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comparison 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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-1:000000000000 0:54a25f1139b4
1 <tool id="flowsom_tree" name="Generate a reference Self Organizing Map" version="1.0+galaxy1">
2 <description>using FlowSOM.</description>
3 <requirements>
4 <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="10" level="fatal" description="Please provide a valid input (FCS or flowFrame)." />
8 <exit_code range="11" level="fatal" description="Please provide integers for columns you want to analyze, in a comma separated list." />
9 <exit_code range="12" level="fatal" description="Provided indices are out of range in the FCS file / flowframe given as input." />
10 <exit_code range="13" level="fatal" description="Please provide integers for the number of expected clusters." />
11 <exit_code range="14" level="fatal" description="Please provide integers for the grid size." />
12 <exit_code range="15" level="fatal" description="Please provide an integer to set the seed." />
13 </stdio>
14 <command><![CDATA[
15 Rscript $__tool_directory__/FlowSOMGenerateTree.R '${input}' '${output}' '${cols}' '${cluster}' '${xdim}' '${ydim}' '${seed}'
16 #if $plotoutput.plot == "TRUE"
17 '${treeplot}' '${plotoutput.plotformat}' '${plotoutput.nodesize}'
18 #end if
19 #if $mplot == "TRUE"
20 '${mrkrplot}'
21 #end if
22 #if $txtoutput.table == "TRUE"
23 '${txtoutput.tablecontent}' '${txttable}' '${mappingtable}' 'mm' 'mm'
24 #end if
25 ]]>
26 </command>
27 <inputs>
28 <param format="fcs, flowframe" name="input" type="data" label="FCS file or flowFrame" />
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." />
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" />
31 <param name="xdim" type="integer" value="10" label="Grid size, width"/>
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." />
33 <param name="seed" type="integer" value="42" label="Seed" help="Let's be geeks, default is set to 42." />
34 <conditional name="txtoutput">
35 <param name="table" type="boolean" label="Output text?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
36 <when value="TRUE">
37 <param name="tablecontent" type="select" label="Associate each event to SOM clusters or meta-clusters?">
38 <option value="FlowSOM">FlowSOM Clusters</option>
39 <option value="meta">Meta-Clusters</option>
40 </param>
41 </when>
42 </conditional>
43 <conditional name="plotoutput">
44 <param name="plot" type="boolean" label="Plot SOM Tree?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
45 <when value="TRUE">
46 <param name="nodesize" type="boolean" label="Make all nodes the same size?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
47 <param name="plotformat" type="select" label="Graph output Format">
48 <option value="PNG">PNG</option>
49 <option value="PDF">PDF</option>
50 </param>
51 </when>
52 </conditional>
53 <param name="mplot" type="boolean" label="Plot individual marker trees?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
54 </inputs>
55 <outputs>
56 <data format="fsom" name="output" label="FlowSOM tree from ${input.name}">
57 </data>
58 <data format="flowclr" name="txttable" label="FlowSOM tree on ${input.name} with ${txtoutput.tablecontent} clusters">
59 <filter>txtoutput['table']</filter>
60 </data>
61 <data format="tabular" name="mappingtable" label="Mapping of nodes to meta-clusters from FlowSOM tree on ${input.name}">
62 <filter>txtoutput['table']</filter>
63 </data>
64 <data format="png" name="treeplot" label="Representation of FlowSOM tree on ${input.name} in ${plotoutput.plotformat}">
65 <filter>plotoutput['plot']</filter>
66 <change_format>
67 <when input="plotoutput.plotformat" value="PDF" format="pdf" />
68 </change_format>
69 </data>
70 <data format="pdf" name="mrkrplot" label="Marker trees from FlowSOM on ${input.name}">
71 <filter>(mplot)</filter>
72 </data>
73 </outputs>
74 <tests>
75 <test>
76 <param name="input" value="input.fcs"/>
77 <param name="cols" value="3,4,5"/>
78 <param name="cluster" value="10"/>
79 <param name="xdim" value="10"/>
80 <param name="ydim" value="10"/>
81 <param name="seed" value="33"/>
82 <param name="plot" value="FALSE"/>
83 <param name="table" value="FALSE" />
84 <param name="mplot" value="FALSE"/>
85 <output name="output" file="output1.fsom" compare="sim_size"/>
