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1 <tool id="extract_fcs_keywords" name="Extract keywords" version="1.0">
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2 <description>from 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="1:" />
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9 </stdio>
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10 <command><![CDATA[
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11 Rscript --slave --vanilla $__tool_directory__/FCSKeyword.R --args "${input}" "${keyword_file}"
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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="tabular" name="keyword_file" label="Extract Keywords on ${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="keyword_file" file="out.tabular" lines_diff="2"/>
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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 extracts the Keywords from a FCS file.
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28
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29 -----
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30
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31 **Input files**
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32
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33 This tool uses 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 The list of FCS file headers is output.
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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 FCSversion=2
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44
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45 $BYTEORD=4,3,2,1
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46
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47 $DATATYPE=I
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48
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49 $NEXTDATA=0
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50
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51 $SYS=Macintosh System Software 9.2.2
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52
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53 CREATOR=CELLQuest 3.3
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54
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55 $TOT=20000
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56
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57 $MODE=L
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58
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59 $PAR=6
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60
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61 $P1N=FSC-H
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62
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63 .
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64
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65 ..
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66
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67 ...
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68 ]]>
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69 </help>
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70 </tool>
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