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comparison grep.xml @ 10:c78b1767db2b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
author bgruening
date Fri, 26 Feb 2016 12:22:54 -0500
parents fa7f88da29d7
children 062ed2bb4f2e
comparison
equal deleted inserted replaced
9:d9819ccb9ca7 10:c78b1767db2b
11 <![CDATA[ 11 <![CDATA[
12 #if str($color) == "COLOR": 12 #if str($color) == "COLOR":
13 GREP_COLOR='1;34' 13 GREP_COLOR='1;34'
14 grep 14 grep
15 --color=always 15 --color=always
16 -P 16 $regex_type
17 -A $lines_after 17 -A $lines_after
18 -B $lines_before 18 -B $lines_before
19 $invert 19 $invert
20 $case_sensitive 20 $case_sensitive
21 -- "${url_paste}" 21 -- "${url_paste}"
22 '${infile}' | $__tool_directory__/ansi2html.sh > "${output}" 22 '${infile}' | $__tool_directory__/ansi2html.sh > "${output}"
23 #else: 23 #else:
24 grep 24 grep
25 -P 25 $regex_type
26 -A $lines_after 26 -A $lines_after
27 -B $lines_before 27 -B $lines_before
28 $invert 28 $invert
29 $case_sensitive 29 $case_sensitive
30 -- "${url_paste}" 30 -- "${url_paste}"
39 39
40 <param name="invert" type="select" label="that"> 40 <param name="invert" type="select" label="that">
41 <option value="">Match</option> 41 <option value="">Match</option>
42 <option value="-v">Don't Match</option> 42 <option value="-v">Don't Match</option>
43 </param> 43 </param>
44 44
45 <param name="url_paste" type="text" size="40" label="Regular Expression" help="See below for more details"> 45 <param name="regex_type" type="select" label="Type of regex">
46 <option value="-G">Basic</option>
47 <option value="-P" selected="true">Perl</option>
48 <option value="-E">Extended (egrep)</option>
49 </param>
50
51 <param name="url_paste" type="text" label="Regular Expression" help="See below for more details">
46 <sanitizer> 52 <sanitizer>
47 <valid initial="string.printable"> 53 <valid initial="string.printable">
48 <remove value="&apos;"/> 54 <remove value="&apos;"/>
49 </valid> 55 </valid>
50 </sanitizer> 56 </sanitizer>
74 <tests> 80 <tests>
75 <test> 81 <test>
76 <!-- grep a FASTA file for sequences with specific motif --> 82 <!-- grep a FASTA file for sequences with specific motif -->
77 <param name="infile" value="grep1.txt" /> 83 <param name="infile" value="grep1.txt" />
78 <param name="case_sensitive" value="case sensitive" /> 84 <param name="case_sensitive" value="case sensitive" />
85 <param name="regex_type" value="-P" />
79 <param name="invert" value="" /> 86 <param name="invert" value="" />
80 <param name="url_paste" value="AA.{2}GT" /> 87 <param name="url_paste" value="AA.{2}GT" />
81 <param name="lines_before" value="1" /> 88 <param name="lines_before" value="1" />
82 <param name="lines_after" value="0" /> 89 <param name="lines_after" value="0" />
83 <param name="color" value="NOCOLOR" /> 90 <param name="color" value="NOCOLOR" />
86 <test> 93 <test>
87 <!-- grep a FASTA file for sequences with specific motif - 94 <!-- grep a FASTA file for sequences with specific motif -
88 show highlighed output --> 95 show highlighed output -->
89 <param name="infile" value="grep1.txt" /> 96 <param name="infile" value="grep1.txt" />
90 <param name="case_sensitive" value="case sensitive" /> 97 <param name="case_sensitive" value="case sensitive" />
98 <param name="regex_type" value="-P" />
91 <param name="invert" value="" /> 99 <param name="invert" value="" />
92 <param name="url_paste" value="AA.{2}GT" /> 100 <param name="url_paste" value="AA.{2}GT" />
93 <param name="lines_before" value="0" /> 101 <param name="lines_before" value="0" />
94 <param name="lines_after" value="0" /> 102 <param name="lines_after" value="0" />
95 <param name="color" value="COLOR" /> 103 <param name="color" value="COLOR" />
96 <output name="output" file="grep_results2.html" /> 104 <output name="output" file="grep_results2.html" />
105 </test>
106 <test><!-- tests egrep -->
107 <param name="infile" value="egrep1.txt" />
108 <param name="case_sensitive" value="case sensitive" />
109 <param name="regex_type" value="-E" />
110 <param name="invert" value="" />
111 <param name="url_paste" value="[^ ]+" />
112 <param name="lines_before" value="0" />
113 <param name="lines_after" value="0" />
114 <param name="color" value="NOCOLOR" />
115 <output name="output" file="egrep_results1.txt" />
116 </test>
117 <test><!-- same regex as egrep test, but different outcome with basic regex -->
118 <param name="infile" value="egrep1.txt" />
119 <param name="case_sensitive" value="case sensitive" />
120 <param name="regex_type" value="-G" />
121 <param name="invert" value="" />
122 <param name="url_paste" value="[^ ]+" />
123 <param name="lines_before" value="0" />
124 <param name="lines_after" value="0" />
125 <param name="color" value="NOCOLOR" />
126 <output name="output" file="egrep_results2.txt" />>
97 </test> 127 </test>
98 </tests> 128 </tests>
99 <help> 129 <help>
100 <![CDATA[ 130 <![CDATA[
101 **What it does** 131 **What it does**