Mercurial > repos > immport-devteam > txt_diagnosis
changeset 1:b94872d65050 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
| author | azomics |
|---|---|
| date | Thu, 16 Jul 2020 07:35:26 -0400 |
| parents | e1f0194cf8fc |
| children | |
| files | test-data/input_error.txt test-data/input_noerror.txt test-data/output_error.txt test-data/output_noerror.txt txtDiagnosis.xml txt_diagnosis/test-data/input_error.txt txt_diagnosis/test-data/input_noerror.txt txt_diagnosis/test-data/output_error.txt txt_diagnosis/test-data/output_noerror.txt txt_diagnosis/txtDiagnosis.xml txt_diagnosis/txtdiagnosis.py txtdiagnosis.py |
| diffstat | 12 files changed, 165 insertions(+), 179 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_error.txt Thu Jul 16 07:35:26 2020 -0400 @@ -0,0 +1,16 @@ +Forward Scatter Side Scatter FITC CD4 PE CD25 PP CD3 APC CD45RA +289 56 438 0 626 nan +352 153 30 147 483 386 +383 190 156 228 734 408 +261 62 432 121 598 555 +451 120 537 338 568 nba +373 104 3 110 621 584 +418 105 561 0 610 562 +358 185 0 292 641 327 +733 970 139 227 293 259 +765 1023 71 239 bkl 253 +762 957 143 158 271 255 +406 191 513 122 646 264 +695 1023 168 251 234 283 +336 178 0 146 128 we +668 1023 167 306 302 253
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_noerror.txt Thu Jul 16 07:35:26 2020 -0400 @@ -0,0 +1,16 @@ +Forward Scatter Side Scatter FITC CD4 PE CD25 PP CD3 APC CD45RA +289 56 438 0 626 0 +352 153 30 147 483 386 +383 190 156 228 734 408 +261 62 432 121 598 555 +451 120 537 338 568 111 +373 104 3 110 621 584 +418 105 561 0 610 562 +358 185 0 292 641 327 +733 970 139 227 293 259 +765 1023 71 239 54 253 +762 957 143 158 271 255 +406 191 513 122 646 264 +695 1023 168 251 234 283 +336 178 0 146 128 35 +668 1023 167 306 302 253
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_error.txt Thu Jul 16 07:35:26 2020 -0400 @@ -0,0 +1,3 @@ +WARNING: line 6 in input_error.txt contains non-numeric results +WARNING: line 11 in input_error.txt contains non-numeric results +WARNING: line 15 in input_error.txt contains non-numeric results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_noerror.txt Thu Jul 16 07:35:26 2020 -0400 @@ -0,0 +1,1 @@ +No errors in the file.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/txtDiagnosis.xml Thu Jul 16 07:35:26 2020 -0400 @@ -0,0 +1,64 @@ +<tool id="txt_diagnosis" name="Check data" version="1.1+galaxy0" profile="18.01"> + <description> in txt-converted FCS files</description> + <requirements> + <requirement type="package" version="0.17.1">pandas</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + python '$__tool_directory__/txtdiagnosis.py' -i '${input}' -o '${output}' -n '${input.name}' + ]]> + </command> + <inputs> + <param format="flowtext" name="input" type="data" label="Text file to check"/> + </inputs> + <outputs> + <data format="txt" name="output" label="Report on ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input" value="input_error.txt"/> + <output name="output" file="output_error.txt"> + <assert_contents> + <has_text_matching expression="WARNING: line 6 in .* contains non-numeric results"/> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="input_noerror.txt"/> + <output name="output" file="output_noerror.txt"> + <assert_contents> + <has_text text="No errors in the file."/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + This tool looks for potential errors in txt-converted FCS files. +----- +**Input** +This diagnosis tools reads in text files, and checks that the data is all numeric. +**Output** +The output is a report with the errors and corresponding line numbers. +----- +**Example** +*Input*:: + Marker1 Marker2 Marker3 + 34 45 12 + NaN 65 10 + 34 45 12 + 33 NaN 10 + 34 45 12 + 33 65 10 + 34 45 12 + 33 65 NaN + 34 45 12 + 33 65 10 +*Output*:: + WARNING: line 2 in example_file.txt contains non-numeric results + WARNING: line 4 in example_file.txt contains non-numeric results + WARNING: line 8 in example_file.txt contains non-numeric results + ]]> + </help> +</tool>
--- a/txt_diagnosis/test-data/input_error.txt Mon Feb 27 13:07:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -Forward Scatter Side Scatter FITC CD4 PE CD25 PP CD3 APC CD45RA -289 56 438 0 626 nan -352 153 30 147 483 386 -383 190 156 228 734 408 -261 62 432 121 598 555 -451 120 537 338 568 nba -373 104 3 110 621 584 -418 105 561 0 610 562 -358 185 0 292 641 327 -733 970 139 227 293 259 -765 1023 71 239 bkl 253 -762 957 143 158 271 255 -406 191 513 122 646 264 -695 1023 168 251 234 283 -336 178 0 146 128 we -668 1023 167 306 302 253
--- a/txt_diagnosis/test-data/input_noerror.txt Mon Feb 27 13:07:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -Forward Scatter Side Scatter FITC CD4 PE CD25 PP CD3 APC CD45RA -289 56 438 0 626 0 -352 153 30 147 483 386 -383 190 156 228 734 408 -261 62 432 121 598 555 -451 120 537 338 568 111 -373 104 3 110 621 584 -418 105 561 0 610 562 -358 185 0 292 641 327 -733 970 139 227 293 259 -765 1023 71 239 54 253 -762 957 143 158 271 255 -406 191 513 122 646 264 -695 1023 168 251 234 283 -336 178 0 146 128 35 -668 1023 167 306 302 253
--- a/txt_diagnosis/test-data/output_error.txt Mon Feb 27 13:07:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -WARNING: line 6 in input_error.txt contains non-numeric results -WARNING: line 11 in input_error.txt contains non-numeric results -WARNING: line 15 in input_error.txt contains non-numeric results
--- a/txt_diagnosis/test-data/output_noerror.txt Mon Feb 27 13:07:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -No errors in the file.
