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comparison runCrossSample.xml @ 4:e80b0f62ffb3 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
author azomics
date Wed, 29 Jul 2020 13:32:17 -0400
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3:5f670146a9af 4:e80b0f62ffb3
1 <tool id="run_cross_sample" name="Run Cross Sample" version="1.1+galaxy0" profile="18.01">
2 <description>using a Flow file that was run using FLOCK</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" level="fatal"/>
10 <exit_code range="2" level="fatal" description="Columns inconsistencies between files and centroids file. See stderr for more details." />
11 <exit_code range="3:" level="fatal"/>
12 </stdio>
13 <command><![CDATA[
14 python '$__tool_directory__/runCrossSample.py' -m '${centroid}' -s '${stats}' -S '${mfistats}' -a '${allstats}' -M '${mfi}' -o crossSampleOutputs
15 #for $f in $input
16 -i $f
17 -n '${f.name}'
18 #end for
19
20 ]]>
21 </command>
22 <inputs>
23 <param format="flowtext" name="input" type="data_collection" collection_type="list" label="Flowtext files Collection"/>
24 <param format="flowmfi" name="centroid" type="data" label="Centroid file"/>
25 <param name="mfi" type="select" label="Calculate centroids using:">
26 <option value="mfi" selected="true">Mean Fluorescence Intensity</option>
27 <option value="mdfi">Median Fluorescence Intensity</option>
28 <option value="gmfi">Geometric Mean Fluorescence Intensity</option>
29 </param>
30 </inputs>
31 <outputs>
32 <collection type="list" label="CrossSample on ${input.name}" name="output">
33 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="crossSampleOutputs" format="flowclr" />
34 </collection>
35 <data format="flowstat1" name="stats" label="Population distribution after CrossSample on ${input.name} using ${mfi}"/>
36 <data format="flowstat2" name="mfistats" label="${mfi} centroids of CrossSample on ${input.name} using ${mfi}"/>
37 <data format="flowstat3" name="allstats" label="${mfi} descriptive stats of CrossSample on ${input.name} using ${mfi}"/>
38 </outputs>
39 <tests>
40 <test>
41 <param name="input">
42 <collection type="list">
43 <element name="input1" value="input1.flowtext"/>
44 <element name="input2" value="input2.flowtext"/>
45 <element name="input3" value="input3.flowtext"/>
46 </collection>
47 </param>
48 <param name="centroid" value="mfi.flowmfi"/>
49 <param name="mfi" value="mfi"/>
50 <output name="stats" file="out1.flowstat1" lines_diff="6"/>
51 <output name="allstats" file="out1.flowstat3"/>
52 <output name="mfistats" file="out1.flowstat2" compare="sim_size"/>
53 <output_collection name="output" count="3">
54 <element name="input1.flowtext.flowclr" file="run1/input1.flowtext.flowclr" compare="sim_size"/>
55 <element name="input2.flowtext.flowclr" file="run1/input2.flowtext.flowclr" compare="sim_size"/>
56 <element name="input3.flowtext.flowclr" file="run1/input3.flowtext.flowclr" compare="sim_size"/>
57 </output_collection>
58 </test>
59 <test>
60 <param name="input">
61 <collection type="list">
62 <element name="input1" value="input1.flowtext"/>
63 <element name="input2" value="input2.flowtext"/>
64 <element name="input3" value="input3.flowtext"/>
65 </collection>
66 </param>
67 <param name="centroid" value="gmfi.flowmfi"/>
68 <param name="mfi" value="gmfi"/>
69 <output name="stats" file="out2.flowstat1" lines_diff="6"/>
70 <output name="allstats" file="out2.flowstat3"/>
71 <output name="mfistats" file="out2.flowstat2" compare="sim_size"/>
72 <output_collection name="output" type="list" count="3">
73 <element name="input1.flowtext.flowclr" file="run2/input1.flowtext.flowclr"/>
74 <element name="input2.flowtext.flowclr" file="run2/input2.flowtext.flowclr"/>
75 <element name="input3.flowtext.flowclr" file="run2/input3.flowtext.flowclr"/>
76 </output_collection>
77 </test>
78 </tests>
79 <help><![CDATA[
80 This tool runs CrossSample using the MFI from FLOCK and text-converted FCS files.
81 -----
82 **Input**
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 .. class:: infomark
85 The option chosen for the centroids (mean, median or geometric mean) should be the same as used to run FLOCK.
86 **Output**
87 Each event within each file of a dataset collection is attributed to a population depending on its intensity profile.
88 A table of the population composition of each file is generated as well as MFI and population descriptive statistics.
89 .. class:: infomark
90 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 Text File Tools section prior to Cross Sample analysis.
91 -----
92 **Example**
93 *Input* - fluorescence intensities per marker per event::
94 Marker1 Marker2 Marker3 ...
95 33 47 11 ...
96 31 64 11 ...
97 21 62 99 ...
98 14 34 60 ...
99 ... ... ... ...
100 *Centroid file* - mean, geometric mean or median fluorescence intensity per marker per population::
101 Population Marker1 Marker2 Marker3 ...
102 1 38 49 10 ...
103 2 21 63 100 ...
104 3 31 52 45 ...
105 4 11 78 25 ...
106 ... ... ... ... ...
107 *Output* for each text file - fluorescence intensities per marker and population ID per event::
108 Marker1 Marker2 Marker3 ... Population
109 33 47 11 ... 1
110 31 64 11 ... 6
111 21 62 99 ... 2
112 14 34 60 ... 7
113 ... ... ... ... ...
114 *Summary table* - distribution of events in each population in each file::
115 Filename SampleName Pop1 Pop2 Pop3 ...
116 File1 Biosample1 0.1 0.25 0.14 ...
117 File2 Biosample2 0.02 0.1 0.17 ...
118 File3 Biosample3 0.4 0.05 0.21 ...
119 File4 Biosample4 0.05 0.3 0.08 ...
120 *Centroid MFI Summary table* - for each file, mean, median or geometric mean fluorescence intensities per marker per population::
121 Marker1 Marker2 Marker3 ... Population Percentage SampleName
122 154 885 24 ... 1 0.2 Biosample1
123 458 74 574 ... 2 0.3 Biosample1
124 3 210 86 ... 3 0.05 Biosample1
125 ... ... ... ... ... ... ...
126 140 921 19 ... 1 0.1 Biosample2
127 428 79 508 ... 2 0.25 Biosample2
128 9 225 90 ... 3 0.3 Biosample2
129 ... ... ... ... ... ... ...
130 *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::
131 Population Marker1_mean Marker1_median Marker1_stdev ... Percentage_mean Percentage_median Percentage_stdev
132 1 94.65 90.86 25.8 ... 1.84 0.55 2.48
133 2 132.18 131.58 5.02 ... 9.89 9.76 0.33
134 3 71.8 69.68 10.53 ... 3.02 1.49 3.45
135 4 84.85 84.85 nan ... 8.52 8.52 nan
136 5 161.82 132.77 61.29 ... 0.95 0.37 1.06
137 ... ... ... ... ... ... ... ...
138 ]]>
139 </help>
140 <citations>
141 <citation type="doi">10.1002/cyto.b.20554</citation>
142 <citation type="doi">10.3389/fimmu.2012.00302</citation>
143 <citation type="doi">10.1371/journal.pone.0038408</citation>
144 <citation type="doi">10.1371/journal.ppat.1003076</citation>
145 <citation type="doi">10.1016/j.clim.2012.12.003</citation>
146 <citation type="doi">10.1038/srep02327</citation>
147 </citations>
148 </tool>