view extract_fcs_keywords/extractKeywords.xml @ 0:dc00746654dc draft

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<tool id="extract_fcs_keywords" name="Extract keywords" version="1.0">
  <description>from 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="1:" />
  </stdio>
  <command><![CDATA[
    Rscript --slave --vanilla $__tool_directory__/FCSKeyword.R --args "${input}" "${keyword_file}"
  ]]>
  </command>
  <inputs>
    <param format="fcs" name="input" type="data" label="FCS file"/>
  </inputs>
  <outputs>
    <data format="tabular" name="keyword_file" label="Extract Keywords on ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="testfcs1.fcs"/>
      <output name="keyword_file" file="out.tabular" lines_diff="2"/>
    </test>
  </tests>
  <help><![CDATA[
   This tool extracts the Keywords from a FCS file.

-----

**Input files**

This tool uses FCS files as input.

**Output file**

The list of FCS file headers is output.

-----

**Example**

FCSversion=2

$BYTEORD=4,3,2,1

$DATATYPE=I

$NEXTDATA=0

$SYS=Macintosh System Software 9.2.2

CREATOR=CELLQuest 3.3

$TOT=20000

$MODE=L

$PAR=6

$P1N=FSC-H

.

..

...
  ]]>
  </help>
</tool>