Mercurial > repos > immport-devteam > flowclr_summary
comparison 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 |
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| children |
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| 0:479ff3a9023c | 1:7a889f2f2e15 |
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| 1 <tool id="flowclr_stats" name="Generate summary statistics" version="1.0+galaxy0"> | |
| 2 <description>of FLOCK output</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.17.1">pandas</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" /> | |
| 8 </stdio> | |
| 9 <command><![CDATA[ | |
| 10 python $__tool_directory__/flowclrstats.py -i '${input}' -p '${output}' -o '${report}' | |
| 11 ]]> | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param format="flowclr" name="input" type="data" collection_type="list" label="FLOCK file"/> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data format="tabular" name="output" label="Summary statistics of ${input.name}"/> | |
| 18 <data format="tabular" name="report" label="Population report of ${input.name}"/> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="input" value="input.flowclr"/> | |
| 23 <output name="output" file="out.tabular" /> | |
| 24 <output name="report" file="report.tabular" /> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help><![CDATA[ | |
| 28 This tool generates summary statistics on FLOCK output. | |
| 29 | |
| 30 ----- | |
| 31 | |
| 32 **Input** | |
| 33 | |
| 34 Any flowclr file, output from FLOCK or Cross Sample, containing fluorescence intensity value par marker and assigned population. | |
| 35 | |
| 36 **Output** | |
| 37 | |
| 38 This tool produces two reports. One indicates the population distribution in the input file, the other gives descriptive summary statistics per population and marker. | |
| 39 | |
| 40 ----- | |
| 41 | |
| 42 **Example** | |
| 43 | |
| 44 *Input* - fluorescence intensities per marker per event:: | |
| 45 | |
| 46 Marker1 Marker2 Marker3 ... Population | |
| 47 33 47 11 ... 1 | |
| 48 31 64 11 ... 6 | |
| 49 21 62 99 ... 2 | |
| 50 14 34 60 ... 7 | |
| 51 ... ... ... ... ... | |
| 52 | |
| 53 | |
| 54 *Output* - Summary statistics:: | |
| 55 | |
| 56 Population . Marker1 Marker2 ... | |
| 57 1 mean 188.7 71.7 ... | |
| 58 1 std 49.6 40.2 ... | |
| 59 1 min 107.0 0.0 ... | |
| 60 1 25% 149.0 40.0 ... | |
| 61 1 50% 183.0 77.0 ... | |
| 62 1 75% 222.0 105.0 ... | |
| 63 1 max 379.0 147.0 ... | |
| 64 2 mean 36.8 186.5 ... | |
| 65 2 std 40.6 50.5 ... | |
| 66 2 min 0.0 119.0 ... | |
| 67 2 25% 0.0 150.0 ... | |
| 68 2 50% 20.0 174.0 ... | |
| 69 2 75% 73.0 208.0 ... | |
| 70 2 max 124.0 433.0 ... | |
| 71 ... ... ... ... ... | |
| 72 | |
| 73 *Output* - Population report:: | |
| 74 | |
| 75 Population Count Percentage | |
| 76 1 3866 43.92 | |
| 77 2 2772 31.50 | |
| 78 3 2163 24.58 | |
| 79 ... ... ... | |
| 80 Total 8801 | |
| 81 ]]> | |
| 82 </help> | |
| 83 </tool> |