Mercurial > repos > immport-devteam > auto_collapse_pop
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/auto_collapse_pop/auto_collapse_pops.xml Mon Feb 27 12:14:29 2017 -0500 @@ -0,0 +1,85 @@ +<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>