| Next changeset 1:d533e4b75800 (2018-09-23) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn commit 045006e0b2fe5b4fe96583949b0c757eb6a734a4 |
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added:
replaceColumn.xml test-data/GRCh38_ensembl2UCSC.txt test-data/empty_mapping test-data/original_file test-data/result_file test-data/result_file_empty_mapping |
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| diff -r 000000000000 -r cc18bac5afdb replaceColumn.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/replaceColumn.xml Fri Feb 24 10:14:15 2017 -0500 |
| [ |
| @@ -0,0 +1,107 @@ +<tool id="replace_column_with_key_value_file" name="Replace column" version="0.1"> + <description>by values which are defined in a convert file</description> + <command> + <![CDATA[ + python '$replaceColumnScript' + ]]> + </command> + <configfiles> + <configfile name="replaceColumnScript"> + <![CDATA[ +import sys + +replace_file = '$replace_information' +original_file = '$original_file' +column = int("$column_replace") - 1 +ignore_start_lines = int("$skip_lines") +delimiter_local = "\t" if str("$delimiter") == "" else str("$delimiter") + +## read conversion information to index +conversion = {} + +with open(replace_file, 'r') as conversion_file: + for line in conversion_file: + conv_key_value = line.strip().split() + if len(conv_key_value) == 2: + conversion[conv_key_value[0]] = conv_key_value[1] + +## read file line by line, search for column entry if it can be replaced. Otherwise it will be skipped. +with open("output_file", 'w') as output: + with open(original_file) as original: + for i, line in enumerate(original): + if i < ignore_start_lines: + output.write(line) + continue + + if str("$delimiter") == "": + line_content = line.split() + else: + line_content = line.split(str("$delimiter")) + + out = list() + for j, line_content_column in enumerate(line_content): + if j == column: + if line_content_column in conversion: + out.append(conversion[line_content_column]) + else: + out.append(line_content_column) + + if len(out) == len(line_content): + output.write('%s\n' % delimiter_local.join(out)) + +]]> + </configfile> + </configfiles> + <inputs> + <param name="original_file" type="data" format="tabular" + label="File in which you want to replace some values" + help="The entries of a specific column are replaced by the information given by the next input file." /> + <param name="replace_information" type="data" format="tabular" + label="Replace information file" + help="This file contains in the first column the entries that should be replaced by the values of the second column." /> + <param name="column_replace" type="data_column" data_ref="original_file" multiple="false" + label="Which column should be replaced?" /> + <param name="skip_lines" type='integer' value='0' label="Skip this many starting lines" /> + <param name="delimiter" type="select" label="Delimited by"> + <option value="" selected="True">Tab</option> + <option value=" ">Whitespace</option> + <option value=".">Dot</option> + <option value=",">Comma</option> + <option