Mercurial > repos > immport-devteam > fcs_gate_trans
view FCSGateTrans.xml @ 1:c28c2e680bf5 draft
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
| author | azomics |
|---|---|
| date | Mon, 22 Jun 2020 20:30:34 -0400 |
| parents | |
| children | 66a54e77aa33 |
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<tool id="fcs_gate_trans_convert" name="Transform FCS data" version="1.2+galaxy0"> <description>with optional compensation and automated gating with flowDensity.</description> <requirements> <requirement type="package" version="1.10.0">bioconductor-flowdensity</requirement> </requirements> <stdio> <exit_code range="2:" level="fatal" description="See stderr for more details." /> </stdio> <command><![CDATA[ Rscript $__tool_directory__/FCSGateTrans.R '${input}' '${output}' $comp '${outformat}' '${graph}' '${report}' '${transform.trans_method}' #if $transform.trans_method == "arcsinh" $transform.scaling_factor #else if $transform.trans_method == "logicle" $transform.w $transform.t $transform.m #end if ]]> </command> <inputs> <param format="fcs" name="input" type="data" label="FCS file"/> <param name="comp" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?"/> <conditional name="transform"> <param name="trans_method" type="select" label="Transformation using:" help="by default, FCSTrans"> <option value="fcstrans">FCSTrans</option> <option value="logicle_auto">logicle, automatic estimation of parameters</option> <option value="logicle">logicle</option> <option value="arcsinh">arcsinh</option> <option value="None">no transformation please.</option> </param> <when value="arcsinh"> <param name="scaling_factor" type="integer" min="1" max="200" value="150" label="Scaling factor b for arcsinh transform:" help="The default value is 150 for standard FCM data. The recommended value for cyTOF data is 5."> </param> </when> <when value="logicle"> <param name="w" type="float" value="0.5" label="Linearization width w for logicle transform:" help="w should be positive and determines the slope of transformation at zero. The default value is 0.5."> </param> <param name="t" type="integer" value="262144" label="Top of the scale data value t for logicle transform:" help=" t should be greater than zero. Recommended values are 10000 for common 4 decade data or 262144 for a 18 bit data range. The default value is 262144."> </param> <param name="m" type="float" value="4.5" label="Full width of the transformed display m for logicle transform:" help="m is expressed in asymptotic decades and should be positive. The default value is 4.5 ."> </param> </when> </conditional> <param name="gate" type="select" label="Automatically gate debris?"> <option value="FALSE">No, thank you</option> <option value="TRUE">Yes, please</option> </param> <param name="gate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Automatically gate debris?"/> <param name="outformat" type="select" label="Output Format"> <option value="flowtext">Text File</option> <option value="FCS">FCS 3.0</option> <option value="flowFrame">R Data, flowFrame</option> </param> </inputs> <outputs> <data format="flowtext" name="output" label="${outformat} FCSGateTrans output with ${transform.trans_method} on ${input.name}"> <change_format> <when input="outformat" value="FCS" format="fcs" /> <when input="outformat" value="flowFrame" format="flowframe" /> </change_format> </data> <data format="png" name="graph" label="Graphs of automated gating on ${input.name} with ${transform.trans_method}"> <filter>(gate)</filter> </data> <data format="txt" name="report" label="Report of automated gating on ${input.name} with ${transform.trans_method}"> <filter>(gate)</filter> </data> </outputs> <tests> <test> <param name="input" value="testfcs1.fcs"/> <param name="comp" value="TRUE"/> <param name="gate" value="FALSE"/> <param name="outformat" value="FCS"/> <param name="trans_method" value="fcstrans"/> <output name="output" file="comp_gated.fcs" compare="sim_size"/> </test> <test> <param name="input" value="testfcs1.fcs"/> <param name="comp" value="TRUE"/> <param name="gate" value="FALSE"/> <param name="outformat" value="flowFrame"/> <param name="trans_method" value="fcstrans"/> <output name="output" file="comp_gated.flowframe" compare="sim_size"/> </test> </tests> <help><![CDATA[ This tool offers data transformation options, optional automated gating of debris using flowDensity and conversion of FCS files to text. ----- **Input files** This tool uses FCS files as input and files are processed serially. Users choose to automatically gate cellular debris, and/or compensate the data. **Output files** Output is tab-separated text containing transformed fluorescence intensity values for each marker. If the option is selected, a FCS file (format FCS3.0) is generated. **Gating output** Automatically gated output includes a summary of data pre- and post-gating as well as density scatter plots pre- and post- gating for each marker pair. ----- Compensation will be implemented according to the spillover matrix included in the FCS files (if available). ----- **Transformation** This tools currently supports 3 transformation algorithms: FCSTrans, arcsinh and logicle. The latter two are implemented using flowCore, FCSTrans is documented in the paper cited below. Transformation algorithms are NOT applied to FSC and SSC channels. ----- **Automated Gating** Automated gating is implemented with flowDensity. Cellular debris removal uses gate coordinates calculated based on the density of the forward scatter channel only. The calculated gate is vertical and located at the largest value of either the 0.1 quantile of the FSC density or the lowest density between the first and second density peaks. Cells smaller than the threshold are removed. .. class:: warningmark Users should verify whether data benefit from being gated. We recommend evaluating the number of events and scatter plots pre- and post-gating. ----- **Example** *Output text file*:: 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 ... ... ... ... ... ... ... ... *Gating summary*:: ========================= == BEFORE GATING == ========================= events parameters 203584 13 FSC-A FSC-H SSC-A SSC-H APC-A APC-H7-A FITC-A PerCP-Cy5-5-A V450-A V500-A PE-A PE-Cy7-A Time Min. 0 78 0 0.0 0 0.0 0 0 0 0 0.0 0 0 1st Qu. 869 769 544 514.0 940 0.0 1023 826 978 1104 358.8 913 4182 Median 1234 1081 754 704.0 1750 31.0 1247 1614 1971 1505 1612.0 1791 8392 Mean 1304 1108 1002 863.6 1629 812.8 1329 1597 1694 1765 1376.0 1813 8536 3rd Qu. 1675 1474 1240 1087.0 2326 1573.0 1629 2565 2326 2640 2261.0 2782 12760 Max. 4095 4061 4095 4012.0 4096 4086.0 4094 4022 4091 4096 4093.0 4096 17740 ========================= == AFTER GATING == ========================= events parameters 171547 13 FSC-A FSC-H SSC-A SSC-H APC-A APC-H7-A FITC-A PerCP-Cy5-5-A V450-A V500-A PE-A PE-Cy7-A Time Min. 403 219 1.0 4.0 0 0.0 0 0 0 0 0 0 0 1st Qu. 949 849 599.0 565.0 979 0.0 1063 943 1203 1119 444 1060 4182 Median 1348 1170 782.0 730.0 1809 0.0 1258 1717 2082 1493 1785 1883 8358 Mean 1353 1177 989.2 885.9 1642 779.4 1330 1678 1778 1753 1458 1873 8504 3rd Qu. 1670 1475 1204.0 1076.0 2322 1559.0 1591 2623 2345 2630 2289 2808 12700 Max. 2953 2406 4055.0 3329.0 4069 4080.0 3498 3868 3612 4076 4093 3764 17730 *Gating plots*: .. image:: ./static/images/flowtools/flowdensity.png ]]> </help> <citations> <citation type="doi">10.1002/cyto.a.22037</citation> <citation type="doi">10.1093/bioinformatics/btu677</citation> <citation type="doi">10.1186/1471-2105-10-106</citation> </citations> </tool>