--- a/txt_diagnosis/txtDiagnosis.xml Mon Feb 27 13:07:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,75 +0,0 @@ -<tool id="txt_diagnosis" name="Check data" version="1.1"> - <description> in txt-converted FCS files.</description> - <requirements> - <requirement type="package" version="0.17.1">pandas</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command><![CDATA[ - python $__tool_directory__/txtdiagnosis.py -i "${input}" -o "${output}" -n "${input.name}" - ]]> - </command> - <inputs> - <param format="flowtext" name="input" type="data" label="Text file to check"/> - </inputs> - <outputs> - <data format="txt" name="output" label="Report on ${input.name}"/> - </outputs> - <tests> - <test> - <param name="input" value="input_error.txt"/> - <output name="output" file="output_error.txt"> - <assert_contents> - <has_text_matching text="WARNING: line 6 in .* contains non-numeric results"/> - </assert_contents> - </output> - </test> - <test> - <param name="input" value="input_noerror.txt"/> - <output name="output" file="output_noerror.txt"> - <assert_contents> - <has_text text="No errors in the file."/> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[ - This tool looks for potential errors in txt-converted FCS files. - ------ - -**Input** - -This diagnosis tools reads in text files, and checks that the data is all numeric. - -**Output** - -The output is a report with the errors and corresponding line numbers. - ------ - -**Example** - -*Input*:: - - Marker1 Marker2 Marker3 - 34 45 12 - NaN 65 10 - 34 45 12 - 33 NaN 10 - 34 45 12 - 33 65 10 - 34 45 12 - 33 65 NaN - 34 45 12 - 33 65 10 - -*Output*:: - - WARNING: line 2 in example_file.txt contains non-numeric results - WARNING: line 4 in example_file.txt contains non-numeric results - WARNING: line 8 in example_file.txt contains non-numeric results - ]]> - </help> -</tool>
--- a/txt_diagnosis/txtdiagnosis.py Mon Feb 27 13:07:11 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ -#!/usr/bin/env python -###################################################################### -# Copyright (c) 2016 Northrop Grumman. -# All rights reserved. -###################################################################### -from __future__ import print_function -from __future__ import division -import pandas as pd -from argparse import ArgumentParser -import sys - - -def is_number(s): - try: - float(s) - return True - except ValueError: - return False - - -def error_report(input_file, fname, output_file): - errors = 0 - df = pd.read_table(input_file) - with open(output_file, "w") as outf: - for cols in df.columns.values: - if df[cols].count() != len(df[cols]): - with open(input_file, "r") as checkfile: - fl = checkfile.readline() - count_lines = 1 - for checklines in checkfile: - to_check = checklines.strip().split("\t") - count_lines += 1 - for item in to_check: - if not is_number(item): - errors += 1 - outf.write(" ".join(["WARNING: line", str(count_lines), "in", fname, "contains non-numeric results\n"])) - if errors == 0: - outf.write("No errors in the file.\n") - return - - -if __name__ == "__main__": - parser = ArgumentParser( - prog="txtDiagnosis", - description="Reports potential errors in text-converted FCS files") - - parser.add_argument( - '-i', - dest="input_file", - required=True, - help="File location for the text file.") - - parser.add_argument( - '-n', - dest="filename", - required=True, - help="Filename location for the text file.") - - parser.add_argument( - '-o', - dest="output_file", - required=True, - help="Name of the output file.") - - args = parser.parse_args() - - error_report(args.input_file, args.filename, args.output_file) - sys.exit(0)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/txtdiagnosis.py Thu Jul 16 07:35:26 2020 -0400 @@ -0,0 +1,65 @@ +#!/usr/bin/env python +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +import pandas as pd +from argparse import ArgumentParser +import sys + + +def is_number(s): + try: + float(s) + return True + except ValueError: + return False + + +def error_report(input_file, fname, output_file): + errors = 0 + df = pd.read_table(input_file) + with open(output_file, "w") as outf: + for cols in df.columns.values: + if df[cols].count() != len(df[cols]): + with open(input_file, "r") as checkfile: + fl = checkfile.readline() + count_lines = 1 + for checklines in checkfile: + to_check = checklines.strip().split("\t") + count_lines += 1 + for item in to_check: + if not is_number(item): + errors += 1 + outf.write(" ".join(["WARNING: line", str(count_lines), "in", fname, "contains non-numeric results\n"])) + if errors == 0: + outf.write("No errors in the file.\n") + return + + +if __name__ == "__main__": + parser = ArgumentParser( + prog="txtDiagnosis", + description="Reports potential errors in text-converted FCS files") + + parser.add_argument( + '-i', + dest="input_file", + required=True, + help="File location for the text file.") + + parser.add_argument( + '-n', + dest="filename", + required=True, + help="Filename location for the text file.") + + parser.add_argument( + '-o', + dest="output_file", + required=True, + help="Name of the output file.") + + args = parser.parse_args() + + error_report(args.input_file, args.filename, args.output_file)