value="-">Dash</option> + <option value="_">Underscore</option> + <option value="|">Pipe</option> + </param> + </inputs> + <outputs> + <data name="outfile_replace" format="txt" from_work_dir="output_file"/> + </outputs> + <tests> + <test> + <param name="replace_information" value="GRCh38_ensembl2UCSC.txt" ftype="tabular" /> + <param name="original_file" value="original_file" ftype="tabular" /> + <param name="column_replace" value="1"/> + <param name="skip_lines" value="1"/> + <param name="delimiter" value="" /> + <output name="outfile_replace" file="result_file"/> + </test> + <test> + <param name="replace_information" value="GRCh38_ensembl2UCSC.txt" ftype="tabular" /> + <param name="original_file" value="empty_mapping" ftype="tabular" /> + <param name="column_replace" value="1"/> + <param name="skip_lines" value="1"/> + <param name="delimiter" value="" /> + <output name="outfile_replace" file="result_file_empty_mapping"/> + </test> + </tests> + <help> + <![CDATA[ +**What it does** + +This tool replaces the entries of a defined column with entries given by a replacement file. +For example the replacement file holds the information of the naming scheme of ensembl annotated chromosomes in the frist column and in the second the UCSC annotation. +A file which is having information about chromosomes in ensembl notation in column x can now be converted to a file which holds the same information but in UCSC annotation. + +A useful repository for ensembl and UCSC chromosomes mapping is: https://github.com/dpryan79/ChromosomeMappings + ]]> + </help> +</tool> |
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| diff -r 000000000000 -r cc18bac5afdb test-data/GRCh38_ensembl2UCSC.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GRCh38_ensembl2UCSC.txt Fri Feb 24 10:14:15 2017 -0500 |
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| b'@@ -0,0 +1,525 @@\n+1\tchr1\n+10\tchr10\n+11\tchr11\n+12\tchr12\n+13\tchr13\n+14\tchr14\n+15\tchr15\n+16\tchr16\n+17\tchr17\n+18\tchr18\n+19\tchr19\n+2\tchr2\n+20\tchr20\n+21\tchr21\n+22\tchr22\n+3\tchr3\n+4\tchr4\n+5\tchr5\n+6\tchr6\n+7\tchr7\n+8\tchr8\n+9\tchr9\n+CHR_HG107_PATCH\t\n+CHR_HG126_PATCH\t\n+CHR_HG1311_PATCH\t\n+CHR_HG1342_HG2282_PATCH\t\n+CHR_HG1362_PATCH\t\n+CHR_HG142_HG150_NOVEL_TEST\tchr11_JH159136v1_alt\n+CHR_HG151_NOVEL_TEST\tchr11_JH159137v1_alt\n+CHR_HG1651_PATCH\t\n+CHR_HG1832_PATCH\t\n+CHR_HG2021_PATCH\t\n+CHR_HG2022_PATCH\t\n+CHR_HG2023_PATCH\t\n+CHR_HG2030_PATCH\t\n+CHR_HG2058_PATCH\t\n+CHR_HG2062_PATCH\t\n+CHR_HG2063_PATCH\t\n+CHR_HG2066_PATCH\t\n+CHR_HG2072_PATCH\t\n+CHR_HG2095_PATCH\t\n+CHR_HG2104_PATCH\t\n+CHR_HG2116_PATCH\t\n+CHR_HG2128_PATCH\t\n+CHR_HG2139_PATCH\t\n+CHR_HG2191_PATCH\t\n+CHR_HG2213_PATCH\t\n+CHR_HG2216_PATCH\t\n+CHR_HG2217_PATCH\t\n+CHR_HG2232_PATCH\t\n+CHR_HG2233_PATCH\t\n+CHR_HG2235_PATCH\t\n+CHR_HG2237_PATCH\t\n+CHR_HG2239_PATCH\t\n+CHR_HG2241_PATCH\t\n+CHR_HG2242_HG2243_PATCH\t\n+CHR_HG2244_HG2245_PATCH\t\n+CHR_HG2247_PATCH\t\n+CHR_HG2249_PATCH\t\n+CHR_HG2288_HG2289_PATCH\t\n+CHR_HG2290_PATCH\t\n+CHR_HG2291_PATCH\t\