# HG changeset patch # User bgruening # Date 1709244920 0 # Node ID 12615d397df7aafc040158766e7b773753928690 # Parent d698c222f3545f99433a17f75d5375ba29a70594 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f diff -r d698c222f354 -r 12615d397df7 awk.xml --- a/awk.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/awk.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,10 +1,11 @@ - + with awk macros.xml + - gawk + gawk awk --version | head -n 1 @@ -15,9 +16,9 @@ -v FS=' ' -v OFS=' ' --re-interval - -f "$awk_script" - "$infile" - > "$outfile" + -f '$awk_script' + '$infile' + > '$outfile' ]]> @@ -119,7 +120,6 @@ - **$** matches the end of a line or string. - **\|** Separates alternate possibilities. -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 cat.xml --- a/cat.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/cat.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,8 +1,9 @@ - + tail-to-head (cat) macros.xml + diff -r d698c222f354 -r 12615d397df7 cut.xml --- a/cut.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/cut.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,4 +1,4 @@ - + columns from a table (cut) macros.xml @@ -8,14 +8,18 @@ '${output}' + '$input' + > '$output' ]]> @@ -24,23 +28,33 @@ - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + @@ -51,15 +65,6 @@ - - - - - - - - - @@ -70,7 +75,7 @@ - + @@ -184,20 +189,26 @@ - + - + - - + + + + + + + + - + diff -r d698c222f354 -r 12615d397df7 easyjoin.xml --- a/easyjoin.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/easyjoin.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,17 +1,18 @@ - + two files macros.xml + - perl + perl join --version | head -n 1 '$output' ]]> @@ -109,7 +110,6 @@ * The header line (**Fruit Color Price**) was joined and kept as first line. * Missing values ( Avocado's color, missing from the first file ) are replaced with a period character. -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 find_and_replace.xml --- a/find_and_replace.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/find_and_replace.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,10 +1,11 @@ - + parts of text macros.xml + - perl + perl diff -r d698c222f354 -r 12615d397df7 grep.xml --- a/grep.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/grep.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,11 +1,12 @@ - + (grep) macros.xml + - grep - sed + grep + sed grep --version | head -n 1 @@ -19,8 +20,8 @@ -B $lines_before $invert $case_sensitive - -- "${url_paste}" - '${infile}' | $__tool_directory__/ansi2html.sh > "${output}" + -- '${url_paste}' + '${infile}' | '$__tool_directory__/ansi2html.sh' > '${output}' #else: grep $regex_type @@ -28,8 +29,8 @@ -B $lines_before $invert $case_sensitive - -- "${url_paste}" - '${infile}' | grep -v "^--$" > "${output}" + -- '${url_paste}' + '${infile}' | grep -v "^--$" > '${output}' #end if ]]> @@ -42,9 +43,9 @@ - - - + + + @@ -113,16 +114,16 @@ - + - + - + @@ -187,7 +188,6 @@ - **$** matches the end of a line or string. - **\|** Separates alternate possibilities. -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 head.xml --- a/head.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/head.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,8 +1,9 @@ - + lines from a dataset (head) macros.xml + head --version | head -n 1 @@ -56,7 +57,6 @@ chr7 56632 56652 D17003_CTCF_R6 310 + chr7 56736 56756 D17003_CTCF_R7 354 + -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 macros.xml --- a/macros.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/macros.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,11 +1,13 @@ - coreutils + coreutils - 1.1 + 9.3 + 0 + 23.1 @@ -16,22 +18,18 @@ - -`_ - -Assaf Gordon (gordon cshl dot edu) -]]> - + 10.5281/zenodo.1419255 + + + + + + + + diff -r d698c222f354 -r 12615d397df7 multijoin.xml --- a/multijoin.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/multijoin.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,10 +1,11 @@ - + (combine multiple files) macros.xml + - perl + perl diff -r d698c222f354 -r 12615d397df7 nl.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nl.xml Thu Feb 29 22:15:20 2024 +0000 @@ -0,0 +1,63 @@ + + + + macros.xml + + + + nl --version | head -n 1 + '$output' + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r d698c222f354 -r 12615d397df7 recurring_lines.xml --- a/recurring_lines.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/recurring_lines.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,8 +1,9 @@ - + with recurring lines macros.xml + yes --version | head -n 1 @@ -13,7 +14,7 @@ #else: times=`wc -l $token.repeat_select.infile | awk '{print $1}'`; #end if - yes -- "${token.line}" 2>/dev/null | head -n \$times >> $outfile; + yes -- '${token.line}' 2>/dev/null | head -n \$times >> '$outfile'; #end for ]]> @@ -72,7 +73,6 @@ The entire string will be printed X times separated by a line break. X can be either given by the use as a number or calculated by a given file. In case the user provides a file, the line number will be used as X. -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 replace_text_in_column.xml --- a/replace_text_in_column.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/replace_text_in_column.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,10 +1,11 @@ - + in a specific column macros.xml + - gawk + gawk awk --version | head -n 1 @@ -19,8 +20,8 @@ \$$replacement.column = gensub( /$replacement.find_pattern/, "$replacement.replace_pattern", "g", \$$replacement.column ) ; #end for print \$0 ; }' - "$infile" - > "$outfile" + '$infile' + > '$outfile' ]]> @@ -151,7 +152,6 @@ **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 replace_text_in_line.xml --- a/replace_text_in_line.