Mercurial > repos > bgruening > text_processing
changeset 5:20344ce0c811 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
| author | bgruening |
|---|---|
| date | Wed, 23 Nov 2016 15:56:41 -0500 |
| parents | 288462ec2630 |
| children | 60edf2f8c28f |
| files | awk.xml cat.xml easyjoin.xml find_and_replace.xml grep.xml macros.xml multijoin multijoin.xml replace_text_in_column.xml replace_text_in_line.xml sed.xml sort.xml sorted_uniq.xml test-data/grep_results2.html tool_dependencies.xml unfold_column.xml |
| diffstat | 16 files changed, 55 insertions(+), 92 deletions(-) [+] |
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--- a/awk.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/awk.xml Wed Nov 23 15:56:41 2016 -0500 @@ -3,9 +3,9 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="4.1.0">gnu_awk</requirement> - </expand> + <requirements> + <requirement type="package" version="4.1.3">gawk</requirement> + </requirements> <version_command>awk --version | head -n 1</version_command> <command> <![CDATA[ @@ -19,6 +19,9 @@ > "$outfile" ]]> </command> + <configfiles> + <configfile name="awk_script">$code</configfile> + </configfiles> <inputs> <param name="infile" format="txt" type="data" label="File to process" /> <param name="code" type="text" area="true" size="5x35" label="AWK Program" help=""> @@ -29,9 +32,6 @@ </sanitizer> </param> </inputs> - <configfiles> - <configfile name="awk_script">$code</configfile> - </configfiles> <outputs> <data name="outfile" format_source="infile" metadata_source="infile"/> </outputs> @@ -61,9 +61,6 @@ - Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1.html) - Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html) -- Learn AWK in 1 hour (http://www.selectorweb.com/awk.html) -- awk cheat-sheet (http://cbi.med.harvard.edu/people/peshkin/sb302/awk_cheatsheets.pdf) -- Collection of useful awk one-liners (http://student.northpark.edu/pemente/awk/awk1line.txt) -----
--- a/cat.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/cat.xml Wed Nov 23 15:56:41 2016 -0500 @@ -1,8 +1,9 @@ <tool id="tp_cat" name="Concatenate datasets" version="0.1.0"> <description>tail-to-head (cat)</description> - <requirements> - <requirement type="package" version="8.22">gnu_coreutils</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> <version_command> <![CDATA[ cat --version | head -n 1 @@ -84,5 +85,7 @@ chr1 151278832 151279227 Z 0 - chr2 100000030 200000955 P 0 + chr2 100000015 200000999 Q 0 + + +@REFERENCES@ ]]></help> </tool>
--- a/easyjoin.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/easyjoin.xml Wed Nov 23 15:56:41 2016 -0500 @@ -3,7 +3,9 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"> + <requirement type="package" version="5.18.1">perl</requirement> + </expand> <version_command>join --version | head -n 1</version_command> <command> <![CDATA[
--- a/find_and_replace.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/find_and_replace.xml Wed Nov 23 15:56:41 2016 -0500 @@ -3,9 +3,12 @@ <macros> <import>macros.xml</import> </macros> - <command interpreter="perl"> + <requirements> + <requirement type="package" version="5.18.1">perl</requirement> + </requirements> + <command> <![CDATA[ - find_and_replace + perl '$__tool_directory__/find_and_replace' #if $searchwhere.searchwhere_select == "column": -c $searchwhere.column #end if
--- a/grep.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/grep.xml Wed Nov 23 15:56:41 2016 -0500 @@ -3,9 +3,10 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="2.14">gnu_grep</requirement> - </expand> + <requirements> + <requirement type="package" version="2.14">grep</requirement> + <requirement type="package" version="4.2.3.dev0">sed</requirement><!-- for ansi2html.sh --> + </requirements> <version_command>grep --version | head -n 1</version_command> <command> <![CDATA[ @@ -30,8 +31,6 @@ -- "${url_paste}" '${infile}' | grep -v "^--$" > "${output}" #end if - - ##grep_wrapper.sh '$infile' '$output' '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitive ]]> </command> <inputs> @@ -123,7 +122,7 @@ <param name="lines_before" value="0" /> <param name="lines_after" value="0" /> <param name="color" value="NOCOLOR" /> - <output name="output" file="egrep_results2.txt" />> + <output name="output" file="egrep_results2.txt" /> </test> </tests> <help>
