Mercurial > repos > immport-devteam > fcs_gate_trans

annotate FCSGateTrans.xml @ 2:66a54e77aa33 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
author azomics
date Mon, 06 Jul 2020 19:39:35 -0400
parents c28c2e680bf5
children
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66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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1 <tool id="fcs_gate_trans_convert" name="Transform FCS data" version="1.2+galaxy1" profile="18.01">
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c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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2 <description>with optional compensation and automated gating with flowDensity.</description>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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3 <requirements>
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4 <requirement type="package" version="1.10.0">bioconductor-flowdensity</requirement>
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66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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5 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
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c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="See stderr for more details." />
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9 </stdio>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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10 <command><![CDATA[
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66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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11 Rscript $__tool_directory__/FCSGateTrans.R '${input}' '${output}' $comp '${outformat}'
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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12 #if $gate
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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13 '${graph}' '${report}'
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14 #else
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15 'None' 'None'
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16 #end if
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17 '${transform.trans_method}'
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18 #if $transform.trans_method == "arcsinh"
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19 $transform.scaling_factor
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20 #else if $transform.trans_method == "logicle"
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21 $transform.w $transform.t $transform.m
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22 #end if
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param format="fcs" name="input" type="data" label="FCS file"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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27 <param name="comp" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?"/>
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28 <conditional name="transform">
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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29 <param name="trans_method" type="select" label="Transformation using:" help="by default, FCSTrans">
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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30 <option value="fcstrans">FCSTrans</option>
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31 <option value="logicle_auto">logicle, automatic estimation of parameters</option>
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32 <option value="logicle">logicle</option>
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33 <option value="arcsinh">arcsinh</option>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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34 <option value="None">no transformation please.</option>
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35 </param>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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36 <when value="arcsinh">
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37 <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.">
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38 </param>
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39 </when>
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40 <when value="logicle">
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41 <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.">
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42 </param>
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43 <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.">
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44 </param>
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45 <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 .">
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46 </param>
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47 </when>
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48 </conditional>
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49 <param name="gate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Automatically gate debris?"/>
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50 <param name="outformat" type="select" label="Output Format">
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51 <option value="flowtext">Text File</option>
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52 <option value="FCS">FCS 3.0</option>
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53 <option value="flowFrame">R Data, flowFrame</option>
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54 </param>
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55 </inputs>
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56 <outputs>
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57 <data format="flowtext" name="output" label="${outformat} FCSGateTrans output with ${transform.trans_method} on ${input.name}">
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58 <change_format>
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59 <when input="outformat" value="FCS" format="fcs" />
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60 <when input="outformat" value="flowFrame" format="flowframe" />
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61 </change_format>
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62 </data>
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63 <data format="png" name="graph" label="Graphs of automated gating on ${input.name} with ${transform.trans_method}">
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64 <filter>(gate)</filter>
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65 </data>
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66 <data format="txt" name="report" label="Report of automated gating on ${input.name} with ${transform.trans_method}">
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67 <filter>(gate)</filter>
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68 </data>
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="input" value="testfcs1.fcs"/>
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73 <param name="comp" value="FALSE"/>
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74 <param name="gate" value="FALSE"/>
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75 <param name="outformat" value="flowtext"/>
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76 <param name="trans_method" value="fcstrans"/>
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77 <output name="output" file="nocomp.flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
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78 </test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
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79 <test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
80 <param name="input" value="testfcs1.fcs"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
81 <param name="comp" value="FALSE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
82 <param name="gate" value="FALSE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
83 <param name="outformat" value="flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
84 <param name="trans_method" value="None"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
85 <output name="output" file="notrans.flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
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86 </test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
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87 <test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
88 <param name="input" value="testfcs1.fcs"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
89 <param name="comp" value="FALSE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
90 <param name="gate" value="FALSE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
91 <param name="outformat" value="flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
92 <param name="trans_method" value="arcsinh"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
93 <param name="scaling_factor" value="150"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
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94 <output name="output" file="arcsinh150.flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
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95 </test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
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96 <test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
97 <param name="input" value="testfcs1.fcs"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
98 <param name="comp" value="TRUE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
99 <param name="gate" value="TRUE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
100 <param name="outformat" value="flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
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diff changeset
101 <param name="trans_method" value="fcstrans"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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102 <output name="output" file="withcomp.flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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103 </test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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104 <test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
105 <param name="input" value="testfcs1.fcs"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
106 <param name="comp" value="TRUE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
diff changeset
107 <param name="gate" value="FALSE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
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108 <param name="outformat" value="flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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diff changeset
109 <param name="trans_method" value="logicle_auto"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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110 <output name="output" file="log_auto.flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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111 </test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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112 <test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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diff changeset
113 <param name="input" value="testfcs1.fcs"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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diff changeset
114 <param name="comp" value="TRUE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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parents: 1
diff changeset
115 <param name="gate" value="FALSE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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116 <param name="outformat" value="flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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117 <param name="trans_method" value="logicle"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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118 <param name="w" value="0.4"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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119 <param name="t" value="10000"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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120 <param name="m" value="4.5"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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121 <output name="output" file="logicle.flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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122 </test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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123 <test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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124 <param name="input" value="testfcs1.fcs"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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parents: 1
diff changeset
125 <param name="comp" value="TRUE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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parents: 1
diff changeset
126 <param name="gate" value="TRUE"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
azomics
parents: 1
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127 <param name="outformat" value="flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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128 <param name="trans_method" value="fcstrans"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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129 <output name="output" file="withcomp.flowtext"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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130 <output name="graph" file="graph.png" compare="sim_size"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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131 <output name="report" file="report.txt"/>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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132 </test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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133 <test>
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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134 <param name="input" value="testfcs1.fcs"/>
1
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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135 <param name="comp" value="TRUE"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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diff changeset
136 <param name="gate" value="FALSE"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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137 <param name="outformat" value="FCS"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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138 <param name="trans_method" value="fcstrans"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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139 <output name="output" file="comp_gated.fcs" compare="sim_size"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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140 </test>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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141 <test>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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142 <param name="input" value="testfcs1.fcs"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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143 <param name="comp" value="TRUE"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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144 <param name="gate" value="FALSE"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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145 <param name="outformat" value="flowFrame"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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146 <param name="trans_method" value="fcstrans"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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147 <output name="output" file="comp_gated.flowframe" compare="sim_size"/>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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148 </test>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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149 </tests>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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150 <help><![CDATA[
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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151 This tool offers data transformation options, optional automated gating of debris using flowDensity and conversion of FCS files to text.
