--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/editFCSmarkers.xml	Mon Jun 22 20:07:30 2020 -0400
@@ -0,0 +1,119 @@
+<tool id="edit_fcs_markers" name="Edit markers or channels" version="1.0">
+  <description>in FCS files</description>
+  <requirements>
+    <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="10" level="fatal" description="Please provide a valid FCS file." />
+    <exit_code range="11" level="fatal" description="Please provide a comma separated list of integers for markers/channels you want to rename." />
+    <exit_code range="12" level="fatal" description="Please provide a comma separated list of names for markers/channels you want to rename." />
+    <exit_code range="13" level="fatal" description="List of marker indices and marker names must match. For instance, indices 1,3,4 and Marker4,Marker6,Marker8." />
+    <exit_code range="14" level="fatal" description="Provided indices are out of range in the FCS file given as input." />
+  </stdio>
+  <command><![CDATA[
+    Rscript --slave --vanilla '$__tool_directory__/editFCSmarkers.R' '${input}' '${output_file}' '${outformat}' '${report}' '${columns}' '${colnames}' '${corm}'
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs" name="input" type="data" label="Text file"/>
+    <param name="columns" type="text" label="Channels or markers to modify" help="These are comma separated (ie.: 'ColX,ColY'). The column names provided need to exist in the flowFrame / FCS file provided as input. If you're not sure, check your markers with the list of markers tool in the FCS File Tools section."/>
+    <param name="colnames" type="text" label="New column headings" help="New names for the column headers, a comma separated list of the same lenght as 'Channels or markers to modify' (i.e.: 'Marker1,Marker6,Marker4'). Check below for more details.">
+    </param>
+    <param name="corm" type="select" label="Modify Channels or Markers?" help="If you are not sure which to modify, check with the list of marker tools in the FCS File Tools section.">
+      <option value="M">Markers</option>
+      <option value="C">Channels</option>
+    </param>
+    <param name="outformat" type="select" label="Output Format">
+      <option value="flowFrame">R Data, flowFrame</option>
+      <option value="FCS">FCS 3.0</option>
+    </param>
+</inputs>
+  <outputs>
+    <data format="txt" name="report" label="Editing Report of FCS markers from ${input.name}"/>
+    <data format="flowframe" name="output_file" label="Edited FCS from ${input.name} in ${outformat}">
+      <change_format>
+        <when input="outformat" value="FCS" format="fcs" />
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="input.fcs"/>
+      <param name="columns" value="Forward Scatter,Side Scatter,APC CD45RA"/>
+      <param name="colnames" value="m1,m2,m3"/>
+      <param name="corm" value="M"/>
+      <param name="outformat" value="flowFrame"/>
+      <output name="report" value="report1.txt"/>
+      <output name="output_file" file="output.flowframe" compare="sim_size" delta="500000"/>
+    </test>
+    <test>
+      <param name="input" value="input.fcs"/>
+      <param name="columns" value="FSC-H,SSC-H,FL4-H"/>
+      <param name="colnames" value="m1,m2,m3"/>
+      <param name="corm" value="C"/>
+      <param name="outformat" value="FCS"/>
+      <output name="report" value="report2.txt"/>
+      <output name="output_file" file="output.fcs" compare="sim_size" delta="500000"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool enables editing FCS markers or channels.
+
+-----
+
+**Input files**
+
+This tool requires FCS files as input.
+
+**Column names**
+
+Please indicate the names of the markers / channels to edit (comma-separated list).
+
+.. class:: infomark
+
+Tip: One of the tools in the FCS File Tools section can help check the markers and channels indices:
+
+- Get list of markers and channels in FCS files.
+
+**Column names**
+
+Please indicate the new marker or channel names in the order in which they should appear in the output file (comma-separated list). The number of names should match the number of indices.
+
+**Output file**
+
+The output contains the input data with new marker or channel names. Output can be provided in FCS format or in a RData object containing a flowFrame.
+
+-----
+
+**Examples**
+
+**Input file**::
+
+   Marker1 Marker2 Marker3 Marker4 Marker5
+   4       45      123     1956    62534
+   3       65      104     1254    36576
+   7       26      767     4124    42235
+   4       56      323     7623    74634
+   5       83      532     6256    34763
+   4       15      877     9312    21265
+   ...     ...     ...     ...     ...
+
+*Example 1*
+
+- Indices: Marker1,Marker3,Marker5
+- Column names: Marker7,Marker8,Marker9
+
+*Output1*::
+
+   Marker7 Marker2 Marker8 Marker4 Marker9
+   4       45      123     1956    62534
+   3       65      104     1254    36576
+   7       26      767     4124    42235
+   4       56      323     7623    74634
+   5       83      532     6256    34763
+   4       15      877     9312    21265
+   ...     ...     ...     ...     ...
+
+  ]]>
+  </help>
+</tool>