Mercurial > repos > immport-devteam > cross_sample
comparison cross_sample/runCrossSample.xml @ 0:8d951baf795f draft
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author | immport-devteam |
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date | Mon, 27 Feb 2017 12:47:17 -0500 |
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-1:000000000000 | 0:8d951baf795f |
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1 <tool id="run_cross_sample" name="Run Cross Sample" version="1.1"> | |
2 <description>using a Flow file that was run using FLOCK</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.16.0">scipy</requirement> | |
5 <requirement type="package" version="0.17.1">pandas</requirement> | |
6 <requirement type="package" version="1.0">flock</requirement> | |
7 </requirements> | |
8 <stdio> | |
9 <exit_code range="2" level="fatal" description="Columns inconsistencies between files and centroids file. See stderr for more details." /> | |
10 </stdio> | |
11 <command><![CDATA[ | |
12 python $__tool_directory__/runCrossSample.py -m "${centroid}" -s "${stats}" -S "${mfistats}" -a "${allstats}" -M "${mfi}" -t $__tool_directory__ -o crossSampleOutputs | |
13 #for $f in $input# | |
14 -i $f | |
15 -n "${f.name}" | |
16 #end for# | |
17 ]]> | |
18 </command> | |
19 <inputs> | |
20 <param format="flowtext" name="input" type="data_collection" collection_type="list" label="Flowtext files Collection"/> | |
21 <param format="flowmfi" name="centroid" type="data" label="Centroid file"/> | |
22 <param name="mfi" type="select" label="Calculate centroids using:"> | |
23 <option value="mfi" selected="true">Mean Fluorescence Intensity</option> | |
24 <option value="mdfi">Median Fluorescence Intensity</option> | |
25 <option value="gmfi">Geometric Mean Fluorescence Intensity</option> | |
26 </param> | |
27 </inputs> | |
28 <outputs> | |
29 <collection type="list" label="CrossSample on ${input.name}" name="output"> | |
30 <discover_datasets pattern="(?P<name>.*)" directory="crossSampleOutputs" format="flowclr" /> | |
31 </collection> | |
32 <data format="flowstat1" name="stats" label="Population distribution after CrossSample on ${input.name} using ${mfi}"/> | |
33 <data format="flowstat2" name="mfistats" label="${mfi} centroids of CrossSample on ${input.name} using ${mfi}"/> | |
34 <data format="flowstat3" name="allstats" label="${mfi} descriptive stats of CrossSample on ${input.name} using ${mfi}"/> | |
35 </outputs> | |
36 <tests> | |
37 <test> | |
38 <param name="input"> | |
39 <collection type="list"> | |
40 <element name="input1" value="input1.flowtext"/> | |
41 <element name="input2" value="input2.flowtext"/> | |
42 <element name="input3" value="input3.flowtext"/> | |
43 </collection> | |
44 </param> | |
45 <param name="centroid" value="mfi.flowmfi"/> | |
46 <param name="mfi" value="mfi"/> | |
47 <output name="stats" file="out1.flowstat1" lines_diff="6"/> | |
48 <output name="allstats" file="out1.flowstat3"/> | |
49 <output name="mfistats" file="out1.flowstat2" compare="sim_size"/> | |
50 <output_collection name="output" type="list" count="3"> | |
51 <element name="input1" file="run1/input1.flowtext.flowclr"/> | |
52 <element name="input2" file="run1/input2.flowtext.flowclr"/> | |
53 <element name="input3" file="run1/input3.flowtext.flowclr"/> | |
54 </output_collection> | |
55 </test> | |
56 <test> | |
57 <param name="input"> | |
58 <collection type="list"> | |
59 <element name="input1" value="input1.flowtext"/> | |
60 <element name="input2" value="input2.flowtext"/> | |
61 <element name="input3" value="input3.flowtext"/> | |
62 </collection> | |
63 </param> | |
64 <param name="centroid" value="gmfi.flowmfi"/> | |
65 <param name="mfi" value="gmfi"/> | |
66 <output name="stats" file="out2.flowstat1" lines_diff="6"/> | |
67 <output name="allstats" file="out2.flowstat3"/> | |
