Mercurial > repos > azomics > flowsom_tree

annotate FlowSOMGenerateTree.xml @ 0:54a25f1139b4 draft

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
author azomics
date Tue, 23 Jun 2020 12:46:08 -0400
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children 6c1721e7d0d6
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54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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1 <tool id="flowsom_tree" name="Generate a reference Self Organizing Map" version="1.0+galaxy1">
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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2 <description>using FlowSOM.</description>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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3 <requirements>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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4 <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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5 </requirements>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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6 <stdio>
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7 <exit_code range="10" level="fatal" description="Please provide a valid input (FCS or flowFrame)." />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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8 <exit_code range="11" level="fatal" description="Please provide integers for columns you want to analyze, in a comma separated list." />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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9 <exit_code range="12" level="fatal" description="Provided indices are out of range in the FCS file / flowframe given as input." />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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10 <exit_code range="13" level="fatal" description="Please provide integers for the number of expected clusters." />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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11 <exit_code range="14" level="fatal" description="Please provide integers for the grid size." />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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12 <exit_code range="15" level="fatal" description="Please provide an integer to set the seed." />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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13 </stdio>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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14 <command><![CDATA[
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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15 Rscript $__tool_directory__/FlowSOMGenerateTree.R '${input}' '${output}' '${cols}' '${cluster}' '${xdim}' '${ydim}' '${seed}'
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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16 #if $plotoutput.plot == "TRUE"
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17 '${treeplot}' '${plotoutput.plotformat}' '${plotoutput.nodesize}'
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18 #end if
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19 #if $mplot == "TRUE"
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20 '${mrkrplot}'
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21 #end if
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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22 #if $txtoutput.table == "TRUE"
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23 '${txtoutput.tablecontent}' '${txttable}' '${mappingtable}' 'mm' 'mm'
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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24 #end if
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25 ]]>
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26 </command>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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27 <inputs>
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28 <param format="fcs, flowframe" name="input" type="data" label="FCS file or flowFrame" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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29 <param name="cols" type="text" value="i.e.:1,2,5" label="Columns to use for analysis" help="By default, all markers except for FSC and SSC will be taken into account." />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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30 <param name="cluster" type="integer" value="10" optional="true" label="Number of expected metaclusters" help="By default, the number of expected metaclusters is set to 10" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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31 <param name="xdim" type="integer" value="10" label="Grid size, width"/>
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32 <param name="ydim" type="integer" value="10" label="Grid size, height" help="By default, the grid size is 10x10. The grid size specifies the number of clusters." />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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33 <param name="seed" type="integer" value="42" label="Seed" help="Let's be geeks, default is set to 42." />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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34 <conditional name="txtoutput">
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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35 <param name="table" type="boolean" label="Output text?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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36 <when value="TRUE">
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37 <param name="tablecontent" type="select" label="Associate each event to SOM clusters or meta-clusters?">
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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38 <option value="FlowSOM">FlowSOM Clusters</option>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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39 <option value="meta">Meta-Clusters</option>
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40 </param>
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41 </when>
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42 </conditional>
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43 <conditional name="plotoutput">
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44 <param name="plot" type="boolean" label="Plot SOM Tree?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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45 <when value="TRUE">
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46 <param name="nodesize" type="boolean" label="Make all nodes the same size?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
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47 <param name="plotformat" type="select" label="Graph output Format">
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48 <option value="PNG">PNG</option>
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49 <option value="PDF">PDF</option>
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50 </param>
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51 </when>
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52 </conditional>
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53 <param name="mplot" type="boolean" label="Plot individual marker trees?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
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54 </inputs>
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55 <outputs>
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56 <data format="fsom" name="output" label="FlowSOM tree from ${input.name}">
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57 </data>
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58 <data format="flowclr" name="txttable" label="FlowSOM tree on ${input.name} with ${txtoutput.tablecontent} clusters">
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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59 <filter>txtoutput['table']</filter>
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60 </data>
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61 <data format="tabular" name="mappingtable" label="Mapping of nodes to meta-clusters from FlowSOM tree on ${input.name}">
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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62 <filter>txtoutput['table']</filter>
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63 </data>
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64 <data format="png" name="treeplot" label="Representation of FlowSOM tree on ${input.name} in ${plotoutput.plotformat}">
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65 <filter>plotoutput['plot']</filter>
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66 <change_format>
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67 <when input="plotoutput.plotformat" value="PDF" format="pdf" />
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68 </change_format>
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69 </data>
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70 <data format="pdf" name="mrkrplot" label="Marker trees from FlowSOM on ${input.name}">
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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71 <filter>(mplot)</filter>
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72 </data>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="input" value="input.fcs"/>
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77 <param name="cols" value="3,4,5"/>
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78 <param name="cluster" value="10"/>
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79 <param name="xdim" value="10"/>
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80 <param name="ydim" value="10"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
81 <param name="seed" value="33"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
82 <param name="plot" value="FALSE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
83 <param name="table" value="FALSE" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
84 <param name="mplot" value="FALSE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
85 <output name="output" file="output1.fsom" compare="sim_size"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
86 </test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
87 <test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
88 <param name="input" value="input.flowframe"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
89 <param name="cols" value="3,4,5"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
90 <param name="cluster" value="15"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
91 <param name="xdim" value="10"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
92 <param name="ydim" value="10"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
93 <param name="seed" value="33"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
94 <param name="plot" value="TRUE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
95 <param name="nodesize" value="FALSE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
96 <param name="mplot" value="FALSE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
97 <param name="plotformat" value="PNG"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
98 <param name="table" value="FALSE" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
99 <output name="output" file="output2.fsom" compare="sim_size"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
100 <output name="treeplot" file="tree.png" compare="sim_size"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
101 </test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
102 <test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
103 <param name="input" value="input.fcs"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
