diff getDensityPlots.xml @ 1:413f3e610295 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_scatterplot commit 82365bd2b90a783f84f497afbb29b435cd25cf9d"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getDensityPlots.xml	Thu Jul 16 08:00:52 2020 -0400
@@ -0,0 +1,76 @@
+<tool id="gen_density_plots" name="Generate scatter plots" version="1.0+galaxy0">
+  <description>for any given markers in FCS file</description>
+  <requirements>
+    <requirement type="package" version="1.10.0">bioconductor-flowdensity</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 --slave --vanilla '$__tool_directory__/getDensityPlots.R' '${input}' '${channels}' '${output}' '${outformat}'
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs" name="input" type="data" label="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="testfcs1.fcs"/>
+      <param name="channels" value="1,3"/>
+      <param name="outformat" value="PDF"/>
+      <output name="output" file="graph.pdf" compare="sim_size" delta="1000000"/>
+    </test>
+    <test>
+      <param name="input" value="testfcs1.fcs"/>
+      <param name="channels" value="i.e.:1,3,4"/>
+      <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 flowDensity.
+
+-----
+
+**Input files**
+
+This tool takes valid 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/densityplots.png
+  ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btu677</citation>
+    <citation type="doi">10.1186/1471-2105-10-106</citation>
+  </citations>
+</tool>