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1 <tool id="get_fcs_stats" name="Get summary" version="1.0">
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2 <description>of FCS files.</description>
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3 <requirements>
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4 <requirement type="package" version="3.3.0">r</requirement>
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5 <requirement type="package" version="1.38.2">bioconductor-flowcore</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="2:" level="fatal" description="See stderr for more details." />
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9 </stdio>
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10 <command><![CDATA[
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11 Rscript --slave --vanilla $__tool_directory__/FCSstats.R --args "${input}" "${output}"
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param format="fcs" name="input" type="data" label="FCS file"/>
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16 </inputs>
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17 <outputs>
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18 <data format="txt" name="output" label="Summary statisitics of ${input.name}"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input" value="testfcs1.fcs"/>
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23 <output name="output" file="summary.txt"/>
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24 </test>
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25 </tests>
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26 <help><![CDATA[
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27 This tool generates a summary of a FCS file and list of markers.
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28
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29 -----
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30
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31 **Input file**
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32
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33 This tool uses valid FCS files as input.
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34
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35 **Output file**
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36
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37 FCS file summary includes number of events, list of markers and parameters, and summary statistics for each.
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38
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39 -----
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40
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41 **Example**
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42
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43 *Output*::
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44
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45 events parameters
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46 20000 6
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47
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48
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49 =========================
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50 == FCS SUMMARY ==
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51 =========================
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52 FSC-H SSC-H FL1-H FL2-H FL3-H FL4-H
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53 Min. 261 23 0.0 0.0 0.0 0.0
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54 1st Qu. 371 120 129.0 153.0 257.0 252.0
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55 Median 432 196 206.0 237.0 432.0 331.0
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56 Mean 512 476 284.8 236.7 433.2 372.3
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57 3rd Qu. 657 1023 499.0 297.0 628.0 510.0
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58 Max. 1023 1023 729.0 925.0 1023.0 1023.0
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59
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60
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61 =========================
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62 == MARKERS IN FCS ==
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63 =========================
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64 channels markers
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65 1 FSC-H Forward Scatter
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66 2 SSC-H Side Scatter
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67 3 FL1-H FITC CD4
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68 4 FL2-H PE CD25
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69 5 FL3-H PP CD3
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70 6 FL4-H APC CD45RA
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71 ]]>
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72 </help>
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73 </tool>
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