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/replace_text_in_line.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,10 +1,11 @@ - + in entire line macros.xml + - sed + sed sed --version | head -n 1 @@ -156,7 +157,6 @@ **Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 sed.xml --- a/sed.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/sed.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,10 +1,11 @@ - + with sed macros.xml + - sed + sed sed --version | head -n 1 @@ -126,7 +127,6 @@ **Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 sort.xml --- a/sort.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/sort.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,10 +1,11 @@ - + data in ascending or descending order macros.xml + - sed + sed sort --version | head -n 1 @@ -170,7 +171,6 @@ If you're planning to use the file with another tool that expected sorted files (such as *join*), you should use the **Alphabetical sort**, not the **Natural Sort**. Natural sort order is easier for humans, but is unnatural for computer programs. -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 sort_rows.xml --- a/sort_rows.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/sort_rows.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,11 +1,15 @@ - + according to their columns macros.xml + + + python + $outfile + python -c 'for line in ( "\t".join(sorted(line.strip().split("\t"))) for line in open("$infile") ): print(line)' > '$outfile' ]]> @@ -31,7 +35,6 @@ That tool sorts each row in a TAB separated file, according to their columns. In other words: It is a sorted reordering of all columns. -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 sorted_uniq.xml --- a/sorted_uniq.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/sorted_uniq.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,10 +1,11 @@ - + assuming sorted input file macros.xml + - sed + sed uniq --version | head -n 1 @@ -23,14 +24,14 @@ $grouping.uniqueonly #end if - "$infile" + '$infile' #if $grouping.grouping_select == 'no' and $grouping.count: ## count will print the count with spaces in front of the line and ## with a space (not a tab) after the number, we need to cahnge that | sed -e 's/ *//' -e 's/ /\t/' #end if - > "$outfile" + > '$outfile' ]]> @@ -99,7 +100,6 @@ You can sort your file using either the "Sort" tool in "Filter and Sort", or the "Sort" tool in "Unix Tools". -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 tac.xml --- a/tac.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/tac.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,8 +1,9 @@ - + reverse a file (reverse cat) macros.xml + tac --version | head -n 1 @@ -15,8 +16,8 @@ "$separator.separator_string" #end if #end if - "$infile" - > "$outfile" + '$infile' + > '$outfile' ]]> @@ -85,7 +86,6 @@ 5 # 6 7 8 9 0 1 2 3 4 -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 tail.xml --- a/tail.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/tail.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,8 +1,9 @@ - + lines from a dataset (tail) macros.xml + tail --version | head -n 1 @@ -61,7 +62,6 @@ chr7 57341 57361 D17003_CTCF_R7 375 + chr7 57457 57477 D17003_CTCF_R3 188 + -@REFERENCES@ ]]> diff -r d698c222f354 -r 12615d397df7 test-data/grep_results2.html --- a/test-data/grep_results2.html Sat Oct 08 21:01:33 2022 +0000 +++ b/test-data/grep_results2.html Thu Feb 29 22:15:20 2024 +0000 @@ -290,11 +290,17 @@

 GCTATAGAAATGTTAACATCGAATGTACATTATAAC
+--
 CAGCTAACAATCAAGCGTTACAGATTAGCCCCCCCC
+--
 GAACTTGCGTAACGTACAAAAATGCAAGCAAAAAGT
+--
 GCTCTGTTAATCTAGAAAATGTGTCTCCCCCCCCCC
+--
 AATCGTATAGCTCGGGCCGGATACTAGTACACCCCC
+--
 GATATAGTGGATAACTAATGCTCCCCCAGAACTGTT
+--
 GAACGGACTATAGCCGGTATCCAAACATAAATGTTC

diff -r d698c222f354 -r 12615d397df7 test-data/nl-out-number-format.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nl-out-number-format.txt Thu Feb 29 22:15:20 2024 +0000 @@ -0,0 +1,4 @@ +1 fruit color weight price +2 apple red 1.4 0.4 +3 orange orange 1.1 0.2 +4 banana yellow 0.9 0.35 diff -r d698c222f354 -r 12615d397df7 test-data/nl-out.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nl-out.txt Thu Feb 29 22:15:20 2024 +0000 @@ -0,0 +1,4 @@ + 1 fruit color weight price + 2 apple red 1.4 0.4 + 3 orange orange 1.1 0.2 + 4 banana yellow 0.9 0.35 diff -r d698c222f354 -r 12615d397df7 test-data/nl-start-incr.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nl-start-incr.txt Thu Feb 29 22:15:20 2024 +0000 @@ -0,0 +1,4 @@ + 10 fruit color weight price + 12 apple red 1.4 0.4 + 14 orange orange 1.1 0.2 + 16 banana yellow 0.9 0.35 diff -r d698c222f354 -r 12615d397df7 unfold_column.xml --- a/unfold_column.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/unfold_column.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,10 +1,11 @@ - + columns from a table macros.xml + - python + python diff -r d698c222f354 -r 12615d397df7 unsorted_uniq.xml --- a/unsorted_uniq.xml Sat Oct 08 21:01:33 2022 +0000 +++ b/unsorted_uniq.xml Thu Feb 29 22:15:20 2024 +0000 @@ -1,8 +1,9 @@ - + occurrences of each record macros.xml + sort --version | head -n 1 @@ -14,8 +15,8 @@ #if $adv_opts.adv_opts_selector == "advanced": -k$adv_opts.column_start,$adv_opts.column_end #end if - -o "$outfile" - "$infile" + -o '$outfile' + '$infile' ]]> @@ -87,7 +88,6 @@ chr2 1000 1900 gene5 chr3 15 1656 gene6 -@REFERENCES@ ]]>