Mercurial > repos > azomics > flowsom_cross_comp

annotate FlowSOMMApIndividualFCS.xml @ 1:a1054bd1060a draft

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planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
author azomics
date Mon, 25 Sep 2023 22:04:40 +0000
parents e796ed5dfd02
children f611ded6c6df
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a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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1 <tool id="flowsom_cross_comp" name="Map individual FCS to reference SOM" version="1.0+galaxy1">
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2 <description>using FlowSOM.</description>
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3 <requirements>
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4 <requirement type="package" version="1.16.0">bioconductor-flowsom</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="10" level="fatal" description="Please provide valid input files (FCS or flowFrame)."/>
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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8 <exit_code range="11" level="fatal" description="Please provide a valid reference SOM tree."/>
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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9 <exit_code range="12" level="fatal" description="Input files should all be in the same format."/>
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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10 <exit_code range="13" level="fatal" description="There are inconsistencies in marker names between FCS files."/>
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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11 <exit_code range="14" level="fatal" description="FCS file and reference tree markers are inconsistent."/>
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12 </stdio>
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13 <command><![CDATA[
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14 Rscript $__tool_directory__/FlowSOMMApIndividualFCS.R '${reftree}' 'newDataOutput' '${cluster}' '${tablecontent}' '${mfi}' '${stats}' '${mfistats}' '${allstats}'
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15 #if $plot == "TRUE"
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16 'newDataTrees'
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17 #end if
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18 #if $mplot == "TRUE"
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19 'newDataMarkers'
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20 #end if
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21 #for $f in $input
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22 '${f}' '${f.name}'
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23 #end for
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24 ]]>
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25 </command>
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26 <inputs>
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27 <param format="fcs, flowframe" name="input" type="data_collection" collection_type="list" label="FCS files or flowFrames Collection"/>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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28 <param format="fsom" name="reftree" type="data" label="Reference SOM tree"/>
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29 <param name="tablecontent" type="select" label="Associate each event to SOM clusters or meta-clusters?">
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30 <option value="FlowSOM">FlowSOM Clusters</option>
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31 <option value="meta">Meta-Clusters</option>
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32 </param>
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33 <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"/>
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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34 <param name="plot" type="boolean" label="Plot SOM Tree?" checked="false" truevalue="TRUE" falsevalue="FALSE"/>
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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35 <param name="mplot" type="boolean" label="Plot individual marker trees?" checked="false" truevalue="TRUE" falsevalue="FALSE"/>
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36 <param name="mfi" type="select" label="Calculate centroids using:">
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37 <option value="mfi" selected="true">Mean Fluorescence Intensity</option>
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38 <option value="mdfi">Median Fluorescence Intensity</option>
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39 <option value="gmfi">Geometric Mean Fluorescence Intensity</option>
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40 </param>
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41 </inputs>
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42 <outputs>
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43 <collection type="list" label="Mapping of ${input.name} to ${reftree.name}" name="output">
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44 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="newDataOutput" format="flowclr"/>
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45 </collection>
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46 <data format="flowstat1" name="stats" label="${tablecontent} cluster distribution in ${input.name}"/>
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47 <data format="flowstat2" name="mfistats" label="${tablecontent} cluster ${mfi} centroids in ${input.name}"/>
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48 <data format="flowstat3" name="allstats" label="${tablecontent} cluster descriptive stats of ${input.name}"/>
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49 <collection type="list" label="Tree representations of mapping ${input.name} to ${reftree.name}" name="trees">
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50 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="newDataTrees" format="png"/>
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51 <filter>(plot)</filter>
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52 </collection>
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53 <collection type="list" label="Marker trees from mapping ${input.name} to ${reftree.name}" name="mtrees">
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54 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="newDataMarkers" format="pdf"/>
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55 <filter>(mplot)</filter>
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56 </collection>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="input">
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61 <collection type="list">
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62 <element name="input1.flowframe" value="input1.flowframe"/>
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63 <element name="input2.flowframe" value="input2.flowframe"/>
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64 <element name="input3.flowframe" value="input3.flowframe"/>
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65 </collection>
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66 </param>
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67 <param name="reftree" value="input.fsom"/>
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68 <param name="tablecontent" value="meta"/>
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69 <param name="cluster" value="10"/>
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70 <param name="plot" value="FALSE"/>
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71 <param name="mplot" value="FALSE"/>
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72 <param name="mfi" value="mfi"/>
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73 <output name="stats" file="out1.flowstat1" compare="sim_size"/>
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74 <output name="mfistats" file="out1.flowstat2" compare="sim_size"/>
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75 <output name="allstats" file="out1.flowstat3" compare="sim_size"/>
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76 <output_collection name="output" type="list" count="3">
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77 <element name="input1.flowframe_clustered.flowclr" file="run1/input1.flowclr" compare="sim_size"/>
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78 <element name="input2.flowframe_clustered.flowclr" file="run1/input2.flowclr" compare="sim_size"/>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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79 <element name="input3.flowframe_clustered.flowclr" file="run1/input3.flowclr" compare="sim_size"/>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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80 </output_collection>
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81 </test>
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82 <test>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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83 <param name="input">
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84 <collection type="list">
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85 <element name="input1.fcs" value="input1.fcs"/>
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86 <element name="input2.fcs" value="input2.fcs"/>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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87 <element name="input3.fcs" value="input3.fcs"/>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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88 </collection>
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89 </param>
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90 <param name="reftree" value="input.fsom"/>
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91 <param name="tablecontent" value="FlowSOM"/>
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92 <param name="cluster" value="10"/>
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93 <param name="plot" value="TRUE"/>
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94 <param name="mplot" value="TRUE"/>
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95 <param name="mfi" value="mfi"/>
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96 <output name="stats" file="out2.flowstat1" compare="sim_size"/>
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97 <output name="mfistats" file="out2.flowstat2" compare="sim_size"/>
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98 <output name="allstats" file="out2.flowstat3" compare="sim_size"/>
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99 <output_collection name="output" type="list" count="3">
