--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getFCSheaders.xml	Thu Jul 23 08:14:29 2020 -0400
@@ -0,0 +1,72 @@
+<tool id="get_fcs_headers" name="Get list of markers" version="2.0+galaxy0">
+  <description>in FCS files.</description>
+  <requirements>
+    <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="10" level="warning" description="Not all files are valid FCS files, see output for details." />
+  </stdio>
+  <command><![CDATA[
+         Rscript '$__tool_directory__/getFCSheader.R' '${output_file}'
+    #for $f in $input
+ 	'${f}' '${f.name}'
+    #end for
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/>
+  </inputs>
+  <outputs>
+      <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input">
+        <collection type="list">
+          <element name="input1.fcs" value="input1.fcs"/>
+          <element name="input2.fcs" value="input2.fcs"/>
+          <element name="input3.fcs" value="input3.fcs"/>
+        </collection>
+      </param>
+      <output name="output_file" file="output.tabular" lines_diff="8"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+  This tool returns a table of the headers of a set of FCS files.
+
+-----
+
+**Input files**
+
+This tool requires collections of FCS files as input.
+
+**Output file**
+
+The output file is a table listing the markers and channels for each file.
+
+-----
+
+**Example**
+
+*File1*::
+
+   Marker1 Marker2 Marker3
+   34      45      12
+   33      65      10
+
+*File2*::
+
+   Marker4 Marker5 Marker3
+   19      62      98
+   12      36      58
+
+*Output*::
+
+   Filename Index    1        2        3
+   File1 channels Channel1 Channel2 Channel3
+   File2 channels Channel4 Channel5 Channel3
+   File1 markers  Marker1  Marker2  Marker3
+   File2 markers  Marker4  Marker5  Marker3
+ ]]>
+  </help>
+</tool>