text_processing: find_and_replace.xml annotate

annotate find_and_replace.xml @ 18:d698c222f354 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc"

author	bgruening
date	Sat, 08 Oct 2022 21:01:33 +0000
parents	fb4ff3c42cd3
children	12615d397df7

rev	line source
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	1 <tool id="tp_find_and_replace" name="Replace" version="@BASE_VERSION@.4">
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	2 <description>parts of text</description>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	3 <macros>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	4 <import>macros.xml</import>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	5 </macros>
5 20344ce0c811 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52 bgruening parents: 3 diff changeset	6 <requirements>
7 01ca80da2266 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6 bgruening parents: 6 diff changeset	7 <requirement type="package" version="5.22.0.1">perl</requirement>
5 20344ce0c811 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52 bgruening parents: 3 diff changeset	8 </requirements>
20344ce0c811 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52 bgruening parents: 3 diff changeset	9 <command>
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	10 <![CDATA[
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	11 #for $i, $el in enumerate($find_and_replace)
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	12 #if $i == (len($find_and_replace) - 1)
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	13 #set $join = ""
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	14 #else
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	15 #set $join = "\|"
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	16 #end if
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	17 perl '$__tool_directory__/find_and_replace'
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	18 #if $el.searchwhere.searchwhere_select == "column":
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	19 -c $el.searchwhere.column
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	20 #end if
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	21 #if $i == (len($find_and_replace) - 1)
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	22 -o '$outfile'
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	23 #end if
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	24 $el.global
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	25 $el.caseinsensitive
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	26 $el.wholewords
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	27 $el.skip_first_line
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	28 $el.is_regex
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	29 '$el.find_pattern'
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	30 '$el.replace_pattern'
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	31 #if $i == 0
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	32 '$infile'
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	33 #end if
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	34 $join
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	35 #end for
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	36 ]]>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	37 </command>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	38 <inputs>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	39 <param name="infile" format="txt" type="data" label="File to process" />
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	40 <repeat name="find_and_replace" title="Find and Replace" min="1">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	41 <param name="find_pattern" type="text" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	42 <sanitizer>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	43 <valid initial="string.printable">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	44 <remove value="'"/>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	45 </valid>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	46 </sanitizer>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	47 </param>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	48 <param name="replace_pattern" type="text" label="Replace with"
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	49 help="Use simple text, or $& (dollar-ampersand) and $1 $2 $3 to refer to matched text. See examples below." >
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	50 <sanitizer>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	51 <valid initial="string.printable">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	52 <remove value="'"/>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	53 </valid>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	54 </sanitizer>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	55 </param>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	56 <param name="is_regex" type="boolean" checked="false" truevalue="-r" falsevalue=""
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	57 label="Find-Pattern is a regular expression" help="see help section for details." />
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	58
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	59 <param name="global" type="boolean" checked="false" truevalue="-g" falsevalue=""
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	60 label="Replace all occurences of the pattern" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	61
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	62 <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue=""
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	63 label="Case-Insensitive search" help="" />
13 0a8c6b61f0f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 4f79443517baf378fbfe1f81be361d97f2938601 bgruening parents: 7 diff changeset	64
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	65 <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue=""
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	66 label="Find whole-words" help="ignore partial matches (e.g. 'apple' will not match 'snapple')" />
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	67
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	68 <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue=""
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	69 label="Ignore first line" help="Select this option if the first line contains column headers. Text in the line will not be replaced. " />
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	70
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	71 <conditional name="searchwhere">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	72 <param name="searchwhere_select" type="select" label="Find and Replace text in">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	73 <option value="line" selected="true">entire line</option>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	74 <option value="column">specific column</option>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	75 </param>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	76 <when value="line" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	77 <when value="column">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	78 <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	79 </when>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	80 </conditional>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	81 </repeat>
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	82 </inputs>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	83 <outputs>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	84 <data format_source="infile" name="outfile" metadata_source="infile" />
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	85 </outputs>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	86 <tests>
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	87 <test expect_num_outputs="1">
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	88 <param name="infile" value="find_and_replace1.txt" />
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	89 <repeat name="find_and_replace">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	90 <param name="find_pattern" value="day" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	91 <param name="replace_pattern" value="great day" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	92 <param name="is_regex" value="False" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	93 <param name="global" value="true" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	94 <param name="caseinsensitive" value="False" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	95 <param name="wholewords" value="True" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	96 </repeat>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	97 <output name="outfile" file="find_and_replace_results1.txt" />
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	98 </test>
14 fb4ff3c42cd3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208" bgruening parents: 13 diff changeset	99 <!-- test that columns are split by tab not space. input has no tab loads of spaces
fb4ff3c42cd3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208" bgruening parents: 13 diff changeset	100 .. therefore the ftype needs to be set.
fb4ff3c42cd3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208" bgruening parents: 13 diff changeset	101 result should be the same as in test 1 which works on whole line -->
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	102 <test expect_num_outputs="1">
14 fb4ff3c42cd3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208" bgruening parents: 13 diff changeset	103 <param name="infile" value="find_and_replace1.txt" ftype="tabular" />
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	104 <repeat name="find_and_replace">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	105 <param name="find_pattern" value="day" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	106 <param name="replace_pattern" value="great day" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	107 <param name="is_regex" value="False" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	108 <param name="global" value="true" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	109 <param name="caseinsensitive" value="False" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	110 <param name="wholewords" value="True" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	111 <conditional name="searchwhere">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	112 <param name="searchwhere_select" value="column"/>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	113 <param name="column" value="1" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	114 </conditional>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	115 </repeat>
14 fb4ff3c42cd3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208" bgruening parents: 13 diff changeset	116 <output name="outfile" file="find_and_replace_results1.txt" />
fb4ff3c42cd3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208" bgruening parents: 13 diff changeset	117 </test>
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	118 <test expect_num_outputs="1">
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	119 <param name="infile" value="find_and_replace2.txt" />
