--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metacyto_checkpanel.xml	Tue Jul 27 21:47:56 2021 +0000
@@ -0,0 +1,81 @@
+<tool id="metacyto_checkpanel" name="Check markers in analysis panels" version="1.0+galaxy0" profile="18.01">
+  <description>for MetaCyto</description>
+  <requirements>
+    <requirement type="package" version="1.4.0">bioconductor-metacyto</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:9" />
+    <exit_code range="10" level="fatal" description="The input file cannot be used. Please check input format." />
+    <exit_code range="11:" />
+  </stdio>
+  <command><![CDATA[
+    Rscript --slave --vanilla '$__tool_directory__/metacyto_checkpanel.R' '${input_file}' '${output_file}';
+    #if $graph=="TRUE"
+      mv panel_summary.pdf '${pdf_out}'
+    #end if
+  ]]>
+  </command>
+  <inputs>
+    <param format="metacyto_summary.txt" name="input_file" type="data" label="MetaCyto preprocessing summary"/>
+    <param name="graph" type="boolean" label="Output visual summary?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output_file" label="Panel Summary of ${input_file.name}"/>
+    <data format="pdf" name="pdf_out" label="Visual Panel Summary of ${input_file.name}">
+      <filter>(graph)</filter>
+    </data>
+  </outputs>
+  <tests>
+      <test>
+        <param name="input_file" value="mc_preprocesss_summary.metacyto_summary.txt"/>
+        <param name="graph" value="True"/>
+        <output name="output_file" ftype="tabular">
+          <assert_contents>
+            <has_n_columns n="3" />
+            <has_text text="CD95" />
+            <has_n_lines n="14" />
+          </assert_contents>
+        </output>
+        <output name="pdf_out" ftype="pdf">
+          <assert_contents>
+            <has_size value="4569" delta="500" />
+          </assert_contents>
+        </output>
+      </test>
+  </tests>
+  <help><![CDATA[
+    Metacyto Check Markers in analysis panels
+    -----------------------------------------
+
+    This tool uses MetaCyto's panel summary function to compare marker names between groups of FCS files.
+
+    **Input**
+    This tool requires the MetaCyto pre-processing Summary as input.
+
+    **Output**
+    This tool generates a table and an optional visual representation in PDF of how markers are distributed in the FCS file sets.
+
+
+    **Example**
+
+    *Input* - Summary Table::
+
+       study_id antibodies                  filenames
+       group1   Marker1|Marker2|Marker3|... file1.fcs
+       group2   Marker1|Marker2|Marker3|... file2.fcs
+       ...      ...                         ...
+
+    *Output* - Panel Summary::
+
+       Markers group1 group2 ...
+       Marker1 1      1      ...
+       Marker2 1      1      ...
+       Marker3 0      1      ...
+       ...     ...    ...    ...
+
+    *Graphical output*
+
+    .. image:: ./images/checkpanel.png
+  ]]>
+  </help>
+</tool>