Mercurial > repos > immport-devteam > auto_collapse_pop
comparison auto_collapse_pops.xml @ 1:08b71aee9b80 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
| author | azomics |
|---|---|
| date | Mon, 22 Jun 2020 17:22:03 -0400 |
| parents | |
| children |
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| 0:7632562ada41 | 1:08b71aee9b80 |
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| 1 <tool id="auto_collapse_populations" name="Collapse populations automatically" version="1.0+galaxy1"> | |
| 2 <description>based on quartile binning from FLOCK results</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 '$__tool_directory__/auto_collapse_pops.py' -o '${output}' -i '${input}' -p '${profile}' -r '${report}' | |
| 11 ]]> | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param format="flowclr" name="input" type="data" label="FLOCK or Cross-Sample output file"/> | |
| 15 <param format="flowscore" name="profile" type="data" label="Population score profiles from FLOCK"/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="flowclr" name="output" label="Auto-collapsed pops in ${input.name}"/> | |
| 19 <data format="tabular" name="report" label="Auto-collapse report for ${input.name} with ${profile.name}"/> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="input" value="input.flowclr"/> | |
| 24 <param name="profile" value="profile.flowscore"/> | |
| 25 <param name="report" value="report.txt"/> | |
| 26 <output name="output" file="output.flowclr" compare="sim_size"/> | |
| 27 </test> | |
| 28 </tests> | |
| 29 <help><![CDATA[ | |
| 30 This tool automatically collapses populations together based on FLOCK score profiles. | |
| 31 | |
| 32 ----- | |
| 33 | |
| 34 .. class:: warningmark | |
| 35 | |
| 36 *FLOCK score profiles are assigned based on quartile binning of the data. As always, use this tool with caution and be critical of your results* | |
| 37 | |
| 38 ----- | |
| 39 | |
| 40 **Input** | |
| 41 | |
| 42 FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each, as well as the file containing the score profiles for each FLOCK population. | |
| 43 | |
| 44 **Output** | |
| 45 | |
| 46 The input file with selected populations replaced by the indicated population. This tool also generates a report. | |
| 47 | |
| 48 ----- | |
| 49 | |
| 50 **Example** | |
| 51 | |
| 52 *Input* - fluorescence intensities per marker and population ID per event:: | |
| 53 | |
| 54 Marker1 Marker2 Marker3 ... Population | |
| 55 34 45 12 ... 1 | |
| 56 33 65 10 ... 5 | |
| 57 19 62 98 ... 2 | |
| 58 12 36 58 ... 3 | |
| 59 ... ... ... ... ... | |
| 60 | |
| 61 *Population profile file*:: | |
| 62 | |
| 63 Population_ID Marker1 Marker2 Marker3 ... Count Percentage | |
| 64 1 2 2 3 ... 3885 6.44 | |
| 65 2 1 3 4 ... 2774 4.62 | |
| 66 3 2 2 3 ... 2151 3.59 | |
| 67 4 1 3 2 ... 1207 2.01 | |
| 68 ... ... ... ... ... ... ... | |
| 69 | |
| 70 *Output* - fluorescence intensities per marker and population ID per event:: | |
| 71 | |
| 72 Marker1 Marker2 Marker3 ... Population | |
| 73 34 45 12 ... 1 | |
| 74 33 65 10 ... 4 | |
| 75 19 62 98 ... 2 | |
| 76 12 36 58 ... 1 | |
| 77 ... ... ... ... ... | |
| 78 | |
| 79 *Output* - fluorescence intensities per marker and population ID per event:: | |
| 80 | |
| 81 New_Population Former_Populations Marker1 Marker2 Marker3 ... | |
| 82 1 1, 3 2 2 3 ... | |
| 83 2 2 1 3 4 ... | |
| 84 3 4 1 3 2 ... | |
| 85 4 5, 8, 12 3 1 1 ... | |
| 86 ... ... ... ... ... ... | |
| 87 ]]> | |
| 88 </help> | |
| 89 </tool> |