n+CHR_HG2334_PATCH\t\n+CHR_HG23_PATCH\t\n+CHR_HG26_PATCH\t\n+CHR_HG986_PATCH\t\n+CHR_HSCHR10_1_CTG1\tchr10_GL383545v1_alt\n+CHR_HSCHR10_1_CTG2\tchr10_GL383546v1_alt\n+CHR_HSCHR10_1_CTG3\tchr10_KI270824v1_alt\n+CHR_HSCHR10_1_CTG4\tchr10_KI270825v1_alt\n+CHR_HSCHR10_1_CTG6\t\n+CHR_HSCHR11_1_CTG1_1\tchr11_GL383547v1_alt\n+CHR_HSCHR11_1_CTG1_2\t\n+CHR_HSCHR11_1_CTG2\tchr11_KI270826v1_alt\n+CHR_HSCHR11_1_CTG3\tchr11_KI270827v1_alt\n+CHR_HSCHR11_1_CTG5\tchr11_KI270829v1_alt\n+CHR_HSCHR11_1_CTG6\tchr11_KI270830v1_alt\n+CHR_HSCHR11_1_CTG7\tchr11_KI270831v1_alt\n+CHR_HSCHR11_1_CTG8\tchr11_KI270832v1_alt\n+CHR_HSCHR11_2_CTG1\tchr11_KI270902v1_alt\n+CHR_HSCHR11_2_CTG1_1\tchr11_KI270903v1_alt\n+CHR_HSCHR11_3_CTG1\tchr11_KI270927v1_alt\n+CHR_HSCHR12_1_CTG1\tchr12_GL877875v1_alt\n+CHR_HSCHR12_1_CTG2\tchr12_GL383549v1_alt\n+CHR_HSCHR12_1_CTG2_1\tchr12_GL383550v2_alt\n+CHR_HSCHR12_2_CTG1\t\n+CHR_HSCHR12_2_CTG2\tchr12_GL877876v1_alt\n+CHR_HSCHR12_2_CTG2_1\tchr12_GL383552v1_alt\n+CHR_HSCHR12_3_CTG2\tchr12_KI270904v1_alt\n+CHR_HSCHR12_3_CTG2_1\tchr12_GL383553v2_alt\n+CHR_HSCHR12_4_CTG2\tchr12_KI270835v1_alt\n+CHR_HSCHR12_4_CTG2_1\tchr12_GL383551v1_alt\n+CHR_HSCHR12_5_CTG2\tchr12_KI270837v1_alt\n+CHR_HSCHR12_5_CTG2_1\tchr12_KI270833v1_alt\n+CHR_HSCHR12_6_CTG2_1\tchr12_KI270834v1_alt\n+CHR_HSCHR12_7_CTG2_1\tchr12_KI270836v1_alt\n+CHR_HSCHR13_1_CTG1\tchr13_KI270838v1_alt\n+CHR_HSCHR13_1_CTG2\tchr13_KI270839v1_alt\n+CHR_HSCHR13_1_CTG3\tchr13_KI270840v1_alt\n+CHR_HSCHR13_1_CTG4\tchr13_KI270841v1_alt\n+CHR_HSCHR13_1_CTG5\tchr13_KI270842v1_alt\n+CHR_HSCHR13_1_CTG6\tchr13_KI270843v1_alt\n+CHR_HSCHR13_1_CTG7\t\n+CHR_HSCHR13_1_CTG8\t\n+CHR_HSCHR14_1_CTG1\tchr14_KI270844v1_alt\n+CHR_HSCHR14_2_CTG1\tchr14_KI270845v1_alt\n+CHR_HSCHR14_3_CTG1\tchr14_KI270846v1_alt\n+CHR_HSCHR14_7_CTG1\tchr14_KI270847v1_alt\n+CHR_HSCHR15_1_CTG1\tchr15_KI270852v1_alt\n+CHR_HSCHR15_1_CTG3\tchr15_KI270848v1_alt\n+CHR_HSCHR15_1_CTG8\tchr15_GL383554v1_alt\n+CHR_HSCHR15_2_CTG3\tchr15_KI270906v1_alt\n+CHR_HSCHR15_2_CTG8\tchr15_GL383555v2_alt\n+CHR_HSCHR15_3_CTG3\tchr15_KI270851v1_alt\n+CHR_HSCHR15_3_CTG8\tchr15_KI270849v1_alt\n+CHR_HSCHR15_4_CTG8\tchr15_KI270905v1_alt\n+CHR_HSCHR15_5_CTG8\tchr15_KI270850v1_alt\n+CHR_HSCHR15_6_CTG8\t\n+CHR_HSCHR16_1_CTG1\tchr16_KI270853v1_alt\n+CHR_HSCHR16_1_CTG3_1\tchr16_GL383556v1_alt\n+CHR_HSCHR16_2_CTG3_1\tchr16_GL383557v1_alt\n+CHR_HSCHR16_3_CTG1\tchr16_KI270855v1_alt\n+CHR_HSCHR16_3_CTG3_1\t\n+CHR_HSCHR16_4_CTG1\tchr16_KI270856v1_alt\n+CHR_HSCHR16_4_CTG3_1\t\n+CHR_HSCHR16_5_CTG1\t\n+CHR_HSCHR16_CTG2\tchr16_KI270854v1_alt\n+CHR_HSCHR17_10_CTG4\tchr17_KI270909v1_alt\n+CHR_HSCHR17_1_CTG1\tchr17_GL383563v3_alt\n+CHR_HSCHR17_1_CTG2\tchr17_KI270861v1_alt\n+CHR_HSCHR17_1_CTG4\tchr17_GL383564v2_alt\n+CHR_HSCHR17_1_CTG5\tchr17_GL000258v2_alt\n+CHR_HSCHR17_1_CTG9\tchr17_KI270860v1_alt\n+CHR_HSCHR17_2_CTG1\tchr17_KI270907v1_alt\n+CHR_HSCHR17_2_CTG2\tchr17_KI270862v1_alt\n+CHR_HSCHR17_2_CTG4\tchr17_GL383565v1_alt\n+CHR_HSCHR17_2_CTG5\tchr17_KI270908v1_alt\n+CHR_HSCHR17_3_CTG2\tchr17_KI270910v1_alt\n+CHR_HSCHR17_3_CTG4\tchr17_GL383566v1_alt\n+