Mercurial > repos > immport-devteam > extract_pop
changeset 1:4f28ee74079b draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_pop commit 117c0e4a5c00dfd2e190359badf77d5643fccefa"
| author | azomics |
|---|---|
| date | Fri, 24 Jul 2020 19:24:49 -0400 |
| parents | 21b2dc3934ed |
| children | |
| files | extract_pop/extractpop.py extract_pop/extractpop.xml extract_pop/test-data/input.txt extract_pop/test-data/output.flowtext extractpop.py extractpop.xml test-data/input.txt test-data/output.flowtext |
| diffstat | 8 files changed, 191 insertions(+), 190 deletions(-) [+] |
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--- a/extract_pop/extractpop.py Mon Feb 27 12:50:08 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ -#!/usr/bin/env python - -###################################################################### -# Copyright (c) 2016 Northrop Grumman. -# All rights reserved. -###################################################################### - -from __future__ import print_function -import sys -import pandas as pd - -from argparse import ArgumentParser - - -def is_int(s): - try: - int(s) - return True - except ValueError: - return False - - -def extract_pop(in_file, pop_list, out_file): - df = pd.read_table(in_file, dtype={'Population': object}) - dfout = df.loc[df['Population'].isin(pop_list)] - dfout.to_csv(out_file, sep="\t", index=False) - return - - -def remove_pop(in_file, pop_list, out_file): - df = pd.read_table(in_file, dtype={'Population': object}) - dfout = df.loc[~df['Population'].isin(pop_list)] - dfout.to_csv(out_file, sep="\t", index=False) - return - - -if __name__ == "__main__": - parser = ArgumentParser( - prog="ExtractPop", - description="Extract events associated to given population numbers.") - - parser.add_argument( - '-i', - dest="input_file", - required=True, - help="File location for the text file.") - - parser.add_argument( - '-p', - dest="pops", - required=True, - help="List of populations to extract.") - - parser.add_argument( - '-o', - dest="output_file", - required=True, - help="Name of the output file.") - - parser.add_argument( - '-m', - dest="method", - required=True, - help="What to do with the populations.") - - args = parser.parse_args() - - # check populations - default_values = ["i.e.:2,3,11,25", "default", "Default"] - populations = [] - if args.pops: - if args.pops not in default_values: - tmp_pops = args.pops.split(",") - for popn in tmp_pops: - populations.append(popn.strip()) - else: - sys.exit(2) - for pops in populations: - if not is_int(pops): - sys.exit(3) - if args.method == "selected": - extract_pop(args.input_file, populations, args.output_file) - else: - remove_pop(args.input_file, populations, args.output_file) - sys.exit(0)
--- a/extract_pop/extractpop.xml Mon Feb 27 12:50:08 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,90 +0,0 @@ -<tool id="extract_pop" name="Extract populations" version="1.0"> - <description>of interest from FLOCK or Cross Sample output.</description> - <requirements> - <requirement type="package" version="0.17.1">pandas</requirement> - </requirements> - <stdio> - <exit_code range="2" level="fatal" description="Please provide a comma separated list of populations to extract." /> - <exit_code range="3" level="fatal" description="The populations to extract must be integers (i.e,: 1,2,4.)" /> - </stdio> - <command><![CDATA[ - python $__tool_directory__/extractpop.py -i "${input}" -o "${output}" -p "${population}" -m "${method}" - ]]> - </command> - <inputs> - <param format="flowclr" name="input" type="data" label="Source file"/> - <param name="population" type="text" label="Populations:" value="i.e.:2,3,11,25"/> - <param name="method" type="select" label="What would you like to do?"> - <option value="selected">Keep only these populations.</option> - <option value="removed">Remove these populations.</option> - </param> - </inputs> - <outputs> - <data format="flowtext" name="output" label="Populations ${population} ${method} from ${input.name}"/> - </outputs> - <tests> - <test> - <param name="input" value="input.txt"/> - <param name="population" value="2,4"/> - <param name="method" value="selected"/> - <output name="output" file="output.flowtext"/> - </test> - </tests> - <help><![CDATA[ - This tool extracts events from given populations from FLOCK or Cross Sample outputs. - ------ - -**Input** - -FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each. - -**Output** - -The input file filtered for selected populations. - ------ - -**Example 1** - -*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 1 - -*Populations selected:* 2 - -*Method:* Keep only the selected populations - -*Output* - fluorescence intensities per marker and population ID per event:: - - Marker1 Marker2 Marker3 Population - 19 62 98 2 - -**Example 2** - -*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 1 - - *Populations selected:* 2 - - *Method:* Remove the selected populations - - *Output* - fluorescence intensities per marker and population ID per event:: - - Marker1 Marker2 Marker3 Population - 34 45 12 1 - 33 65 10 5 - 12 36 58 1 - - ]]> - </help> -</tool>
--- a/extract_pop/test-data/input.txt Mon Feb 27 12:50:08 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -Forward Scatter Side Scatter FITC CD4 PE CCR3 PP CD8 APC CCR4 Population -449 157 551 129 169 292 1 -894 1023 199 277 320 227 4 -262 73 437 69 0 146 1 -340 115 509 268 0 74 2 -316 76 50 0 60 129 5 -394 144 83 138 335 194 3 -383 139 499 0 0 224 6 -800 1023 239 284 288 280 2 -388 97 534 111 83 177 4
