Mercurial > repos > immport-devteam > cross_sample
diff 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 |
|---|---|
| date | Wed, 29 Jul 2020 13:32:17 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/runCrossSample.xml Wed Jul 29 13:32:17 2020 -0400 @@ -0,0 +1,148 @@ +<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>