Mercurial > repos > immport-devteam > convert_fcs_to_text

diff convert_fcs_to_text/convertFCSToText.xml @ 0:8e10184368a0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author immport-devteam
date Mon, 27 Feb 2017 12:45:51 -0500
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_fcs_to_text/convertFCSToText.xml	Mon Feb 27 12:45:51 2017 -0500
@@ -0,0 +1,58 @@
+<tool id="convert_fcs_to_text" name="Convert FCS to Text" version="1.0">
+  <description>with no transformation.</description>
+  <requirements>
+    <requirement type="package" version="3.3.0">r</requirement>
+    <requirement type="package" version="1.38.2">bioconductor-flowcore</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command><![CDATA[
+      Rscript --slave --vanilla $__tool_directory__/FCSConvert.R --args "${input}" "${output_file}" $compensate
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs" name="input" type="data" label="FCS file"/>
+    <param name="compensate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?">
+    </param>
+  </inputs>
+  <outputs>
+    <data format="flowtext" name="output_file" label="No Transformation ${input.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="testfcs1.fcs"/>
+      <param name="compensate" value="FALSE"/>
+      <output name="output_file" file="nocomp.flowtext"/>
+    </test>
+    <test>
+      <param name="input" value="testfcs1.fcs"/>
+      <param name="compensate" value="TRUE"/>
+      <output name="output_file" file="withcomp.flowtext"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool converts FCS files to text format with no tranformation.
+
+-----
+
+**Input files**
+
+This tool requires valid FCS files as input. Files are processed serially. Applying compensation is an option for FCS files including a compensation matrix.
+
+**Output file**
+
+The output is tab-separated text, containing the fluorescence intensity values for each marker.
+
+-----
+
+**Example**::
+
+   Forward Scatter Side Scatter Marker1 Marker2 Marker3 Marker4
+   449             157          551     129     169     292
+   894             1023	        199     277     320     227
+   262             73           437     69      0       146
+   340             115          509     268     0       74
+  ]]>
+  </help>
+</tool>