68 <output name="mfistats" file="out2.flowstat2" compare="sim_size"/> | |
69 <output_collection name="output" type="list" count="3"> | |
70 <element name="input1" file="run2/input1.flowtext.flowclr"/> | |
71 <element name="input2" file="run2/input2.flowtext.flowclr"/> | |
72 <element name="input3" file="run2/input3.flowtext.flowclr"/> | |
73 </output_collection> | |
74 </test> | |
75 </tests> | |
76 <help><![CDATA[ | |
77 This tool runs CrossSample using the MFI from FLOCK and text-converted FCS files. | |
78 | |
79 ----- | |
80 | |
81 **Input** | |
82 | |
83 This tool compares text-converted FCS files from a data collection to the MFI generated by a FLOCK run. The same data collection merged and run with FLOCK should be used to ensure consistency in the attribution of events to populations. | |
84 | |
85 .. class:: infomark | |
86 | |
87 The option chosen for the centroids (mean, median or geometric mean) should be the same as used to run FLOCK. | |
88 | |
89 **Output** | |
90 | |
91 Each event within each file of a dataset collection is attributed to a population depending on its intensity profile. | |
92 A table of the population composition of each file is generated as well as MFI and population descriptive statistics. | |
93 | |
94 .. class:: infomark | |
95 | |
96 Tip: If headers in each text-converted FCS file do not match those in the centroid file, the program will not run. Edit the input file using the Remove, rearrange and/or rename columns tool in the Flow File Tools section prior to Cross Sample analysis. | |
97 | |
98 ----- | |
99 | |
100 **Example** | |
101 | |
102 *Input* - fluorescence intensities per marker per event:: | |
103 | |
104 Marker1 Marker2 Marker3 | |
105 33 47 11 | |
106 31 64 11 | |
107 21 62 99 | |
108 14 34 60 | |
109 | |
110 *Centroid file* - mean, geometric mean or median fluorescence intensity per marker per population:: | |
111 | |
112 Population Marker1 Marker2 Marker3 | |
113 1 38 49 10 | |
114 2 21 63 100 | |
115 3 31 52 45 | |
116 4 11 78 25 | |
117 | |
118 *Output* for each text file - fluorescence intensities per marker and population ID per event:: | |
119 | |
120 Marker1 Marker2 Marker3 Population | |
121 33 47 11 1 | |
122 31 64 11 6 | |
123 21 62 99 2 | |
124 14 34 60 7 | |
125 | |
126 *Summary table* - counts of events in each population in each file:: | |
127 | |
128 Filename SampleName Pop1 Pop2 Pop3 ... | |
129 File1 Biosample1 255 147 18 ... | |
130 File2 Biosample2 27 61 965 ... | |
131 File3 Biosample3 201 546 221 ... | |
132 File4 Biosample4 11 77 327 ... | |
133 | |
134 *Centroid MFI Summary table* - for each file, mean, median or geometric mean fluorescence intensities per marker per population:: | |
135 | |
136 Marker1 Marker2 Marker3 ... Population Percentage SampleName | |
137 154 885 24 ... 1 0.2 Biosample1 | |
138 458 74 574 ... 2 0.3 Biosample1 | |
139 3 210 86 ... 3 0.05 Biosample1 | |
140 140 921 19 ... 1 0.1 Biosample2 | |
141 428 79 508 ... 2 0.25 Biosample2 | |
142 9 225 90 ... 3 0.3 Biosample2 | |
143 | |
144 *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:: | |
145 | |
146 Population Marker1_mean Marker1_median Marker1_stdev ... Percentage_mean Percentage_median Percentage_stdev | |
147 1 94.65 90.86 25.8 ... 1.84 0.55 2.48 | |
148 2 132.18 131.58 5.02 ... 9.89 9.76 0.33 | |
149 3 71.8 69.68 10.53 ... 3.02 1.49 3.45 | |
150 4 84.85 84.85 nan ... 8.52 8.52 nan | |
151 5 161.82 132.77 61.29 ... 0.95 0.37 1.06 | |
152 ]]> | |
153 </help> | |
154 <citations> | |
155 <citation type="doi">10.1002/cyto.b.20554</citation> | |
156 <citation type="doi">10.3389/fimmu.2012.00302</citation> | |
157 <citation type="doi">10.1371/journal.pone.0038408</citation> | |
158 <citation type="doi">10.1371/journal.ppat.1003076</citation> | |
159 <citation type="doi">10.1016/j.clim.2012.12.003</citation> | |
160 <citation type="doi">10.1038/srep02327</citation> | |
161 </citations> | |
162 </tool> |