Mercurial > repos > immport-devteam > check_fcs_headers
view check_fcs_headers/getFCSheaders.xml @ 0:d3957a51cc51 draft
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author | immport-devteam |
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date | Mon, 27 Feb 2017 12:16:44 -0500 |
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<tool id="get_fcs_headers" name="Get list of markers" version="1.0"> <description>in 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[ python $__tool_directory__/getFCSheaders.py -o "${output_file}" -t $__tool_directory__ #for $f in $input# -i "${f}" -n "${f.name}" #end for# ]]> </command> <inputs> <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/> </inputs> <outputs> <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/> </outputs> <tests> <test> <param name="input"> <collection type="list"> <element name="input1.fcs" value="input1.fcs"/> <element name="input2.fcs" value="input2.fcs"/> <element name="input3.fcs" value="input3.fcs"/> </collection> </param> <output name="output_file" file="output.tabular"/> </test> </tests> <help><![CDATA[ This tool returns a table of the headers of a set of FCS files. ----- **Input files** This tool requires collections of FCS files as input. **Output file** The output file is a table listing the markers and channels for each file. ----- **Example** *File1*:: Marker1 Marker2 Marker3 34 45 12 33 65 10 *File2*:: Marker4 Marker5 Marker3 19 62 98 12 36 58 *Output*:: File1 channels Channel1 Channel2 Channel3 File2 channels Channel4 Channel5 Channel3 File1 markers Marker1 Marker2 Marker3 File2 markers Marker4 Marker5 Marker3 ]]> </help> </tool>