Mercurial > repos > immport-devteam > run_flock
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runFlockMFI.xml Fri Jul 17 09:06:54 2020 -0400 @@ -0,0 +1,166 @@ +<tool id="run_flock" name="Run FLOCK" version="1.2+galaxy0" profile="18.01"> + <description>using a FCS file that was converted/transformed to a text file</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:" /> + </stdio> + <command><![CDATA[ + python3 '$__tool_directory__/runFlockMFI.py' -i '${input}' -m '${method}' -o '${output}' -c '${centroid}' -M '${mfi}' -p '${profile}' + #if $bins + -b $bins + #end if + #if $density + -d $density + #end if + ]]> + </command> + <inputs> + <param format="flowtext" name="input" type="data" label="Source file"/> + <param name="method" type="select" label="Method"> + <option value="flock1" selected="true">Flock Version 1</option> + <option value="flock2">Flock Version 2</option> + </param> + <param name="bins" type="integer" min="6" max="30" optional="true" value="" label="bins (6-30)"/> + <param name="density" type="integer" min="2" max="100" optional="true" value="" label="density (2-100)"/> + <param name="mfi" type="select" label="Calculate centroids using:"> + <option value="mfi" selected="true">Mean Fluorescence Intensity</option> + <option value="mdfi">Median Fluorescence Intensity</option> + <option value="gmfi">Geometric Mean Fluorescence Intensity</option> + </param> + </inputs> + <outputs> + <data format="flowclr" name="output" label="${method} with ${mfi} on ${input.name}"/> + <data format="flowmfi" name="centroid" label="${mfi} centroids from ${method} on ${input.name}"/> + <data format="flowscore" name="profile" label="Population score profiles from ${method} on ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input" value="input.flowtext"/> + <param name="method" value="flock1"/> + <param name="bins" value=""/> + <param name="density" value=""/> + <param name="mfi" value="mfi"/> + <output name="output" file="out1.flowclr"/> + <output name="centroid" file="mfi.flowmfi"/> + <output name="profile" file="out1.flowscore"/> + </test> + <test> + <param name="input" value="input.flowtext"/> + <param name="method" value="flock2"/> + <param name="bins" value=""/> + <param name="density" value=""/> + <param name="mfi" value="mfi"/> + <output name="output" file="out2.flowclr"/> + <output name="centroid" file="mfi2.flowmfi"/> + <output name="profile" file="out2.flowscore"/> + </test> + <test> + <param name="input" value="input.flowtext"/> + <param name="method" value="flock1"/> + <param name="bins" value="7"/> + <param name="density" value="3"/> + <param name="mfi" value="mfi"/> + <output name="output" file="out3.flowclr"/> + <output name="centroid" file="mfi3.flowmfi"/> + <output name="profile" file="out3.flowscore"/> + </test> + </tests> + <help><![CDATA[ + This tool runs FLOCK using a FCS file that was converted to a text file. + +----- + +.. image:: ./static/images/flowtools/flock_logo.png + +FLOCK (FLOw Clustering without K) is a computational approach to flow cytometry analysis which: + + 1. Computationally determines the number of unique populations in high dimensional flow data using a rapid binning approach + 2. Can handle non-spherical hyper-shapes + 3. Maps populations across independent samples + 4. Calculates many useful summary statistics + 5. Finds the most informative parameters + 6. Reduces subjective factors in manual gating + +.. class:: warningmark + +This tool is not intended to analyze CyTOF data as is. + +----- + +**Input** + +FLOCK requires a text file, generated from a FCS file, as input. +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. + +.. class:: infomark + +Tip: Make sure to keep only columns containing data from markers. + +**Output** + +*FLOCK* + +FLOCK attributes each event to a population and generates a text file. + +*Centroids* + +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. + +*Population scores* + +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: + +- 1 implies negative expression +- 2 implies low expression +- 3 implies positive expression +- 4 implies highly positive expression + +----- + +**Example** + +*Input* - fluorescence intensities per marker per event:: + + Marker1 Marker2 Marker3 ... + 34 45 12 ... + 33 65 10 ... + 19 62 98 ... + 12 36 58 ... + ... ... ... ... + +*FLOCK Output* - fluorescence intensities per marker and population ID per event:: + + Marker1 Marker2 Marker3 ... Population + 34 45 12 ... 1 + 33 65 10 ... 5 + 19 62 98 ... 2 + 12 36 58 ... 1 + ... ... ... ... ... + +*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 ... + ... ... ... ... ... + +*Population profile file*:: + + Population_ID Marker1 Marker2 Marker3 ... Count Percentage + 1 1 3 2 ... 3885 6.44 + 2 1 3 4 ... 2774 4.62 + 3 2 2 3 ... 2151 3.59 + 4 1 3 2 ... 1207 2.01 + ... ... ... ... ... ... ... + ]]> + </help> + <citations> + <citation type="doi">10.1002/cyto.b.20554</citation> + </citations> +</tool>