# HG changeset patch # User bgruening # Date 1768611416 0 # Node ID 5907d248dee36f3a2cd9bc38beebe0c84e56974d # Parent 4f7cade041cba85ffe0be217dd4b6ee3702b40d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d diff -r 4f7cade041cb -r 5907d248dee3 grep.xml --- a/grep.xml Wed Jun 04 15:11:51 2025 +0000 +++ b/grep.xml Sat Jan 17 00:56:56 2026 +0000 @@ -6,7 +6,7 @@ grep - sed + sed diff -r 4f7cade041cb -r 5907d248dee3 macros.xml --- a/macros.xml Wed Jun 04 15:11:51 2025 +0000 +++ b/macros.xml Sat Jan 17 00:56:56 2026 +0000 @@ -6,7 +6,7 @@ 9.5 - 2 + 3 23.1 diff -r 4f7cade041cb -r 5907d248dee3 replace_text_in_line.xml --- a/replace_text_in_line.xml Wed Jun 04 15:11:51 2025 +0000 +++ b/replace_text_in_line.xml Sat Jan 17 00:56:56 2026 +0000 @@ -5,7 +5,7 @@ - sed + sed sed --version | head -n 1 @@ -26,7 +26,7 @@ - + @@ -38,7 +38,7 @@ - + @@ -50,7 +50,7 @@ - + diff -r 4f7cade041cb -r 5907d248dee3 sed.xml --- a/sed.xml Wed Jun 04 15:11:51 2025 +0000 +++ b/sed.xml Sat Jan 17 00:56:56 2026 +0000 @@ -5,7 +5,7 @@ - sed + sed sed --version | head -n 1 @@ -88,7 +88,7 @@ - Short sed tutorial (http://www.linuxhowtos.org/System/sed_tutorial.htm) - Long sed tutorial (http://www.grymoire.com/Unix/Sed.html) -- sed faq with good examples (http://sed.sourceforge.net/sedfaq.html) +- sed faq with good examples (https://www.pement.org/sed/sedfaq.html) - sed cheat-sheet (http://www.catonmat.net/download/sed.stream.editor.cheat.sheet.pdf) ----- diff -r 4f7cade041cb -r 5907d248dee3 sort.xml --- a/sort.xml Wed Jun 04 15:11:51 2025 +0000 +++ b/sort.xml Sat Jan 17 00:56:56 2026 +0000 @@ -5,7 +5,7 @@ - sed + sed sort --version | head -n 1 @@ -16,10 +16,18 @@ sed -u '${header}'q && #end if - sort $unique $ignore_case --stable -t ' ' + sort $unique --stable -t ' ' #for $key in $sortkeys: - -k '${key.column}${key.order}${key.style},${key.column}' + #if $key.start_charpos and $key.end_charpos: + -k ${key.column}.${key.start_charpos}${key.ignore_leading_blanks},${key.column}.${key.end_charpos}${key.ignore_leading_blanks}${key.order}${key.style}${key.ignore_case} + #elif $key.start_charpos: + -k ${key.column}.${key.start_charpos}${key.ignore_leading_blanks},${key.column}${key.order}${key.style}${key.ignore_case} + #elif $key.end_charpos: + -k ${key.column}${key.ignore_leading_blanks},${key.column}.${key.end_charpos}${key.ignore_leading_blanks}${key.order}${key.style}${key.ignore_case} + #else: + -k ${key.column}${key.ignore_leading_blanks},${key.column}${key.order}${key.style}${key.ignore_case} + #end if #end for ) < '${infile}' > '${outfile}' @@ -28,17 +36,19 @@ + label="Number of header lines" help="Header lines will be copied to the output unchanged without operating on them."> - + - + + + - + @@ -46,18 +56,20 @@ + + - - + @@ -72,7 +84,7 @@ - + @@ -87,7 +99,7 @@ - + @@ -96,6 +108,80 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 4f7cade041cb -r 5907d248dee3 sorted_uniq.xml --- a/sorted_uniq.xml Wed Jun 04 15:11:51 2025 +0000 +++ b/sorted_uniq.xml Sat Jan 17 00:56:56 2026 +0000 @@ -5,7 +5,7 @@ - sed + sed uniq --version | head -n 1 diff -r 4f7cade041cb -r 5907d248dee3 test-data/1_dup.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1_dup.bed Sat Jan 17 00:56:56 2026 +0000 @@ -0,0 +1,71 @@ +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r 4f7cade041cb -r 5907d248dee3 test-data/sort3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sort3.tabular Sat Jan 17 00:56:56 2026 +0000 @@ -0,0 +1,4 @@ +Alice 22.10.2025 +Bob 28.01.2024 +Charlie 13.06.2025 +Alex 25.06.2025 diff -r 4f7cade041cb -r 5907d248dee3 test-data/sort4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sort4.tabular Sat Jan 17 00:56:56 2026 +0000 @@ -0,0 +1,5 @@ +Motif Length Obs Code +AGCTAAGG 8 10 A + GCTTAAGGC 9 6 A + CCCGTAG 7 13 A +agcTAAgg 8 40 a diff -r 4f7cade041cb -r 5907d248dee3 test-data/sorted3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sorted3.tabular Sat Jan 17 00:56:56 2026 +0000 @@ -0,0 +1,4 @@ +Bob 28.01.2024 +Alex 25.06.2025 +Charlie 13.06.2025 +Alice 22.10.2025 diff -r 4f7cade041cb -r 5907d248dee3 test-data/sorted4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sorted4.tabular Sat Jan 17 00:56:56 2026 +0000 @@ -0,0 +1,5 @@ +Motif Length Obs Code +agcTAAgg 8 40 a +AGCTAAGG 8 10 A + CCCGTAG 7 13 A + GCTTAAGGC 9 6 A diff -r 4f7cade041cb -r 5907d248dee3 test-data/sorted4_partial.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sorted4_partial.tabular Sat Jan 17 00:56:56 2026 +0000 @@ -0,0 +1,5 @@ +Motif Length Obs Code + GCTTAAGGC 9 6 A + CCCGTAG 7 13 A +agcTAAgg 8 40 a +AGCTAAGG 8 10 A diff -r 4f7cade041cb -r 5907d248dee3 test-data/unique_results2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unique_results2.bed Sat Jan 17 00:56:56 2026 +0000 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - diff -r 4f7cade041cb -r 5907d248dee3 test-data/unique_results3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unique_results3.bed Sat Jan 17 00:56:56 2026 +0000 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - 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+ + sed + sort --version | head -n 1 0: + sed -u '${header}'q && #end if - -o '$outfile' - '$infile' + sort -u + $ignore_case + $is_numeric + -t ' ' + #if $adv_opts.adv_opts_selector == "advanced": + -k$adv_opts.column_start,$adv_opts.column_end + #end if + ) < '$infile' > '$outfile' ]]> - - + + + + - + @@ -43,8 +52,8 @@ - - + + @@ -52,6 +61,24 @@ + + + + + + + + + + + + + + + + + +