86 </test>
87 <test>
88 <param name="input" value="input.flowframe"/>
89 <param name="cols" value="3,4,5"/>
90 <param name="cluster" value="15"/>
91 <param name="xdim" value="10"/>
92 <param name="ydim" value="10"/>
93 <param name="seed" value="33"/>
94 <param name="plot" value="TRUE"/>
95 <param name="nodesize" value="FALSE"/>
96 <param name="mplot" value="FALSE"/>
97 <param name="plotformat" value="PNG"/>
98 <param name="table" value="FALSE" />
99 <output name="output" file="output2.fsom" compare="sim_size"/>
100 <output name="treeplot" file="tree.png" compare="sim_size"/>
101 </test>
102 <test>
103 <param name="input" value="input.fcs"/>
104 <param name="cols" value="3,4,5"/>
105 <param name="cluster" value="15"/>
106 <param name="xdim" value="10"/>
107 <param name="ydim" value="10"/>
108 <param name="seed" value="33"/>
109 <param name="plot" value="TRUE"/>
110 <param name="nodesize" value="FALSE"/>
111 <param name="mplot" value="TRUE"/>
112 <param name="plotformat" value="PDF"/>
113 <param name="table" value="FALSE" />
114 <output name="output" file="output3.fsom" compare="sim_size"/>
115 <output name="treeplot" file="tree.pdf" compare="sim_size" delta="100000"/>
116 <output name="mrkrplot" file="mrkrplot.pdf" compare="sim_size" delta="100000"/>
117 </test>
118 <test>
119 <param name="input" value="input.fcs"/>
120 <param name="cols" value="3,4,5"/>
121 <param name="cluster" value="10"/>
122 <param name="xdim" value="7"/>
123 <param name="ydim" value="7"/>
124 <param name="seed" value="33"/>
125 <param name="plot" value="FALSE"/>
126 <param name="mplot" value="FALSE"/>
127 <param name="table" value="TRUE" />
128 <param name="tablecontent" value="FlowSOM" />
129 <output name="output" file="output4.fsom" compare="sim_size"/>
130 <output name="txttable" file="output5.flowclr" compare="sim_size"/>
131 <output name="mappingtable" file="mapping1.tabular" compare="sim_size"/>
132 </test>
133 <test>
134 <param name="input" value="input.fcs"/>
135 <param name="cols" value="3,4,5"/>
136 <param name="cluster" value="10"/>
137 <param name="xdim" value="7"/>
138 <param name="ydim" value="7"/>
139 <param name="seed" value="33"/>
140 <param name="plot" value="FALSE"/>
141 <param name="mplot" value="FALSE"/>
142 <param name="table" value="TRUE" />
143 <param name="tablecontent" value="meta" />
144 <output name="output" file="output6.fsom" compare="sim_size"/>
145 <output name="txttable" file="output7.flowclr" compare="sim_size"/>
146 <output name="mappingtable" file="mapping2.tabular" compare="sim_size"/>
147 </test>
148 </tests>
149 <help><![CDATA[
150 Generate reference SOM
151 -----
152
153 This tool generates a reference Self-Organizing Map using FlowSOM.
154
155 **Input files**
156
157 This tool require a valid FCS file or flowFrame as input.
158
159 .. class:: warningmark
160
161 Compensation and Transformation will NOT be applied with this tool.
162
163 **Parameters**
164
165 *Columns to use*
166
167 Please indicate the indices of the markers to use in the computation of the SOM in a comma-separated list.
168
169 .. class:: infomark
170
171 Tip: One of the tools in the FCS File Tools section can help check the markers and channels indices:
172
173 - Get list of markers and channels in FCS files.
174
175 *Number of meta-clusters*
176
177 Please indicate the exact number of meta-clusters expected.
178
179 *Grid dimension*
180
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)
182
183 *Seed*
184
185 Please indicate a random number to use as seed. To make your analysis reproducible, use the same seed.
186
187 **Output files**
188
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.
190
191 .. class:: warningmark
192
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.
194
195 -----
196
197 **Example**
198
199 *Output text file*::
200
201 Marker1 Marker2 Marker3 ... Population
202 34 45 12 ... 1
203 33 65 10 ... 5
204 19 62 98 ... 2
205 12 36 58 ... 1
206 ... ... ... ... ...
207
208 *Node/Meta-cluster mapping file*::
209
210 Node Meta-Cluster
211 1 10
212 2 9
213 3 1
214 4 9
215 ... ...
216
217 *FlowSOM tree*:
218
219 .. image :: .static/images/flowtools/FlowSOM_tree.png
220
221 *Marker plots*:
222
223 .. image:: .static/images/flowtools/flowSOM_marker.png
224 ]]>
225 </help>
226 <citations>
227 <citation type="doi">10.1002/cyto.a.22625</citation>
228 </citations>
229 </tool>