--- a/macros.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/macros.xml Wed Nov 23 15:56:41 2016 -0500 @@ -1,11 +1,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="8.22">gnu_coreutils</requirement> + <requirement type="package" version="8.25">coreutils</requirement> <yield/> </requirements> </xml> - <token name="@BASE_VERSION@">1.0</token> + <token name="@BASE_VERSION@">1.1</token> <xml name="stdio"> <stdio> <!-- Anything other than zero is an error -->
--- a/multijoin Fri Mar 18 15:17:27 2016 -0400 +++ b/multijoin Wed Nov 23 15:56:41 2016 -0500 @@ -5,7 +5,6 @@ use Data::Dumper; use Carp; use File::Basename; -use Sort::Key::Natural qw(natsort); my $version = "0.1.1"; my $field_sep = "\t"; @@ -68,7 +67,7 @@ sub print_combined_data() { - my @keys = natsort keys %data ; + my @keys = sort keys %data ; foreach my $key ( @keys ) { my @outputs; @@ -247,7 +246,7 @@ --filler X Fill missing values with X. (Default: '$filler'). - --labels When printning output headers with '-h', instead of using the file name, + --labels When printing output headers with '-h', instead of using the file name, use specific labels. Each file name must be followed by a name.
--- a/multijoin.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/multijoin.xml Wed Nov 23 15:56:41 2016 -0500 @@ -3,13 +3,12 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> + <requirements> <requirement type="package" version="5.18.1">perl</requirement> - <requirement type="package" version="1.0">text_processing_perl_packages</requirement> - </expand> - <command interpreter="perl"> + </requirements> + <command> <![CDATA[ - multijoin + perl '$__tool_directory__/multijoin' --key '$key_column' --values '$value_columns' --filler '$filler' @@ -54,7 +53,7 @@ <param name="key_column" value="4" /> <param name="value_columns" value="c7,c8,c9" /> <param name="output_header" value="True" /> - <output name="outfile" file="multijoin_result1.txt" /> + <output name="outfile" file="multijoin_result1.txt" lines_diff="2" /> </test> </tests> <help>
--- a/replace_text_in_column.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/replace_text_in_column.xml Wed Nov 23 15:56:41 2016 -0500 @@ -3,9 +3,9 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="4.1.0">gnu_awk</requirement> - </expand> + <requirements> + <requirement type="package" version="4.1.3">gawk</requirement> + </requirements> <version_command>awk --version | head -n 1</version_command> <command> <![CDATA[
--- a/replace_text_in_line.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/replace_text_in_line.xml Wed Nov 23 15:56:41 2016 -0500 @@ -3,9 +3,9 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement> - </expand> + <requirements> + <requirement type="package" version="4.2.3.dev0">sed</requirement> + </requirements> <version_command>sed --version | head -n 1</version_command> <command> <![CDATA[
--- a/sed.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/sed.xml Wed Nov 23 15:56:41 2016 -0500 @@ -3,9 +3,9 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement> - </expand> + <requirements> + <requirement type="package" version="4.2.3.dev0">sed</requirement> + </requirements> <version_command>sed --version | head -n 1</version_command> <command> <![CDATA[ @@ -20,6 +20,11 @@ > '$output' ]]> </command> + <configfiles> + <configfile name="sed_script"> + $code + </configfile> + </configfiles> <inputs> <param format="txt" name="infile" type="data" label="File to process" /> <param name="code" type="text" area="true" size="5x35" label="SED Program" help=""> @@ -43,11 +48,6 @@ </when> </conditional> </inputs> - <configfiles> - <configfile name="sed_script"> - $code - </configfile> - </configfiles> <outputs> <data name="output" format_source="infile" metadata_source="infile" /> </outputs> @@ -84,7 +84,6 @@ - Long sed tutorial (http://www.grymoire.com/Unix/Sed.html) - sed faq with good examples (http://sed.sourceforge.net/sedfaq.html) - sed cheat-sheet (http://www.catonmat.net/download/sed.stream.editor.cheat.sheet.pdf) -- Collection of useful sed one-liners (http://student.northpark.edu/pemente/sed/sed1line.txt) -----
