Mercurial > repos > immport-devteam > flowclr_summary
diff flowclrstats.xml @ 1:7a889f2f2e15 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowclr_summary commit ce895377ed593ace77016bd019a7998e13e470cc"
| author | azomics |
|---|---|
| date | Mon, 22 Jun 2020 19:55:57 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowclrstats.xml Mon Jun 22 19:55:57 2020 -0400 @@ -0,0 +1,83 @@ +<tool id="flowclr_stats" name="Generate summary statistics" version="1.0+galaxy0"> + <description>of FLOCK output</description> + <requirements> + <requirement type="package" version="0.17.1">pandas</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + python $__tool_directory__/flowclrstats.py -i '${input}' -p '${output}' -o '${report}' + ]]> + </command> + <inputs> + <param format="flowclr" name="input" type="data" collection_type="list" label="FLOCK file"/> + </inputs> + <outputs> + <data format="tabular" name="output" label="Summary statistics of ${input.name}"/> + <data format="tabular" name="report" label="Population report of ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input" value="input.flowclr"/> + <output name="output" file="out.tabular" /> + <output name="report" file="report.tabular" /> + </test> + </tests> + <help><![CDATA[ + This tool generates summary statistics on FLOCK output. + +----- + +**Input** + +Any flowclr file, output from FLOCK or Cross Sample, containing fluorescence intensity value par marker and assigned population. + +**Output** + +This tool produces two reports. One indicates the population distribution in the input file, the other gives descriptive summary statistics per population and marker. + +----- + +**Example** + +*Input* - fluorescence intensities per marker per event:: + + Marker1 Marker2 Marker3 ... Population + 33 47 11 ... 1 + 31 64 11 ... 6 + 21 62 99 ... 2 + 14 34 60 ... 7 + ... ... ... ... ... + + +*Output* - Summary statistics:: + + Population . Marker1 Marker2 ... + 1 mean 188.7 71.7 ... + 1 std 49.6 40.2 ... + 1 min 107.0 0.0 ... + 1 25% 149.0 40.0 ... + 1 50% 183.0 77.0 ... + 1 75% 222.0 105.0 ... + 1 max 379.0 147.0 ... + 2 mean 36.8 186.5 ... + 2 std 40.6 50.5 ... + 2 min 0.0 119.0 ... + 2 25% 0.0 150.0 ... + 2 50% 20.0 174.0 ... + 2 75% 73.0 208.0 ... + 2 max 124.0 433.0 ... + ... ... ... ... ... + +*Output* - Population report:: + + Population Count Percentage + 1 3866 43.92 + 2 2772 31.50 + 3 2163 24.58 + ... ... ... + Total 8801 + ]]> + </help> +</tool>