Mercurial > repos > azomics > flowsom_tree

annotate FlowSOMGenerateTree.xml @ 1:6c1721e7d0d6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit 6a60b44dd06df7be2eb851a5328cfc9e76c1d44e"
author azomics
date Mon, 06 Jul 2020 19:50:37 -0400
parents 54a25f1139b4
children 0efc47dba930
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
6c1721e7d0d6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit 6a60b44dd06df7be2eb851a5328cfc9e76c1d44e"
azomics
parents: 0
diff changeset
1 <tool id="flowsom_tree" name="Generate a reference Self Organizing Map" version="1.0+galaxy1" profile="18.01">
0
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
2 <description>using FlowSOM.</description>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
3 <requirements>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
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"
azomics
parents:
diff changeset
5 </requirements>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
6 <stdio>
1
6c1721e7d0d6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit 6a60b44dd06df7be2eb851a5328cfc9e76c1d44e"
azomics
parents: 0
diff changeset
7 <exit_code range="1:9" level="fatal" description="See stderr for more details." />
0
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
8 <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"
azomics
parents:
diff changeset
9 <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"
azomics
parents:
diff changeset
10 <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"
azomics
parents:
diff changeset
11 <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"
azomics
parents:
diff changeset
12 <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"
azomics
parents:
diff changeset
13 <exit_code range="15" level="fatal" description="Please provide an integer to set the seed." />
1
6c1721e7d0d6 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit 6a60b44dd06df7be2eb851a5328cfc9e76c1d44e"
azomics
parents: 0
diff changeset
14 <exit_code range="16:" level="fatal" description="See stderr for more details." />
0
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
15 </stdio>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
16 <command><![CDATA[
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
17 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"
azomics
parents:
diff changeset
18 #if $plotoutput.plot == "TRUE"
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
19 '${treeplot}' '${plotoutput.plotformat}' '${plotoutput.nodesize}'
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
20 #end if
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
21 #if $mplot == "TRUE"
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
22 '${mrkrplot}'
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
23 #end if
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
24 #if $txtoutput.table == "TRUE"
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
25 '${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"
azomics
parents:
diff changeset
26 #end if
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
27 ]]>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
28 </command>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
29 <inputs>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
30 <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"
azomics
parents:
diff changeset
31 <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"
azomics
parents:
diff changeset
32 <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"
azomics
parents:
diff changeset
33 <param name="xdim" type="integer" value="10" label="Grid size, width"/>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
34 <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"
azomics
parents:
diff changeset
35 <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"
azomics
parents:
diff changeset
36 <conditional name="txtoutput">
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
37 <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"
azomics
parents:
diff changeset
38 <when 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
39 <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"
azomics
parents:
diff changeset
40 <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"
azomics
parents:
diff changeset
41 <option value="meta">Meta-Clusters</option>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
42 </param>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
43 </when>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
44 </conditional>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
45 <conditional name="plotoutput">
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
46 <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"
azomics
parents:
diff changeset
47 <when 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
48 <param name="nodesize" type="boolean" label="Make all nodes the same size?" 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"
azomics
parents:
diff changeset
49 <param name="plotformat" type="select" label="Graph output Format">
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
50 <option value="PNG">PNG</option>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
51 <option value="PDF">PDF</option>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
52 </param>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
53 </when>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
54 </conditional>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
55 <param name="mplot" type="boolean" label="Plot individual marker trees?" 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"
azomics
parents:
diff changeset
56 </inputs>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
57 <outputs>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
58 <data format="fsom" name="output" label="FlowSOM tree from ${input.name}">
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
59 </data>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
60 <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"
azomics
parents:
diff changeset
61 <filter>txtoutput['table']</filter>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
62 </data>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
63 <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"
azomics
parents:
diff changeset
64 <filter>txtoutput['table']</filter>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
65 </data>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
66 <data format="png" name="treeplot" label="Representation of FlowSOM tree on ${input.name} in ${plotoutput.plotformat}">
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
67 <filter>plotoutput['plot']</filter>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
68 <change_format>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
69 <when input="plotoutput.plotformat" value="PDF" format="pdf" />
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
70 </change_format>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
71 </data>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
72 <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"
azomics
parents:
diff changeset
73 <filter>(mplot)</filter>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
74 </data>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
75 </outputs>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
76 <tests>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
77 <test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
78 <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
79 <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
80 <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
81 <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
82 <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
83 <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
84 <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
85 <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
86 <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
87 <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
88 </test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
89 <test>
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="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
91 <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
92 <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
93 <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
94 <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
95 <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
96 <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
97 <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
98 <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
99 <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
100 <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
101 <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
102 <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
103 </test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
104 <test>
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="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
106 <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
107 <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
108 <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
109 <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
110 <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
111 <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
112 <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
113 <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
114 <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
115 <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
116 <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
117 <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
118 <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
119 </test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
120 <test>
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="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
122 <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
123 <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
124 <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
125 <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
126 <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
127 <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
128 <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
129 <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
130 <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
131 <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
132 <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
133 <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
parents:
diff changeset
134 </test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
135 <test>
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="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
137 <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
138 <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
139 <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
140 <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
141 <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
142 <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
143 <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
144 <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
145 <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
parents:
diff changeset
146 <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
147 <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
parents:
diff changeset
148 <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
parents:
diff changeset
149 </test>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
150 </tests>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
151 <help><![CDATA[
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
152 Generate reference SOM
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
153 -----
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
154
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
155 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
parents:
diff changeset
156
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
157 **Input files**
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
158
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
159 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
parents:
diff changeset
160
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
161 .. class:: warningmark
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
162
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
163 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
parents:
diff changeset
164
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
165 **Parameters**
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
166
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
167 *Columns to use*
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
168
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
169 Please indicate the indices of the markers to use in the computation of the SOM in a comma-separated list.
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
170
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
171 .. class:: infomark
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
172
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
173 Tip: One of the tools in the FCS File Tools section can help check the markers and channels indices:
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
174
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
175 - Get list of markers and channels in FCS files.
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
176
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
177 *Number of meta-clusters*
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
178
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
179 Please indicate the exact number of meta-clusters expected.
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
180
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
181 *Grid dimension*
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
182
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
183 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)
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
184
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
185 *Seed*
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
186
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
187 Please indicate a random number to use as seed. To make your analysis reproducible, use the same seed.
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
188
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
189 **Output files**
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
190
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
191 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.
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
192
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
193 .. class:: warningmark
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
194
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
195 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.
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
196
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
197 -----
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
198
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
199 **Example**
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
200
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
201 *Output text file*::
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
202
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
203 Marker1 Marker2 Marker3 ... Population
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
204 34 45 12 ... 1
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
205 33 65 10 ... 5
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
206 19 62 98 ... 2
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
207 12 36 58 ... 1
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
208 ... ... ... ... ...
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
209
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
210 *Node/Meta-cluster mapping file*::
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
211
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
212 Node Meta-Cluster
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
213 1 10
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
214 2 9
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
215 3 1
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
216 4 9
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
217 ... ...
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
218
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
219 *FlowSOM tree*:
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
220
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
221 .. image :: .static/images/flowtools/FlowSOM_tree.png
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
222
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
223 *Marker plots*:
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
224
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
225 .. image:: .static/images/flowtools/flowSOM_marker.png
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
226 ]]>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
227 </help>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
228 <citations>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
229 <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"
azomics
parents:
diff changeset
230 </citations>
54a25f1139b4 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit b183455dde52e5b870fe898df9863b924e5370bd"
azomics
parents:
diff changeset
231 </tool>