--- a/sort.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/sort.xml Wed Nov 23 15:56:41 2016 -0500 @@ -4,7 +4,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement> + <requirement type="package" version="4.2.3.dev0">sed</requirement> </expand> <version_command>sort --version | head -n 1</version_command> <command>
--- a/sorted_uniq.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/sorted_uniq.xml Wed Nov 23 15:56:41 2016 -0500 @@ -4,7 +4,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement> + <requirement type="package" version="4.2.3.dev0">sed</requirement> </expand> <version_command>uniq --version | head -n 1</version_command> <command>
--- a/test-data/grep_results2.html Fri Mar 18 15:17:27 2016 -0400 +++ b/test-data/grep_results2.html Wed Nov 23 15:56:41 2016 -0500 @@ -290,17 +290,11 @@ <body class="f9 b9"> <pre> GCTATAG<span class="bold"><span class="f4">AAATGT</span></span>TAACATCGAATGTACATTATAAC -<span class="f6">--</span> CAGCTAACAATC<span class="bold"><span class="f4">AAGCGT</span></span>TACAGATTAGCCCCCCCC -<span class="f6">--</span> GAACTTGCGTAACGTACAAAAATGCAAGCA<span class="bold"><span class="f4">AAAAGT</span></span> -<span class="f6">--</span> GCTCTGTTAATCTAGA<span class="bold"><span class="f4">AAATGT</span></span>GTCTCCCCCCCCCC -<span class="f6">--</span> <span class="bold"><span class="f4">AATCGT</span></span>ATAGCTCGGGCCGGATACTAGTACACCCCC -<span class="f6">--</span> GATATAGTGGATAACTAATGCTCCCCCAG<span class="bold"><span class="f4">AACTGT</span></span>T -<span class="f6">--</span> GAACGGACTATAGCCGGTATCCAAACAT<span class="bold"><span class="f4">AAATGT</span></span>TC </pre> </body>
--- a/tool_dependencies.xml Fri Mar 18 15:17:27 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="gnu_coreutils" version="8.22"> - <repository changeset_revision="ac64dfe4b1fb" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="gnu_awk" version="4.1.0"> - <repository changeset_revision="f145f856ec57" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="gnu_grep" version="2.14"> - <repository changeset_revision="d4d4eb7a0123" name="package_gnu_grep_2_14" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="gnu_sed" version="4.2.2-sandbox"> - <repository changeset_revision="76cc52f79dd4" name="package_gnu_sed_4_2_2_sandbox" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="perl" version="5.18.1"> - <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="text_processing_perl_packages" version="1.0"> - <install version="1.0"> - <actions> - <action type="setup_perl_environment"> - <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="perl" version="5.18.1" /> - </repository> - <!-- allow downloading and installing an Perl package from cpan.org--> - <package>https://cpan.metacpan.org/authors/id/S/SA/SALVA/Sort-Key-1.33.tar.gz</package> - </action> - </actions> - </install> - <readme> - Needed perl packages. - </readme> - </package> -</tool_dependency>
--- a/unfold_column.xml Fri Mar 18 15:17:27 2016 -0400 +++ b/unfold_column.xml Wed Nov 23 15:56:41 2016 -0500 @@ -3,10 +3,12 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> - <command interpreter="python"> + <requirements> + <requirement type="package" version="2.7.12">python</requirement> + </requirements> + <command> <![CDATA[ - unfold_column.py + python '$__tool_directory__/unfold_column.py' '${infile}' $column "${delimiter}"