Mercurial > repos > immport-devteam > run_flock
comparison runFlockMFI.xml @ 2:b6b4d08b6858 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"
author | azomics |
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date | Fri, 17 Jul 2020 09:06:54 -0400 |
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1:81f9b44f5242 | 2:b6b4d08b6858 |
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1 <tool id="run_flock" name="Run FLOCK" version="1.2+galaxy0" profile="18.01"> | |
2 <description>using a FCS file that was converted/transformed to a text file</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.5.1">scipy</requirement> | |
5 <requirement type="package" version="1.0.5">pandas</requirement> | |
6 <requirement type="package" version="1.0">flock</requirement> | |
7 </requirements> | |
8 <stdio> | |
9 <exit_code range="1:" /> | |
10 </stdio> | |
11 <command><![CDATA[ | |
12 python3 '$__tool_directory__/runFlockMFI.py' -i '${input}' -m '${method}' -o '${output}' -c '${centroid}' -M '${mfi}' -p '${profile}' | |
13 #if $bins | |
14 -b $bins | |
15 #end if | |
16 #if $density | |
17 -d $density | |
18 #end if | |
19 ]]> | |
20 </command> | |
21 <inputs> | |
22 <param format="flowtext" name="input" type="data" label="Source file"/> | |
23 <param name="method" type="select" label="Method"> | |
24 <option value="flock1" selected="true">Flock Version 1</option> | |
25 <option value="flock2">Flock Version 2</option> | |
26 </param> | |
27 <param name="bins" type="integer" min="6" max="30" optional="true" value="" label="bins (6-30)"/> | |
28 <param name="density" type="integer" min="2" max="100" optional="true" value="" label="density (2-100)"/> | |
29 <param name="mfi" type="select" label="Calculate centroids using:"> | |
30 <option value="mfi" selected="true">Mean Fluorescence Intensity</option> | |
31 <option value="mdfi">Median Fluorescence Intensity</option> | |
32 <option value="gmfi">Geometric Mean Fluorescence Intensity</option> | |
33 </param> | |
34 </inputs> | |
35 <outputs> | |
36 <data format="flowclr" name="output" label="${method} with ${mfi} on ${input.name}"/> | |
37 <data format="flowmfi" name="centroid" label="${mfi} centroids from ${method} on ${input.name}"/> | |
38 <data format="flowscore" name="profile" label="Population score profiles from ${method} on ${input.name}"/> | |
39 </outputs> | |
40 <tests> | |
41 <test> | |
42 <param name="input" value="input.flowtext"/> | |
43 <param name="method" value="flock1"/> | |
44 <param name="bins" value=""/> | |
45 <param name="density" value=""/> | |
46 <param name="mfi" value="mfi"/> | |
47 <output name="output" file="out1.flowclr"/> | |
48 <output name="centroid" file="mfi.flowmfi"/> | |
49 <output name="profile" file="out1.flowscore"/> | |
50 </test> | |
51 <test> | |
52 <param name="input" value="input.flowtext"/> | |
53 <param name="method" value="flock2"/> | |
54 <param name="bins" value=""/> | |
55 <param name="density" value=""/> | |
56 <param name="mfi" value="mfi"/> | |
57 <output name="output" file="out2.flowclr"/> | |
58 <output name="centroid" file="mfi2.flowmfi"/> | |
59 <output name="profile" file="out2.flowscore"/> | |
60 </test> | |
61 <test> | |
62 <param name="input" value="input.flowtext"/> | |
63 <param name="method" value="flock1"/> | |
64 <param name="bins" value="7"/> | |
65 <param name="density" value="3"/> | |
66 <param name="mfi" value="mfi"/> | |
67 <output name="output" file="out3.flowclr"/> | |
68 <output name="centroid" file="mfi3.flowmfi"/> | |
69 <output name="profile" file="out3.flowscore"/> | |
70 </test> | |
71 </tests> | |
72 <help><![CDATA[ | |
73 This tool runs FLOCK using a FCS file that was converted to a text file. | |
74 | |
75 ----- | |
76 | |
77 .. image:: ./static/images/flowtools/flock_logo.png | |
78 | |
79 FLOCK (FLOw Clustering without K) is a computational approach to flow cytometry analysis which: | |
80 | |
81 1. Computationally determines the number of unique populations in high dimensional flow data using a rapid binning approach | |
82 2. Can handle non-spherical hyper-shapes | |
83 3. Maps populations across independent samples | |
84 4. Calculates many useful summary statistics | |
85 5. Finds the most informative parameters | |
86 6. Reduces subjective factors in manual gating | |
87 | |
88 .. class:: warningmark | |
89 | |
90 This tool is not intended to analyze CyTOF data as is. | |
91 | |
92 ----- | |
93 | |
94 **Input** | |
95 | |
96 FLOCK requires a text file, generated from a FCS file, as input. | |
97 In order to define the populations in a given dataset collection for a given set of markers, run FLOCK on a super-set of FCS file. Use the Downsample and merge tool to concatenate and/or downsample datasets, and remove, edit or rearrange markers before running FLOCK on your favorite set of markers. | |
98 | |
99 .. class:: infomark | |
100 | |
101 Tip: Make sure to keep only columns containing data from markers. | |
102 | |
103 **Output** | |
104 | |
105 *FLOCK* | |
106 | |
107 FLOCK attributes each event to a population and generates a text file. | |
108 | |
109 *Centroids* | |
110 | |
111 The centroid file is a table containing the mean, median or geometric mean fluorescent intensity values of each marker within each population defined by FLOCK, as determined by the user. | |
112 | |
113 *Population scores* | |
114 | |
115 This output is a table containing marker scores for each population. The score value is a number indicating the degree to which this population expresses each marker, as follows: | |
116 | |
117 - 1 implies negative expression | |
118 - 2 implies low expression | |
119 - 3 implies positive expression | |
120 - 4 implies highly positive expression | |
121 | |
122 ----- | |
123 | |
124 **Example** | |
125 | |
126 *Input* - fluorescence intensities per marker per event:: | |
127 | |
128 Marker1 Marker2 Marker3 ... | |
129 34 45 12 ... | |
130 33 65 10 ... | |
131 19 62 98 ... | |
132 12 36 58 ... | |
133 ... ... ... ... | |
134 | |
135 *FLOCK Output* - fluorescence intensities per marker and population ID per event:: | |
136 | |
137 Marker1 Marker2 Marker3 ... Population | |
138 34 45 12 ... 1 | |
139 33 65 10 ... 5 | |
140 19 62 98 ... 2 | |
141 12 36 58 ... 1 | |
142 ... ... ... ... ... | |
143 | |
144 *Centroid file* - mean, geometric mean or median fluorescence intensity per marker per population:: | |
145 | |
146 Population Marker1 Marker2 Marker3 ... | |
147 1 38 49 10 ... | |
148 2 21 63 100 ... | |
149 3 31 52 45 ... | |
150 4 11 78 25 ... | |
151 ... ... ... ... ... | |
152 | |
153 *Population profile file*:: | |
154 | |
155 Population_ID Marker1 Marker2 Marker3 ... Count Percentage | |
156 1 1 3 2 ... 3885 6.44 | |
157 2 1 3 4 ... 2774 4.62 | |
158 3 2 2 3 ... 2151 3.59 | |
159 4 1 3 2 ... 1207 2.01 | |
160 ... ... ... ... ... ... ... | |
161 ]]> | |
162 </help> | |
163 <citations> | |
164 <citation type="doi">10.1002/cyto.b.20554</citation> | |
165 </citations> | |
166 </tool> |