--- a/extract_pop/test-data/output.flowtext Mon Feb 27 12:50:08 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -Forward Scatter Side Scatter FITC CD4 PE CCR3 PP CD8 APC CCR4 Population -894 1023 199 277 320 227 4 -340 115 509 268 0 74 2 -800 1023 239 284 288 280 2 -388 97 534 111 83 177 4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extractpop.py Fri Jul 24 19:24:49 2020 -0400 @@ -0,0 +1,84 @@ +#!/usr/bin/env python + +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### + +from __future__ import print_function +import sys +import pandas as pd + +from argparse import ArgumentParser + + +def is_int(s): + try: + int(s) + return True + except ValueError: + return False + + +def extract_pop(in_file, pop_list, out_file): + df = pd.read_table(in_file, dtype={'Population': object}) + dfout = df.loc[df['Population'].isin(pop_list)] + dfout.to_csv(out_file, sep="\t", index=False) + return + + +def remove_pop(in_file, pop_list, out_file): + df = pd.read_table(in_file, dtype={'Population': object}) + dfout = df.loc[~df['Population'].isin(pop_list)] + dfout.to_csv(out_file, sep="\t", index=False) + return + + +if __name__ == "__main__": + parser = ArgumentParser( + prog="ExtractPop", + description="Extract events associated to given population numbers.") + + parser.add_argument( + '-i', + dest="input_file", + required=True, + help="File location for the text file.") + + parser.add_argument( + '-p', + dest="pops", + required=True, + help="List of populations to extract.") + + parser.add_argument( + '-o', + dest="output_file", + required=True, + help="Name of the output file.") + + parser.add_argument( + '-m', + dest="method", + required=True, + help="What to do with the populations.") + + args = parser.parse_args() + + # check populations + default_values = ["i.e.:2,3,11,25", "default", "Default"] + populations = [] + if args.pops: + if args.pops not in default_values: + tmp_pops = args.pops.split(",") + for popn in tmp_pops: + populations.append(popn.strip()) + else: + sys.exit(2) + for pops in populations: + if not is_int(pops): + sys.exit(3) + if args.method == "selected": + extract_pop(args.input_file, populations, args.output_file) + else: + remove_pop(args.input_file, populations, args.output_file)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extractpop.xml Fri Jul 24 19:24:49 2020 -0400 @@ -0,0 +1,92 @@ +<tool id="extract_pop" name="Extract populations" version="1.0+galaxy0" profile="18.01"> + <description>of interest from FLOCK or Cross Sample output</description> + <requirements> + <requirement type="package" version="1.0.5">pandas</requirement> + </requirements> + <stdio> + <exit_code range="1"/> + <exit_code range="2" level="fatal" description="Please provide a comma separated list of populations to extract." /> + <exit_code range="3" level="fatal" description="The populations to extract must be integers (i.e,: 1,2,4.)" /> + <exit_code range="4:"/> + </stdio> + <command><![CDATA[ + python '$__tool_directory__/extractpop.py' -i '${input}' -o '${output}' -p '${population}' -m '${method}' + ]]> + </command> + <inputs> + <param format="flowclr" name="input" type="data" label="Source file"/> + <param name="population" type="text" label="Populations:" value="i.e.:2,3,11,25"/> + <param name="method" type="select" label="What would you like to do?"> + <option value="selected">Keep only these populations.</option> + <option value="removed">Remove these populations.</option> + </param> + </inputs> + <outputs> + <data format="flowtext" name="output" label="Populations ${population} ${method} from ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input" value="input.txt"/> + <param name="population" value="2,4"/> + <param name="method" value="selected"/> + <output name="output" file="output.flowtext"/> + </test> + </tests> + <help><![CDATA[ + This tool extracts events from given populations from FLOCK or Cross Sample outputs. + +----- + +**Input** + +FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each. + +**Output** + +The input file filtered for selected populations. + +----- + +**Example 1** + +*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 1 + +*Populations selected:* 2 + +*Method:* Keep only the selected populations + +*Output* - fluorescence intensities per marker and population ID per event:: + + Marker1 Marker2 Marker3 Population + 19 62 98 2 + +**Example 2** + +*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 1 + + *Populations selected:* 2 + + *Method:* Remove the selected populations + + *Output* - fluorescence intensities per marker and population ID per event:: + + Marker1 Marker2 Marker3 Population + 34 45 12 1 + 33 65 10 5 + 12 36 58 1 + + ]]> + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.txt Fri Jul 24 19:24:49 2020 -0400 @@ -0,0 +1,10 @@ +Forward Scatter Side Scatter FITC CD4 PE CCR3 PP CD8 APC CCR4 Population +449 157 551 129 169 292 1 +894 1023 199 277 320 227 4 +262 73 437 69 0 146 1 +340 115 509 268 0 74 2 +316 76 50 0 60 129 5 +394 144 83 138 335 194 3 +383 139 499 0 0 224 6 +800 1023 239 284 288 280 2 +388 97 534 111 83 177 4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.flowtext Fri Jul 24 19:24:49 2020 -0400 @@ -0,0 +1,5 @@ +Forward Scatter Side Scatter FITC CD4 PE CCR3 PP CD8 APC CCR4 Population +894 1023 199 277 320 227 4 +340 115 509 268 0 74 2 +800 1023 239 284 288 280 2 +388 97 534 111 83 177 4