download the PDF output once generated to open it locally.
+
+-----
+
+**Example**
+
+*Output*:
+
+.. image:: ./static/images/flowtools/flowtextgraph.png
+  ]]>
+  </help>
+  <citations>
+    <citation type="bibtex">@BOOK{,
+      author = {Hadley Wickham},
+      title = {ggplot2: Elegant Graphics for Data Analysis},
+      publisher = {Springer-Verlag New York},
+      year = {2009},
+      isbn = {978-0-387-98140-6},
+      url = {http://ggplot2.org},
+   }</citation>
+  </citations>
+</tool>