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	120 <repeat name="find_and_replace">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	121 <param name="find_pattern" value="^chr" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	122 <param name="replace_pattern" value="" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	123 <param name="is_regex" value="True" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	124 <param name="caseinsensitive" value="False" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	125 <param name="wholewords" value="False" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	126 <conditional name="searchwhere">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	127 <param name="searchwhere_select" value="column" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	128 <param name="column" value="3" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	129 </conditional>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	130 </repeat>
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	131 <output name="outfile" file="find_and_replace_results2.txt" />
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	132 </test>
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	133 <test expect_num_outputs="1">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	134 <param name="infile" value="find_and_replace1.txt" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	135 <repeat name="find_and_replace">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	136 <param name="find_pattern" value="day" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	137 <param name="replace_pattern" value="great day" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	138 <param name="is_regex" value="False" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	139 <param name="global" value="true" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	140 <param name="caseinsensitive" value="False" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	141 <param name="wholewords" value="True" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	142 </repeat>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	143 <param name="infile" value="find_and_replace1.txt" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	144 <repeat name="find_and_replace">
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	145 <param name="find_pattern" value="great" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	146 <param name="replace_pattern" value="best" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	147 <param name="is_regex" value="False" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	148 <param name="global" value="False" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	149 <param name="caseinsensitive" value="False" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	150 <param name="wholewords" value="True" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	151 </repeat>
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	152 <output name="outfile" file="find_and_replace_results3.txt" />
d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	153 </test>
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	154 </tests>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	155 <help>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	156 <![CDATA[
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	157 What it does
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	158
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	159 This tool finds $ replaces text in an input dataset.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	160
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	161 .. class:: infomark
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	162
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	163 The pattern to find can be a simple text string, or a perl regular expression string (depending on pattern is a regex check-box).
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	164
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	165 .. class:: infomark
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	166
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	167 When using regular expressions, the replace pattern can contain back-references ( e.g. \\1 )
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	168
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	169 .. class:: infomark
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	170
18 d698c222f354 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 378e99cde623698fb44ee7ac9873f455fb51fdbc" bgruening parents: 14 diff changeset	171 This tool uses `Perl regular expression <https://perldoc.perl.org/perlre>`_ syntax.
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	172
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	173 -----
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	174
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	175 *Examples of regular-expression* Find Patterns**
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	176
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	177 - HELLO The word 'HELLO' (case sensitive).
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	178 - AG.T The letters A,G followed by any single character, followed by the letter T.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	179 - A{4,} Four or more consecutive A's.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	180 - chr2[012]\\t The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	181 - hsa-mir-([^ ]+) The text 'hsa-mir-' followed by one-or-more non-space characters. When using parenthesis, the matched content of the parenthesis can be accessed with \1 in the replace pattern.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	182
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	183
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	184 Examples of Replace Patterns
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	185
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	186 - WORLD The word 'WORLD' will be placed whereever the find pattern was found.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	187 - FOO-$&-BAR Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. $& (dollar-ampersand) represents the matched find pattern.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	188 - $1 The text which matched the first parenthesis in the Find Pattern.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	189
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	190
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	191 -----
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	192
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	193 Example 1
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	194
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	195 Find Pattern: HELLO
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	196 Replace Pattern: WORLD
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	197 Regular Expression: no
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	198 Replace what: entire line
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	199
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	200 Every time the word HELLO is found, it will be replaced with the word WORLD.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	201
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	202 -----
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	203
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	204 Example 2
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	205
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	206 Find Pattern: ^chr
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	207 Replace Pattern: (empty)
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	208 Regular Expression: yes
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	209 Replace what: column 11
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	210
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	211 If column 11 (of every line) begins with ther letters 'chr', they will be removed. Effectively, it'll turn "chr4" into "4" and "chrXHet" into "XHet"
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	212
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	213
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	214 -----
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	215
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	216 Perl's Regular Expression Syntax
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	217
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	218 The Find & Replace tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	219
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	220 - *( ) { } [ ] . ? + \\ ^ $ are all special characters. \\** can be used to "escape" a special character, allowing that special character to be searched for.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	221 - ^ matches the beginning of a string(but not an internal line).
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	222 - ( .. ) groups a particular pattern.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	223 - { n or n, or n,m } specifies an expected number of repetitions of the preceding pattern.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	224
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	225 - {n} The preceding item is matched exactly n times.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	226 - {n,} The preceding item ismatched n or more times.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	227 - {n,m} The preceding item is matched at least n times but not more than m times.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	228
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	229 - [ ... ] creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as a-z.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	230 - . Matches any single character except a newline.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	231 - ***** The preceding item will be matched zero or more times.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	232 - ? The preceding item is optional and matched at most once.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	233 - + The preceding item will be matched one or more times.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	234 - ^ has two meaning:
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	235 - matches the beginning of a line or string.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	236 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	237 - $ matches the end of a line or string.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	238 - \\\| Separates alternate possibilities.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	239 - \\d matches a single digit
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	240 - \\w matches a single letter or digit or an underscore.
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	241 - \\s matches a single white-space (space or tabs).
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	242
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	243 @REFERENCES@
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	244 ]]>
5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	245 </help>
6 60edf2f8c28f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: 5 diff changeset	246 <expand macro="citations" />
0 5314e5d6f040 Imported from capsule None bgruening parents: diff changeset	247 </tool>

Mercurial > repos > bgruening > text_processing

annotate find_and_replace.xml @ 18:d698c222f354 draft