Mercurial > repos > immport-devteam > cross_sample
view runCrossSample.xml @ 4:e80b0f62ffb3 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cross_sample commit e7eab2dca0c1f73f580362f61425a78d4c8892ce"
| author | azomics |
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| date | Wed, 29 Jul 2020 13:32:17 -0400 |
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<tool id="run_cross_sample" name="Run Cross Sample" version="1.1+galaxy0" profile="18.01"> <description>using a Flow file that was run using FLOCK</description> <requirements> <requirement type="package" version="1.5.1">scipy</requirement> <requirement type="package" version="1.0.5">pandas</requirement> <requirement type="package" version="1.0">flock</requirement> </requirements> <stdio> <exit_code range="1" level="fatal"/> <exit_code range="2" level="fatal" description="Columns inconsistencies between files and centroids file. See stderr for more details." /> <exit_code range="3:" level="fatal"/> </stdio> <command><![CDATA[ python '$__tool_directory__/runCrossSample.py' -m '${centroid}' -s '${stats}' -S '${mfistats}' -a '${allstats}' -M '${mfi}' -o crossSampleOutputs #for $f in $input -i $f -n '${f.name}' #end for ]]> </command> <inputs> <param format="flowtext" name="input" type="data_collection" collection_type="list" label="Flowtext files Collection"/> <param format="flowmfi" name="centroid" type="data" label="Centroid file"/> <param name="mfi" type="select" label="Calculate centroids using:"> <option value="mfi" selected="true">Mean Fluorescence Intensity</option> <option value="mdfi">Median Fluorescence Intensity</option> <option value="gmfi">Geometric Mean Fluorescence Intensity</option> </param> </inputs> <outputs> <collection type="list" label="CrossSample on ${input.name}" name="output"> <discover_datasets pattern="(?P<name>.*)" directory="crossSampleOutputs" format="flowclr" /> </collection> <data format="flowstat1" name="stats" label="Population distribution after CrossSample on ${input.name} using ${mfi}"/> <data format="flowstat2" name="mfistats" label="${mfi} centroids of CrossSample on ${input.name} using ${mfi}"/> <data format="flowstat3" name="allstats" label="${mfi} descriptive stats of CrossSample on ${input.name} using ${mfi}"/> </outputs> <tests> <test> <param name="input"> <collection type="list"> <element name="input1" value="input1.flowtext"/> <element name="input2" value="input2.flowtext"/> <element name="input3" value="input3.flowtext"/> </collection> </param> <param name="centroid" value="mfi.flowmfi"/> <param name="mfi" value="mfi"/> <output name="stats" file="out1.flowstat1" lines_diff="6"/> <output name="allstats" file="out1.flowstat3"/> <output name="mfistats" file="out1.flowstat2" compare="sim_size"/> <output_collection name="output" count="3"> <element name="input1.flowtext.flowclr" file="run1/input1.flowtext.flowclr" compare="sim_size"/> <element name="input2.flowtext.flowclr" file="run1/input2.flowtext.flowclr" compare="sim_size"/> <element name="input3.flowtext.flowclr" file="run1/input3.flowtext.flowclr" compare="sim_size"/> </output_collection> </test> <test> <param name="input"> <collection type="list"> <element name="input1" value="input1.flowtext"/> <element name="input2" value="input2.flowtext"/> <element name="input3" value="input3.flowtext"/> </collection> </param> <param name="centroid" value="gmfi.flowmfi"/> <param name="mfi" value="gmfi"/> <output name="stats" file="out2.flowstat1" lines_diff="6"/> <output name="allstats" file="out2.flowstat3"/> <output name="mfistats" file="out2.flowstat2" compare="sim_size"/> <output_collection name="output" type="list" count="3"> <element name="input1.flowtext.flowclr" file="run2/input1.flowtext.flowclr"/> <element name="input2.flowtext.flowclr" file="run2/input2.flowtext.flowclr"/> <element name="input3.flowtext.flowclr" file="run2/input3.flowtext.flowclr"/> </output_collection> </test> </tests> <help><![CDATA[ This tool runs CrossSample using the MFI from FLOCK and text-converted FCS files. ----- **Input** 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. .. class:: infomark The option chosen for the centroids (mean, median or geometric mean) should be the same as used to run FLOCK. **Output** Each event within each file of a dataset collection is attributed to a population depending on its intensity profile. A table of the population composition of each file is generated as well as MFI and population descriptive statistics. .. class:: infomark 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. ----- **Example** *Input* - fluorescence intensities per marker per event:: Marker1 Marker2 Marker3 ... 33 47 11 ... 31 64 11 ... 21 62 99 ... 14 34 60 ... ... ... ... ... *Centroid file* - mean, geometric mean or median fluorescence intensity per marker per population:: Population Marker1 Marker2 Marker3 ... 1 38 49 10 ... 2 21 63 100 ... 3 31 52 45 ... 4 11 78 25 ... ... ... ... ... ... *Output* for each text file - fluorescence intensities per marker and population ID per event:: Marker1 Marker2 Marker3 ... Population 33 47 11 ... 1 31 64 11 ... 6 21 62 99 ... 2 14 34 60 ... 7 ... ... ... ... ... *Summary table* - distribution of events in each population in each file:: Filename SampleName Pop1 Pop2 Pop3 ... File1 Biosample1 0.1 0.25 0.14 ... File2 Biosample2 0.02 0.1 0.17 ... File3 Biosample3 0.4 0.05 0.21 ... File4 Biosample4 0.05 0.3 0.08 ... *Centroid MFI Summary table* - for each file, mean, median or geometric mean fluorescence intensities per marker per population:: Marker1 Marker2 Marker3 ... Population Percentage SampleName 154 885 24 ... 1 0.2 Biosample1 458 74 574 ... 2 0.3 Biosample1 3 210 86 ... 3 0.05 Biosample1 ... ... ... ... ... ... ... 140 921 19 ... 1 0.1 Biosample2 428 79 508 ... 2 0.25 Biosample2 9 225 90 ... 3 0.3 Biosample2 ... ... ... ... ... ... ... *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:: Population Marker1_mean Marker1_median Marker1_stdev ... Percentage_mean Percentage_median Percentage_stdev 1 94.65 90.86 25.8 ... 1.84 0.55 2.48 2 132.18 131.58 5.02 ... 9.89 9.76 0.33 3 71.8 69.68 10.53 ... 3.02 1.49 3.45 4 84.85 84.85 nan ... 8.52 8.52 nan 5 161.82 132.77 61.29 ... 0.95 0.37 1.06 ... ... ... ... ... ... ... ... ]]> </help> <citations> <citation type="doi">10.1002/cyto.b.20554</citation> <citation type="doi">10.3389/fimmu.2012.00302</citation> <citation type="doi">10.1371/journal.pone.0038408</citation> <citation type="doi">10.1371/journal.ppat.1003076</citation> <citation type="doi">10.1016/j.clim.2012.12.003</citation> <citation type="doi">10.1038/srep02327</citation> </citations> </tool>