CHR_HSCHR17_4_CTG4\tchr17_JH'..b'4v1\n+KI270366.1\tchrUn_KI270366v1\n+KI270371.1\tchrUn_KI270371v1\n+KI270372.1\tchrUn_KI270372v1\n+KI270373.1\tchrUn_KI270373v1\n+KI270374.1\tchrUn_KI270374v1\n+KI270375.1\tchrUn_KI270375v1\n+KI270376.1\tchrUn_KI270376v1\n+KI270378.1\tchrUn_KI270378v1\n+KI270379.1\tchrUn_KI270379v1\n+KI270381.1\tchrUn_KI270381v1\n+KI270382.1\tchrUn_KI270382v1\n+KI270383.1\tchrUn_KI270383v1\n+KI270384.1\tchrUn_KI270384v1\n+KI270385.1\tchrUn_KI270385v1\n+KI270386.1\tchrUn_KI270386v1\n+KI270387.1\tchrUn_KI270387v1\n+KI270388.1\tchrUn_KI270388v1\n+KI270389.1\tchrUn_KI270389v1\n+KI270390.1\tchrUn_KI270390v1\n+KI270391.1\tchrUn_KI270391v1\n+KI270392.1\tchrUn_KI270392v1\n+KI270393.1\tchrUn_KI270393v1\n+KI270394.1\tchrUn_KI270394v1\n+KI270395.1\t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|
| b |
| diff -r 000000000000 -r cc18bac5afdb test-data/empty_mapping --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/empty_mapping Fri Feb 24 10:14:15 2017 -0500 |
| b |
| @@ -0,0 +1,27 @@ +track type="bedGraph" description="BT089 CpG merged methylation fractions" +1 92832422 92832424 0.000000 +1 244369376 244369378 0.728477 +10 113126863 113126865 0.009709 +11 78895197 78895199 0.904412 +12 74427787 74427789 1.000000 +CHR_HSCHR12_2_CTG1 11351 11353 0.071429 +13 87191374 87191376 0.976190 +15 18999871 18999873 1.000000 +16 12923268 12923270 0.900000 +17 14341606 14341608 0.666667 +18 13183090 13183092 0.825000 +19 29900920 29900922 1.000000 +2 59783044 59783046 0.964286 +2 205330110 205330112 0.916667 +20 62500278 62500280 0.000000 +3 8821953 8821955 1.000000 +3 150336614 150336616 0.891304 +4 93832475 93832477 0.315789 +5 64863618 64863620 0.936937 +6 15110182 15110184 1.000000 +6 159932526 159932528 0.000000 +7 101038815 101038817 0.980132 +8 56525279 56525281 0.687500 +9 77037217 77037219 0.916667 +X 40465092 40465094 0.419355 +CHR_HG2063_PATCH 11351 11353 0.071429 \ No newline at end of file |
| b |
| diff -r 000000000000 -r cc18bac5afdb test-data/original_file --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/original_file Fri Feb 24 10:14:15 2017 -0500 |
| b |
| @@ -0,0 +1,51 @@ +track type="bedGraph" description="BT089 CpG merged methylation fractions" +1 10468 10470 0.209302 +1 10470 10472 0.611111 +1 10483 10485 0.428571 +1 10488 10490 0.846154 +1 10492 10494 0.666667 +1 10496 10498 0.916667 +1 10524 10526 0.916667 +1 10541 10543 0.818182 +1 10562 10564 0.615385 +1 10570 10572 0.916667 +1 10576 10578 0.615385 +1 10578 10580 0.538462 +1 10588 10590 0.909091 +1 10608 10610 0.700000 +1 10616 10618 0.875000 +1 10619 10621 0.714286 +1 10630 10632 0.428571 +1 10632 10634 0.444444 +1 10635 10637 0.400000 +1 10637 10639 0.400000 +1 10640 10642 0.900000 +1 10643 10645 0.600000 +1 10649 10651 0.727273 +1 10659 10661 0.857143 +1 10661 10663 0.428571 +1 10664 10666 0.846154 +1 10666 10668 0.750000 +1 10669 10671 0.916667 +1 10672 10674 0.916667 +1 10678 10680 1.000000 +1 10688 10690 0.900000 +1 10690 10692 0.545455 +1 10693 10695 1.000000 +1 10695 10697 0.909091 +1 10698 10700 0.916667 +1 10701 10703 1.000000 +1 10707 10709 1.000000 +1 10717 10719 0.866667 +1 10719 10721 0.692308 +1 10722 10724 1.000000 +1 10724 10726 0.933333 +1 10727 10729 0.933333 +1 10730 10732 1.000000 +1 10736 10738 0.933333 +1 10746 10748 0.857143 +1 10748 10750 0.500000 +1 10751 10753 0.928571 +1 10753 10755 0.857143 +1 10756 10758 1.000000 +1 10759 10761 0.857143 |
