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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c4f50d1ee81c1618344ede1f04a46a28d8068bcc |
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modified:
grep.xml macros.xml |
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| diff -r 12615d397df7 -r fbf99087e067 grep.xml --- a/grep.xml Thu Feb 29 22:15:20 2024 +0000 +++ b/grep.xml Thu Mar 28 13:20:16 2024 +0000 |
| [ |
| @@ -8,6 +8,9 @@ <requirement type="package" version="3.11">grep</requirement> <requirement type="package" version="4.8">sed</requirement><!-- for ansi2html.sh --> </requirements> + <stdio> + <exit_code range="2:" level="fatal" description="grep failed" /> + </stdio> <version_command>grep --version | head -n 1</version_command> <command> <![CDATA[ @@ -27,10 +30,11 @@ $regex_type -A $lines_after -B $lines_before + --no-group-separator $invert $case_sensitive -- '${url_paste}' - '${infile}' | grep -v "^--$" > '${output}' + '${infile}' > '${output}' #end if ]]> </command> @@ -78,8 +82,8 @@ </data> </outputs> <tests> + <!-- grep a FASTA file for sequences with specific motif --> <test> - <!-- grep a FASTA file for sequences with specific motif --> <param name="infile" value="grep1.txt" /> <param name="case_sensitive" value="case sensitive" /> <param name="regex_type" value="-P" /> @@ -90,9 +94,9 @@ <param name="color" value="NOCOLOR" /> <output name="output" file="grep_results1.txt" /> </test> + <!-- grep a FASTA file for sequences with specific motif - + show highlighed output --> <test> - <!-- grep a FASTA file for sequences with specific motif - - show highlighed output --> <param name="infile" value="grep1.txt" /> <param name="case_sensitive" value="case sensitive" /> <param name="regex_type" value="-P" /> @@ -103,7 +107,8 @@ <param name="color" value="COLOR" /> <output name="output" file="grep_results2.html" /> </test> - <test><!-- tests egrep --> + <!-- tests egrep --> + <test> <param name="infile" value="egrep1.txt" /> <param name="case_sensitive" value="case sensitive" /> <param name="regex_type" value="-E" /> @@ -114,7 +119,8 @@ <param name="color" value="NOCOLOR" /> <output name="output" file="egrep_results1.txt" /> </test> - <test><!-- tests basic regex; + must be backslashed to match --> + <!-- tests basic regex; + must be backslashed to match --> + <test> <param name="infile" value="egrep1.txt" /> <param name="case_sensitive" value="case sensitive" /> <param name="regex_type" value="-G" /> @@ -125,6 +131,33 @@ <param name="color" value="NOCOLOR" /> <output name="output" file="egrep_results1.txt" /> </test> + <!-- tests regex;matching nothing --> + <test> + <param name="infile" value="egrep1.txt" /> + <param name="case_sensitive" value="case sensitive" /> + <param name="regex_type" value="-G" /> + <param name="invert" value="" /> + <param name="url_paste" value="not existent pattern" /> + <param name="lines_before" value="0" /> + <param name="lines_after" value="0" /> + <param name="color" value="NOCOLOR" /> + <output name="output"> + <assert_contents> + <has_size value="0"/> + </assert_contents> + </output> + </test> + <!-- tests invalid regex; i.e. that we still get exit code 2 --> + <test expect_failure="true" expect_exit_code="2"> + <param name="infile" value="egrep1.txt" /> + <param name="case_sensitive" value="case sensitive" /> + <param name="regex_type" value="-G" /> + <param name="invert" value="" /> + <param name="url_paste" value="\(" /> + <param name="lines_before" value="0" /> + <param name="lines_after" value="0" /> + <param name="color" value="NOCOLOR" /> + </test> </tests> <help> <![CDATA[ |
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| diff -r 12615d397df7 -r fbf99087e067 macros.xml --- a/macros.xml Thu Feb 29 22:15:20 2024 +0000 +++ b/macros.xml Thu Mar 28 13:20:16 2024 +0000 |
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| @@ -6,7 +6,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">9.3</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">23.1</token> <xml name="stdio"> <stdio> |