Mercurial > repos > immport-devteam > convert_fcs_to_text
diff convertFCSToText.xml @ 1:99bf034c674d draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/convert_fcs_to_text commit 5ac9759a4f1850b200cd7a301e6662ef8adca55d"
| author | azomics |
|---|---|
| date | Mon, 22 Jun 2020 17:26:06 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convertFCSToText.xml Mon Jun 22 17:26:06 2020 -0400 @@ -0,0 +1,58 @@ +<tool id="convert_fcs_to_text" name="Convert FCS to Text" version="1.0+galaxy1"> + <description>with no transformation</description> + <requirements> + <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + Rscript $__tool_directory__/FCSConvert.R '${input}' '${output_file}' $compensate + ]]> + </command> + <inputs> + <param format="fcs" name="input" type="data" label="FCS file"/> + <param name="compensate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?"> + </param> + </inputs> + <outputs> + <data format="flowtext" name="output_file" label="No Transformation ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="compensate" value="FALSE"/> + <output name="output_file" file="nocomp.flowtext" compare="sim_size"/> + </test> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="compensate" value="TRUE"/> + <output name="output_file" file="withcomp.flowtext" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + This tool converts FCS files to text format with no tranformation. + +----- + +**Input files** + +This tool requires valid FCS files as input. Files are processed serially. Applying compensation is an option for FCS files including a compensation matrix. + +**Output file** + +The output is tab-separated text, containing the fluorescence intensity values for each marker. + +----- + +**Example**:: + + Forward Scatter Side Scatter Marker1 Marker2 Marker3 Marker4 ... + 449 157 551 129 169 292 ... + 894 1023 199 277 320 227 ... + 262 73 437 69 0 146 ... + 340 115 509 268 0 74 ... + ... ... ... ... ... ... ... + ]]> + </help> +</tool>