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100 <element name="input1.fcs_clustered.flowclr" file="run2/input1.flowclr" compare="sim_size"/>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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101 <element name="input2.fcs_clustered.flowclr" file="run2/input2.flowclr" compare="sim_size"/>
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102 <element name="input3.fcs_clustered.flowclr" file="run2/input3.flowclr" compare="sim_size"/>
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103 </output_collection>
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104 <output_collection name="trees" type="list" count="3">
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105 <element name="input1.fcs_tree.png" file="run2/input1.png" compare="sim_size"/>
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106 <element name="input2.fcs_tree.png" file="run2/input2.png" compare="sim_size"/>
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107 <element name="input3.fcs_tree.png" file="run2/input3.png" compare="sim_size"/>
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108 </output_collection>
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109 <output_collection name="mtrees" type="list" count="3">
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110 <element name="input1.fcs_marker_plots.pdf" file="run2/input1.pdf" compare="sim_size" delta="100000"/>
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111 <element name="input2.fcs_marker_plots.pdf" file="run2/input2.pdf" compare="sim_size" delta="100000"/>
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112 <element name="input3.fcs_marker_plots.pdf" file="run2/input3.pdf" compare="sim_size" delta="100000"/>
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113 </output_collection>
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114 </test>
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115 </tests>
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116 <help><![CDATA[
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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117 Map fcs samples to SOM
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118 -------------------
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119
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120 This tool uses FlowSOM to compare individual FCS or flowframes to a SOM reference tree.
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121
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122 **Input**
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123
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124 This tool compares FCS files or flowframes from a data collection to the reference Self-Organizing Map generated by a FlowSOM run. The same data collection merged and run with FlowSOM should ideally be used to ensure consistency in the attribution of events to clusters or meta-clusters.
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125
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126 .. class:: infomark
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127
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128 The option chosen for the centroids (mean, median or geometric mean) is used to generate descriptive statistics.
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129
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130 **Output**
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131
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132 Each individual FCS files or flowframe from the input collection is mapped to the reference tree, and a table mapping events to FlowSOM clusters or meta-clusters is generated for each. Two sets of plots can be optionally generated, one representing the resulting SOM Trees, and the other displaying each marker's contribution to the trees. The text files can be used as input for vizualisation tools. A table of the custer or meta-cluster composition of each file is generated as well as MFI and population descriptive statistics.
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133
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134 -----
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135
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136 **Example**
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137
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138 *Input*::
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139
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140 - FCS files or flowFrame (binary formats)
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141 - FlowSOM tree (binary format)
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142
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143 *Output* for each text file - fluorescence intensities per marker and cluster ID per event::
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144
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145 Marker1 Marker2 Marker3 ... Population
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146 33 47 11 ... 1
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147 31 64 11 ... 6
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148 21 62 99 ... 2
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149 14 34 60 ... 7
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150 ... ... ... ... ...
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151
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152 *Summary table* - distribution of events in each population in each file::
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153
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154 Filename SampleName Pop1 Pop2 Pop3 ...
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155 File1 Biosample1 0.1 0.25 0.14 ...
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156 File2 Biosample2 0.02 0.1 0.17 ...
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157 File3 Biosample3 0.4 0.05 0.21 ...
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158 File4 Biosample4 0.05 0.3 0.08 ...
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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159 ... ... ... ... ... ...
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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160
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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161 *Cluster MFI Summary table* - for each file, mean, median or geometric mean fluorescence intensities per marker per population::
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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162
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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163 Marker1 Marker2 Marker3 ... Population Percentage SampleName
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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164 154 885 24 ... 1 0.2 Biosample1
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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165 458 74 574 ... 2 0.3 Biosample1
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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166 3 210 86 ... 3 0.05 Biosample1
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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167 140 921 19 ... 1 0.1 Biosample2
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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168 428 79 508 ... 2 0.25 Biosample2
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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169 9 225 90 ... 3 0.3 Biosample2
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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170 ... ... ... ... ... ... ...
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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171
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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172 *Cluster MFI Descriptive Statistics table* - for the set of files, mean, median and standard deviation of each centroid per marker per population, as well as mean, median and standard deviation of the population's proportion::
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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173
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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174 Population Marker1_mean Marker1_median Marker1_stdev ... Percentage_mean Percentage_median Percentage_stdev
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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175 1 94.65 90.86 25.8 ... 1.84 0.55 2.48
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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176 2 132.18 131.58 5.02 ... 9.89 9.76 0.33
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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177 3 71.8 69.68 10.53 ... 3.02 1.49 3.45
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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178 4 84.85 84.85 nan ... 8.52 8.52 nan
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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179 5 161.82 132.77 61.29 ... 0.95 0.37 1.06
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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180 ... ... ... ... ... ... ... ...
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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181
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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182 *FlowSOM tree*:
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183
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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184 .. image:: ./static/images/flowtools/tree_mapflowSOM.png
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185
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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186 *Marker plots*:
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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187
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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188 .. image:: ./static/images/flowtools/flowSOM_marker.png
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189 ]]>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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190 </help>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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191 <citations>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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192 <citation type="doi">10.1002/cyto.a.22625</citation>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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193 </citations>
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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194 </tool>