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1 <tool id="get_txt_fcs_stats" name="Get summary" version="1.0">
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2 <description>of txt-converted FCS files.</description>
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3 <requirements>
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4 <requirement type="package" version="0.17.1">pandas</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="2:" level="fatal" description="See stderr for more details." />
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8 </stdio>
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9 <command><![CDATA[
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10 python $__tool_directory__/FCSstats_txt.py -i "${input}" -o "${output}"
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11 ]]>
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12 </command>
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13 <inputs>
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14 <param format="flowtext" name="input" type="data" label="txt-converted FCS file"/>
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15 </inputs>
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16 <outputs>
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17 <data format="tabular" name="output" label="Summary statisitics of ${input.name}"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input" value="input.flowtext"/>
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22 <output name="output" file="output.tabular"/>
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23 </test>
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24 </tests>
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25 <help><![CDATA[
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26 This tool generates a summary of a txt-converted FCS file and list of markers.
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27
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28 -----
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29
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30 **Input file**
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31
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32 This tool uses txt-converted FCS files as input.
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33
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34 **Output file**
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35
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36 File summary includes number of events, list of markers and parameters, and summary statistics for each.
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37
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38 -----
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39
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40 **Example**
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41
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42 *Output*::
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43
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44 FSC SSC CD4 CCR3 CD8 CCR4
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45 mean 475.4 413.4 288.8 157.9 218.1 179.6
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46 std 165.2 390.7 199.9 117.3 201.7 95.7
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47 min 261.0 18.0 0.0 0.0 0.0 0.0
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48 25% 354.0 121.0 112.0 65.0 58.0 109.0
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49 50% 398.0 167.0 209.0 159.0 180.0 179.0
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50 75% 609.0 951.2 512.0 237.0 275.0 245.0
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51 max 1023.0 1023.0 775.0 1023.0 1023.0 841.0
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52 20000 events
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53 ]]>
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54 </help>
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55 </tool>
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