| Next changeset 1:05440ef97f8b (2020-07-14) |
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Commit message:
Uploaded |
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added:
check_headers/getHeaders.py check_headers/getHeaders.xml check_headers/test-data/input1.txt check_headers/test-data/input2.txt check_headers/test-data/input3.txt check_headers/test-data/output.tabular |
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| diff -r 000000000000 -r e88c99a4fb36 check_headers/getHeaders.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_headers/getHeaders.py Mon Feb 27 12:41:17 2017 -0500 |
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| @@ -0,0 +1,50 @@ +#!/usr/bin/env python +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +from __future__ import print_function +import sys + +from argparse import ArgumentParser + + +def print_headers(files, filenames, outfile): + with open(outfile, "w") as outf: + for i, eachfile in enumerate(files): + with open(eachfile, "r") as ef: + headers = ef.readline() + outf.write("\t".join([filenames[i], headers])) + return + + +if __name__ == "__main__": + parser = ArgumentParser( + prog="GetHeaders", + description="Gets the headers of all files in given set.") + + parser.add_argument( + '-i', + dest="input_files", + required=True, + action='append', + help="File location for the text files.") + + parser.add_argument( + '-n', + dest="file_names", + required=True, + action='append', + help="File names.") + + parser.add_argument( + '-o', + dest="output_file", + required=True, + help="Name of the output file.") + + args = parser.parse_args() + input_files = [f for f in args.input_files] + file_names = [fn for fn in args.file_names] + print_headers(input_files, file_names, args.output_file) + sys.exit(0) |
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| diff -r 000000000000 -r e88c99a4fb36 check_headers/getHeaders.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_headers/getHeaders.xml Mon Feb 27 12:41:17 2017 -0500 |
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| @@ -0,0 +1,67 @@ +<tool id="get_headers" name="Check headers" version="1.1"> + <description>of any set of flowtext files.</description> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + python $__tool_directory__/getHeaders.py -o "${output_file}" + #for $f in $input# + -i "${f}" + -n "${f.name}" + #end for# + ]]> + </command> + <inputs> + <param format="flowtext" name="input" type="data_collection" collection_type="list" label="Text files Collection"/> + </inputs> + <outputs> + <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input"> + <collection type="list"> + <element name="input1.txt" value="input1.txt"/> + <element name="input2.txt" value="input2.txt"/> + <element name="input3.txt" value="input3.txt"/> + </collection> + </param> + <output name="output_file" file="output.tabular"/> + </test> + </tests> + <help><![CDATA[ + This tool returns a table of the headers of a set of text files. + +----- + +**Input files** + +This tool requires collections of txt, flowtext or tabular files as input. + +**Output file** + +The output file is a table listing the headers for each file. + +----- + +**Example** + +*File1*:: + + Marker1 Marker2 Marker3 + 34 45 12 + 33 65 10 + +*File2*:: + + Marker4 Marker5 Marker3 + 19 62 98 + 12 36 58 + +*Output*:: + + File1 Marker1 Marker2 Marker3 + File2 Marker4 Marker5 Marker3 + ]]> + </help> +</tool> |
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| diff -r 000000000000 -r e88c99a4fb36 check_headers/test-data/input1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_headers/test-data/input1.txt Mon Feb 27 12:41:17 2017 -0500 |
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| @@ -0,0 +1,10 @@ +Forward Scatter Side Scatter FITC CD4 PE CCR3 PP CD8 APC CCR4 +449 157 551 129 169 292 +894 1023 199 277 320 227 +262 73 437 69 0 146 +340 115 509 268 0 74 +316 76 50 0 60 129 +394 144 83 138 335 194 +383 139 499 0 0 224 +800 1023 239 284 288 280 +388 97 534 111 83 177 |
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| diff -r 000000000000 -r e88c99a4fb36 check_headers/test-data/input2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_headers/test-data/input2.txt Mon Feb 27 12:41:17 2017 -0500 |
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| @@ -0,0 +1,10 @@ +Forward Scatter Side Scatter FITC CD4 PE CXCR3 PP CD8 APC CCR5 +363 76 550 200 0 127 +372 126 519 44 51 148 +1023 1023 289 401 362 254 +770 1023 175 361 225 237 +384 111 525 121 0 138 +602 578 385 286 222 131 +788 1023 216 310 270 294 +420 211 552 479 0 62 +668 1019 73 193 227 132 |
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| diff -r 000000000000 -r e88c99a4fb36 check_headers/test-data/input3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_headers/test-data/input3.txt Mon Feb 27 12:41:17 2017 -0500 |
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| @@ -0,0 +1,10 @@ +Forward Scatter Side Scatter FITC CD4 PE CD25 PP CD3 APC CD45RA +289 56 438 0 626 480 +352 153 30 147 483 386 +383 190 156 228 734 408 +261 62 432 121 598 555 +451 120 537 338 568 201 +373 104 3 110 621 584 +418 105 561 0 610 562 +358 185 0 292 641 327 +733 970 139 227 293 259 |
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| diff -r 000000000000 -r e88c99a4fb36 check_headers/test-data/output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_headers/test-data/output.tabular Mon Feb 27 12:41:17 2017 -0500 |
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| @@ -0,0 +1,3 @@ +input1.txt Forward Scatter Side Scatter FITC CD4 PE CCR3 PP CD8 APC CCR4 +input2.txt Forward Scatter Side Scatter FITC CD4 PE CXCR3 PP CD8 APC CCR5 +input3.txt Forward Scatter Side Scatter FITC CD4 PE CD25 PP CD3 APC CD45RA |