| Previous changeset 5:20344ce0c811 (2016-11-23) Next changeset 7:01ca80da2266 (2017-05-22) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' |
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modified:
awk.xml cat.xml cut.xml easyjoin.xml find_and_replace.xml grep.xml head.xml multijoin.xml recurring_lines.xml replace_text_in_column.xml replace_text_in_line.xml sed.xml sort.xml sort_rows.xml sorted_uniq.xml tac.xml tail.xml unfold_column.xml unsorted_uniq.xml |
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| diff -r 20344ce0c811 -r 60edf2f8c28f awk.xml --- a/awk.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/awk.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -59,7 +59,7 @@ **Further reading** -- Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1.html) +- Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1/index.html) - Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html) ----- @@ -118,4 +118,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f cat.xml --- a/cat.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/cat.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -87,5 +87,7 @@ chr2 100000015 200000999 Q 0 + @REFERENCES@ -]]></help> +]]> + </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f cut.xml --- a/cut.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/cut.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -106,6 +106,10 @@ <filter type="metadata_value" ref="input" name="endCol" column="3" /> </option> </action> + </when> + </conditional> + </when> + </conditional> <conditional name="output"> <when datatype_isinstance="interval"> <action type="metadata" name="chromCol"> @@ -172,15 +176,11 @@ <filter type="metadata_value" ref="input" name="strandCol" column="1" /> </option> </action> - </when> + </when> </conditional> - </when> - </conditional> - </when> + </when> </conditional> - </when> - </conditional> - </actions> + </actions> </data> </outputs> <tests> @@ -256,4 +256,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f easyjoin.xml --- a/easyjoin.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/easyjoin.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -112,4 +112,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f find_and_replace.xml --- a/find_and_replace.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/find_and_replace.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -178,4 +178,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f grep.xml --- a/grep.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/grep.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -190,4 +190,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f head.xml --- a/head.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/head.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -59,4 +59,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f multijoin.xml --- a/multijoin.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/multijoin.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -129,4 +129,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f recurring_lines.xml --- a/recurring_lines.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/recurring_lines.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -75,4 +75,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f replace_text_in_column.xml --- a/replace_text_in_column.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/replace_text_in_column.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.0"> +<tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.1"> <description>in a specific column</description> <macros> <import>macros.xml</import> @@ -10,7 +10,8 @@ <command> <![CDATA[ awk - -v OFS=" " + -v OFS="\t" + -v FS="\t" --re-interval --sandbox '{ \$$column = gensub( /$find_pattern/, "$replace_pattern", "g", \$$column ) ; print \$0 ; }' "$infile" @@ -132,4 +133,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f replace_text_in_line.xml --- a/replace_text_in_line.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/replace_text_in_line.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -73,7 +73,7 @@ **Examples of Replace Patterns** - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. -- **FOO-&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **$** (ampersand) represents the matched find pattern. +- **FOO-&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the beginning and '-BAR' at the end. **&** (ampersand) represents the matched find pattern. - **\\1** The text which matched the first parenthesis in the Find Pattern. @@ -129,4 +129,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f sed.xml --- a/sed.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/sed.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -129,4 +129,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f sort.xml --- a/sort.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/sort.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -173,4 +173,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f sort_rows.xml --- a/sort_rows.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/sort_rows.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -34,4 +34,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f sorted_uniq.xml --- a/sorted_uniq.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/sorted_uniq.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -102,4 +102,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f tac.xml --- a/tac.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/tac.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -87,4 +87,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f tail.xml --- a/tail.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/tail.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -64,4 +64,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f unfold_column.xml --- a/unfold_column.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/unfold_column.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -63,4 +63,5 @@ @REFERENCES@ ]]> </help> + <expand macro="citations" /> </tool> |
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| diff -r 20344ce0c811 -r 60edf2f8c28f unsorted_uniq.xml --- a/unsorted_uniq.xml Wed Nov 23 15:56:41 2016 -0500 +++ b/unsorted_uniq.xml Sat May 06 13:09:05 2017 -0400 |
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| @@ -90,4 +90,5 @@ @REFERENCES@ ]]> </help> +<expand macro="citations" /> </tool> |