Mercurial > repos > immport-devteam > convert_fcs_to_text
comparison 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 |
comparison
equal
deleted
inserted
replaced
| 0:8e10184368a0 | 1:99bf034c674d |
|---|---|
| 1 <tool id="convert_fcs_to_text" name="Convert FCS to Text" version="1.0+galaxy1"> | |
| 2 <description>with no transformation</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" /> | |
| 8 </stdio> | |
| 9 <command><![CDATA[ | |
| 10 Rscript $__tool_directory__/FCSConvert.R '${input}' '${output_file}' $compensate | |
| 11 ]]> | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param format="fcs" name="input" type="data" label="FCS file"/> | |
| 15 <param name="compensate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?"> | |
| 16 </param> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="flowtext" name="output_file" label="No Transformation ${input.name}"/> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="input" value="testfcs1.fcs"/> | |
| 24 <param name="compensate" value="FALSE"/> | |
| 25 <output name="output_file" file="nocomp.flowtext" compare="sim_size"/> | |
| 26 </test> | |
| 27 <test> | |
| 28 <param name="input" value="testfcs1.fcs"/> | |
| 29 <param name="compensate" value="TRUE"/> | |
| 30 <output name="output_file" file="withcomp.flowtext" compare="sim_size"/> | |
| 31 </test> | |
| 32 </tests> | |
| 33 <help><![CDATA[ | |
| 34 This tool converts FCS files to text format with no tranformation. | |
| 35 | |
| 36 ----- | |
| 37 | |
| 38 **Input files** | |
| 39 | |
| 40 This tool requires valid FCS files as input. Files are processed serially. Applying compensation is an option for FCS files including a compensation matrix. | |
| 41 | |
| 42 **Output file** | |
| 43 | |
| 44 The output is tab-separated text, containing the fluorescence intensity values for each marker. | |
| 45 | |
| 46 ----- | |
| 47 | |
| 48 **Example**:: | |
| 49 | |
| 50 Forward Scatter Side Scatter Marker1 Marker2 Marker3 Marker4 ... | |
| 51 449 157 551 129 169 292 ... | |
| 52 894 1023 199 277 320 227 ... | |
| 53 262 73 437 69 0 146 ... | |
| 54 340 115 509 268 0 74 ... | |
| 55 ... ... ... ... ... ... ... | |
| 56 ]]> | |
| 57 </help> | |
| 58 </tool> |