diff fcs_summary/FCSstats.xml @ 0:1d926a8daa92 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fcs_summary/FCSstats.xml	Mon Feb 27 12:53:11 2017 -0500
@@ -0,0 +1,73 @@
+<tool id="get_fcs_stats" name="Get summary" version="1.0">
+  <description>of FCS files.</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="2:" level="fatal" description="See stderr for more details." />
+  </stdio>
+  <command><![CDATA[
+      Rscript --slave --vanilla $__tool_directory__/FCSstats.R --args "${input}" "${output}"
+  ]]>
+  </command>
+  <inputs>
+    <param format="fcs" name="input" type="data" label="FCS file"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" label="Summary statisitics of ${input.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="testfcs1.fcs"/>
+      <output name="output" file="summary.txt"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool generates a summary of a FCS file and list of markers.
+
+-----
+
+**Input file**
+
+This tool uses valid FCS files as input.
+
+**Output file**
+
+FCS file summary includes number of events, list of markers and parameters, and summary statistics for each.
+
+-----
+
+**Example**
+
+*Output*::
+
+       events parameters
+        20000          6
+
+
+   =========================
+   ==     FCS SUMMARY     ==
+   =========================
+           FSC-H SSC-H FL1-H FL2-H  FL3-H  FL4-H
+   Min.      261    23   0.0   0.0    0.0    0.0
+   1st Qu.   371   120 129.0 153.0  257.0  252.0
+   Median    432   196 206.0 237.0  432.0  331.0
+   Mean      512   476 284.8 236.7  433.2  372.3
+   3rd Qu.   657  1023 499.0 297.0  628.0  510.0
+   Max.     1023  1023 729.0 925.0 1023.0 1023.0
+
+
+   =========================
+   ==    MARKERS IN FCS   ==
+   =========================
+     channels         markers
+   1    FSC-H Forward Scatter
+   2    SSC-H    Side Scatter
+   3    FL1-H        FITC CD4
+   4    FL2-H         PE CD25
+   5    FL3-H          PP CD3
+   6    FL4-H      APC CD45RA
+  ]]>
+  </help>
+</tool>