104 <param name="cols" value="3,4,5"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
105 <param name="cluster" value="15"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
106 <param name="xdim" value="10"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
107 <param name="ydim" value="10"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
108 <param name="seed" value="33"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
109 <param name="plot" value="TRUE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
110 <param name="nodesize" value="FALSE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
111 <param name="mplot" value="TRUE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
112 <param name="plotformat" value="PDF"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
113 <param name="table" value="FALSE" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
114 <output name="output" file="output3.fsom" compare="sim_size"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
115 <output name="treeplot" file="tree.pdf" compare="sim_size" delta="100000"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
116 <output name="mrkrplot" file="mrkrplot.pdf" compare="sim_size" delta="100000"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
117 </test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
118 <test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
119 <param name="input" value="input.fcs"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
120 <param name="cols" value="3,4,5"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
121 <param name="cluster" value="10"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
122 <param name="xdim" value="7"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
123 <param name="ydim" value="7"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
124 <param name="seed" value="33"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
125 <param name="plot" value="FALSE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
126 <param name="mplot" value="FALSE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
127 <param name="table" value="TRUE" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
128 <param name="tablecontent" value="FlowSOM" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
129 <output name="output" file="output4.fsom" compare="sim_size"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
130 <output name="txttable" file="output5.flowclr" compare="sim_size"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
131 <output name="mappingtable" file="mapping1.tabular" compare="sim_size"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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diff changeset
132 </test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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diff changeset
133 <test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
134 <param name="input" value="input.fcs"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
135 <param name="cols" value="3,4,5"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
136 <param name="cluster" value="10"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
137 <param name="xdim" value="7"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
138 <param name="ydim" value="7"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
139 <param name="seed" value="33"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
140 <param name="plot" value="FALSE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
141 <param name="mplot" value="FALSE"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
142 <param name="table" value="TRUE" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
143 <param name="tablecontent" value="meta" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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diff changeset
144 <output name="output" file="output6.fsom" compare="sim_size"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
145 <output name="txttable" file="output7.flowclr" compare="sim_size"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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diff changeset
146 <output name="mappingtable" file="mapping2.tabular" compare="sim_size"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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diff changeset
147 </test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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diff changeset
148 </tests>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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diff changeset
149 <help><![CDATA[
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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150 Generate reference SOM
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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diff changeset
151 -----
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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152
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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153 This tool generates a reference Self-Organizing Map using FlowSOM.
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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154
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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155 **Input files**
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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156
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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157 This tool require a valid FCS file or flowFrame as input.
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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158
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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159 .. class:: warningmark
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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diff changeset
160
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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diff changeset
161 Compensation and Transformation will NOT be applied with this tool.
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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162
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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163 **Parameters**
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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164
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
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165 *Columns to use*
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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166
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167 Please indicate the indices of the markers to use in the computation of the SOM in a comma-separated list.
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168
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169 .. class:: infomark
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170
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171 Tip: One of the tools in the FCS File Tools section can help check the markers and channels indices:
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172
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173 - Get list of markers and channels in FCS files.
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174
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175 *Number of meta-clusters*
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176
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177 Please indicate the exact number of meta-clusters expected.
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178
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179 *Grid dimension*
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180
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181 Please indicate the dimension of the grid for establishing the SOM. The dimension of the grid defines the number of clusters (height x width = cluster)
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182
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183 *Seed*
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184
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185 Please indicate a random number to use as seed. To make your analysis reproducible, use the same seed.
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186
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187 **Output files**
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188
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189 This tool produces a FlowSOM object and optionally two sets of plots, one representing the SOM Tree generated, and the other displaying each marker's contribution to the tree. A flat text file can also optionally be generated and used as input for vizualisation tools.
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190
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191 .. class:: warningmark
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192
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193 PDF are larger files that may take some time to load. It might be faster to download the PDF output once generated to open it locally.
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194
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195 -----
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196
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197 **Example**
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198
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199 *Output text file*::
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200
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201 Marker1 Marker2 Marker3 ... Population
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202 34 45 12 ... 1
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203 33 65 10 ... 5
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204 19 62 98 ... 2
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205 12 36 58 ... 1
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206 ... ... ... ... ...
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207
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208 *Node/Meta-cluster mapping file*::
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209
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210 Node Meta-Cluster
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211 1 10
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212 2 9
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213 3 1
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214 4 9
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215 ... ...
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216
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217 *FlowSOM tree*:
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218
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219 .. image :: .static/images/flowtools/FlowSOM_tree.png
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220
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221 *Marker plots*:
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222
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223 .. image:: .static/images/flowtools/flowSOM_marker.png
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224 ]]>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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225 </help>
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226 <citations>
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227 <citation type="doi">10.1002/cyto.a.22625</citation>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
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228 </citations>
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229 </tool>