Mercurial > repos > immport-devteam > auto_collapse_pop
view auto_collapse_pop/auto_collapse_pops.xml @ 0:7632562ada41 draft
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author | immport-devteam |
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date | Mon, 27 Feb 2017 12:14:29 -0500 |
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<tool id="auto_collapse_populations" name="Collapse populations automatically" version="1.0"> <description>based on quartile binning from FLOCK results.</description> <requirements> <requirement type="package" version="0.17.1">pandas</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ python $__tool_directory__/auto_collapse_pops.py -o "${output}" -i "${input}" -p "${profile}" -r "${report}" ]]> </command> <inputs> <param format="flowclr" name="input" type="data" label="FLOCK or Cross-Sample output file"/> <param format="flowscore" name="profile" type="data" label="Population score profiles from FLOCK"/> </inputs> <outputs> <data format="flowclr" name="output" label="Auto-collapsed pops in ${input.name}"/> <data format="tabular" name="report" label="Auto-collapse report for ${input.name} with ${profile.name}"/> </outputs> <tests> <test> <param name="input" value="input.flowclr"/> <param name="profile=" value="profile.flowscore"/> <param name="report" value="report.txt"/> <output name="output" file="output.flowclr"/> </test> </tests> <help><![CDATA[ This tool automatically collapses populations together based on FLOCK score profiles. ----- .. class:: warningmark *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* ----- **Input** 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. **Output** The input file with selected populations replaced by the indicated population. This tool also generates a report. ----- **Example** *Input* - 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 3 *Population profile file*:: Population_ID Marker1 Marker2 Marker3 Count Percentage 1 2 2 3 3885 6.44 2 1 3 4 2774 4.62 3 2 2 3 2151 3.59 4 1 3 2 1207 2.01 *Output* - fluorescence intensities per marker and population ID per event:: Marker1 Marker2 Marker3 Population 34 45 12 1 33 65 10 4 19 62 98 2 12 36 58 1 *Output* - fluorescence intensities per marker and population ID per event:: New_Population Former_Populations Marker1 Marker2 Marker3 1 1, 3 2 2 3 2 2 1 3 4 3 4 1 3 2 4 5, 8, 12 3 1 1 ]]> </help> </tool>