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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152
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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153 -----
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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154
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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155 **Input files**
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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156
2
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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157 This tool uses FCS files as input and files are processed serially. Users choose which transformation algorithm to apply, and whether to automatically gate cellular debris, and/or compensate the data.
1
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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158
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159 **Output files**
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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160
2
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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161 Output is a table of fluorescence intensity values for each marker, as a text file, FCS3.0 or R Object (flowFrame).
1
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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162
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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163 **Gating output**
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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164
2
66a54e77aa33 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
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165 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. Please check to make sure the gating is doing what you think it should be doing.
1
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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166
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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167 -----
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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168
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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169 Compensation will be implemented according to the spillover matrix included in the FCS files (if available).
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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170
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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171 -----
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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172
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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173 **Transformation**
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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174
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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175 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.
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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176
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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177 -----
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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178
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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179 **Automated Gating**
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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180
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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181 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.
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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182
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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183 .. class:: warningmark
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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184
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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185 Users should verify whether data benefit from being gated. We recommend evaluating the number of events and scatter plots pre- and post-gating.
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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186
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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187 -----
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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188
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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189 **Example**
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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190
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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191 *Output text file*::
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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192
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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193 Forward Scatter Side Scatter Marker1 Marker2 Marker3 Marker4 ...
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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194 449 157 551 129 169 292 ...
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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195 894 1023 199 277 320 227 ...
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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196 262 73 437 69 0 146 ...
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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197 340 115 509 268 0 74 ...
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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198 ... ... ... ... ... ... ...
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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199
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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200
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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201 *Gating summary*::
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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202
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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203 =========================
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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204 == BEFORE GATING ==
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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205 =========================
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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206 events parameters
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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207 203584 13
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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208 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
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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209 Min. 0 78 0 0.0 0 0.0 0 0 0 0 0.0 0 0
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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210 1st Qu. 869 769 544 514.0 940 0.0 1023 826 978 1104 358.8 913 4182
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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211 Median 1234 1081 754 704.0 1750 31.0 1247 1614 1971 1505 1612.0 1791 8392
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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212 Mean 1304 1108 1002 863.6 1629 812.8 1329 1597 1694 1765 1376.0 1813 8536
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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213 3rd Qu. 1675 1474 1240 1087.0 2326 1573.0 1629 2565 2326 2640 2261.0 2782 12760
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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214 Max. 4095 4061 4095 4012.0 4096 4086.0 4094 4022 4091 4096 4093.0 4096 17740
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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215
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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216 =========================
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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217 == AFTER GATING ==
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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218 =========================
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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219 events parameters
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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220 171547 13
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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221 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
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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222 Min. 403 219 1.0 4.0 0 0.0 0 0 0 0 0 0 0
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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223 1st Qu. 949 849 599.0 565.0 979 0.0 1063 943 1203 1119 444 1060 4182
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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224 Median 1348 1170 782.0 730.0 1809 0.0 1258 1717 2082 1493 1785 1883 8358
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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225 Mean 1353 1177 989.2 885.9 1642 779.4 1330 1678 1778 1753 1458 1873 8504
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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226 3rd Qu. 1670 1475 1204.0 1076.0 2322 1559.0 1591 2623 2345 2630 2289 2808 12700
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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227 Max. 2953 2406 4055.0 3329.0 4069 4080.0 3498 3868 3612 4076 4093 3764 17730
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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228
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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229 *Gating plots*:
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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230
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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231 .. image:: ./static/images/flowtools/flowdensity.png
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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232 ]]>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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233 </help>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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234 <citations>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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235 <citation type="doi">10.1002/cyto.a.22037</citation>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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236 <citation type="doi">10.1093/bioinformatics/btu677</citation>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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237 <citation type="doi">10.1186/1471-2105-10-106</citation>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
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238 </citations>
c28c2e680bf5 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit f34ed6ca8e77b9792a270890262c2936b13e30b9"
azomics
parents:
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239 </tool>