| b |
| diff -r 000000000000 -r cc18bac5afdb test-data/result_file --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_file Fri Feb 24 10:14:15 2017 -0500 |
| b |
| @@ -0,0 +1,51 @@ +track type="bedGraph" description="BT089 CpG merged methylation fractions" +chr1 10468 10470 0.209302 +chr1 10470 10472 0.611111 +chr1 10483 10485 0.428571 +chr1 10488 10490 0.846154 +chr1 10492 10494 0.666667 +chr1 10496 10498 0.916667 +chr1 10524 10526 0.916667 +chr1 10541 10543 0.818182 +chr1 10562 10564 0.615385 +chr1 10570 10572 0.916667 +chr1 10576 10578 0.615385 +chr1 10578 10580 0.538462 +chr1 10588 10590 0.909091 +chr1 10608 10610 0.700000 +chr1 10616 10618 0.875000 +chr1 10619 10621 0.714286 +chr1 10630 10632 0.428571 +chr1 10632 10634 0.444444 +chr1 10635 10637 0.400000 +chr1 10637 10639 0.400000 +chr1 10640 10642 0.900000 +chr1 10643 10645 0.600000 +chr1 10649 10651 0.727273 +chr1 10659 10661 0.857143 +chr1 10661 10663 0.428571 +chr1 10664 10666 0.846154 +chr1 10666 10668 0.750000 +chr1 10669 10671 0.916667 +chr1 10672 10674 0.916667 +chr1 10678 10680 1.000000 +chr1 10688 10690 0.900000 +chr1 10690 10692 0.545455 +chr1 10693 10695 1.000000 +chr1 10695 10697 0.909091 +chr1 10698 10700 0.916667 +chr1 10701 10703 1.000000 +chr1 10707 10709 1.000000 +chr1 10717 10719 0.866667 +chr1 10719 10721 0.692308 +chr1 10722 10724 1.000000 +chr1 10724 10726 0.933333 +chr1 10727 10729 0.933333 +chr1 10730 10732 1.000000 +chr1 10736 10738 0.933333 +chr1 10746 10748 0.857143 +chr1 10748 10750 0.500000 +chr1 10751 10753 0.928571 +chr1 10753 10755 0.857143 +chr1 10756 10758 1.000000 +chr1 10759 10761 0.857143 |
| b |
| diff -r 000000000000 -r cc18bac5afdb test-data/result_file_empty_mapping --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_file_empty_mapping Fri Feb 24 10:14:15 2017 -0500 |
| b |
| @@ -0,0 +1,25 @@ +track type="bedGraph" description="BT089 CpG merged methylation fractions" +chr1 92832422 92832424 0.000000 +chr1 244369376 244369378 0.728477 +chr10 113126863 113126865 0.009709 +chr11 78895197 78895199 0.904412 +chr12 74427787 74427789 1.000000 +chr13 87191374 87191376 0.976190 +chr15 18999871 18999873 1.000000 +chr16 12923268 12923270 0.900000 +chr17 14341606 14341608 0.666667 +chr18 13183090 13183092 0.825000 +chr19 29900920 29900922 1.000000 +chr2 59783044 59783046 0.964286 +chr2 205330110 205330112 0.916667 +chr20 62500278 62500280 0.000000 +chr3 8821953 8821955 1.000000 +chr3 150336614 150336616 0.891304 +chr4 93832475 93832477 0.315789 +chr5 64863618 64863620 0.936937 +chr6 15110182 15110184 1.000000 +chr6 159932526 159932528 0.000000 +chr7 101038815 101038817 0.980132 +chr8 56525279 56525281 0.687500 +chr9 77037217 77037219 0.916667 +chrX 40465092 40465094 0.419355 |