diff generateMFI.xml @ 1:91e856e5ec7a draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generateMFI.xml	Wed Jul 22 15:41:56 2020 -0400
@@ -0,0 +1,69 @@
+<tool id="generate_mfi" name="Generate the centroids" version="1.0+galaxy0" profile="18.01">
+  <description>from a flow result file</description>
+  <requirements>
+    <requirement type="package" version="1.0.5">pandas</requirement>
+    <requirement type="package" version="1.5.1">scipy</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command><![CDATA[
+      python '$__tool_directory__/generateMFI.py' -i '${input}' -o '${output}' -M '${mfi}'
+  ]]>
+  </command>
+  <inputs>
+    <param format="flowclr" name="input" type="data" label="Flow Text file"/>
+    <param name="mfi" type="select" label="Calculate centroids using:">
+      <option value="mfi" selected="true">Mean Fluorescence Intensity</option>
+      <option value="mdfi">Median Fluorescence Intensity</option>
+      <option value="gmfi">Geometric Mean Fluorescence Intensity</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="flowmfi" name="output" label="${mfi} centroids from ${input.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="input.flowclr"/>
+      <param name="mfi" value="mfi"/>
+      <output name="output" file="mfi.flowmfi"/>
+    </test>
+    <test>
+      <param name="input" value="input.flowclr"/>
+      <param name="mfi" value="mdfi"/>
+      <output name="output" file="mdfi.flowmfi"/>
+    </test>
+    <test>
+      <param name="input" value="input.flowclr"/>
+      <param name="mfi" value="gmfi"/>
+      <output name="output" file="gmfi.flowmfi"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool generates the Mean, Median or Geometric Mean Fluorescence Intensity of clustered flow files.
+.. class:: infomark
+Tip: This tool can be used to generate the centroids table required by the visualization tool multiple samples mapping result.
+-----
+**Input file**
+This tool reads in a tab-separated file containing markers fluorescence intensities for each event as well as population or cluster attribution, for instance text output from a FLOCK or FlowSOM run.
+**Output file**
+The output is a table containing the mean, median or geometric mean fluorescent intensity values of each marker within each population or cluster defined in the input file.
+-----
+**Example**
+*Input*::
+   Marker1 Marker2 Marker3 ... Population
+   34      45      12      ... 1
+   13      65      10      ... 5
+   19      62      98      ... 2
+   32      46      10      ... 1
+   ...     ...     ...     ... ...
+*Output*::
+   Population Marker1 Marker2 Marker3 ...
+   1          38      49      10      ...
+   2          21      63      100     ...
+   3          31      52      45      ...
+   4          11      78      25      ...
+   ...        ...     ...     ...     ...
+  ]]>
+  </help>
+</tool>