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comparison grep.xml @ 27:08cdbfffce67 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
author bgruening
date Fri, 07 Mar 2025 20:43:41 +0000
parents f22a309187a3
children
comparison
equal deleted inserted replaced
26:f22a309187a3 27:08cdbfffce67
83 </outputs> 83 </outputs>
84 <tests> 84 <tests>
85 <!-- grep a FASTA file for sequences with specific motif --> 85 <!-- grep a FASTA file for sequences with specific motif -->
86 <test> 86 <test>
87 <param name="infile" value="grep1.txt" /> 87 <param name="infile" value="grep1.txt" />
88 <param name="case_sensitive" value="case sensitive" /> 88 <param name="case_sensitive" value="-i" />
89 <param name="regex_type" value="-P" /> 89 <param name="regex_type" value="-P" />
90 <param name="invert" value="" /> 90 <param name="invert" value="" />
91 <param name="url_paste" value="AA.{2}GT" /> 91 <param name="url_paste" value="AA.{2}GT" />
92 <param name="lines_before" value="1" /> 92 <param name="lines_before" value="1" />
93 <param name="lines_after" value="0" /> 93 <param name="lines_after" value="0" />
96 </test> 96 </test>
97 <!-- grep a FASTA file for sequences with specific motif - 97 <!-- grep a FASTA file for sequences with specific motif -
98 show highlighed output --> 98 show highlighed output -->
99 <test> 99 <test>
100 <param name="infile" value="grep1.txt" /> 100 <param name="infile" value="grep1.txt" />
101 <param name="case_sensitive" value="case sensitive" /> 101 <param name="case_sensitive" value="-i" />
102 <param name="regex_type" value="-P" /> 102 <param name="regex_type" value="-P" />
103 <param name="invert" value="" /> 103 <param name="invert" value="" />
104 <param name="url_paste" value="AA.{2}GT" /> 104 <param name="url_paste" value="AA.{2}GT" />
105 <param name="lines_before" value="0" /> 105 <param name="lines_before" value="0" />
106 <param name="lines_after" value="0" /> 106 <param name="lines_after" value="0" />
108 <output name="output" file="grep_results2.html" /> 108 <output name="output" file="grep_results2.html" />
109 </test> 109 </test>
110 <!-- tests egrep --> 110 <!-- tests egrep -->
111 <test> 111 <test>
112 <param name="infile" value="egrep1.txt" /> 112 <param name="infile" value="egrep1.txt" />
113 <param name="case_sensitive" value="case sensitive" /> 113 <param name="case_sensitive" value="-i" />
114 <param name="regex_type" value="-E" /> 114 <param name="regex_type" value="-E" />
115 <param name="invert" value="" /> 115 <param name="invert" value="" />
116 <param name="url_paste" value="[^ ]+" /> 116 <param name="url_paste" value="[^ ]+" />
117 <param name="lines_before" value="0" /> 117 <param name="lines_before" value="0" />
118 <param name="lines_after" value="0" /> 118 <param name="lines_after" value="0" />
120 <output name="output" file="egrep_results1.txt" /> 120 <output name="output" file="egrep_results1.txt" />
121 </test> 121 </test>
122 <!-- tests basic regex; + must be backslashed to match --> 122 <!-- tests basic regex; + must be backslashed to match -->
123 <test> 123 <test>
124 <param name="infile" value="egrep1.txt" /> 124 <param name="infile" value="egrep1.txt" />
125 <param name="case_sensitive" value="case sensitive" /> 125 <param name="case_sensitive" value="-i" />
126 <param name="regex_type" value="-G" /> 126 <param name="regex_type" value="-G" />
127 <param name="invert" value="" /> 127 <param name="invert" value="" />
128 <param name="url_paste" value="[^ ]\+" /> 128 <param name="url_paste" value="[^ ]\+" />
129 <param name="lines_before" value="0" /> 129 <param name="lines_before" value="0" />
130 <param name="lines_after" value="0" /> 130 <param name="lines_after" value="0" />
132 <output name="output" file="egrep_results1.txt" /> 132 <output name="output" file="egrep_results1.txt" />
133 </test> 133 </test>
134 <!-- tests regex;matching nothing --> 134 <!-- tests regex;matching nothing -->
135 <test> 135 <test>
136 <param name="infile" value="egrep1.txt" /> 136 <param name="infile" value="egrep1.txt" />
137 <param name="case_sensitive" value="case sensitive" /> 137 <param name="case_sensitive" value="-i" />
138 <param name="regex_type" value="-G" /> 138 <param name="regex_type" value="-G" />
139 <param name="invert" value="" /> 139 <param name="invert" value="" />
140 <param name="url_paste" value="not existent pattern" /> 140 <param name="url_paste" value="not existent pattern" />
141 <param name="lines_before" value="0" /> 141 <param name="lines_before" value="0" />
142 <param name="lines_after" value="0" /> 142 <param name="lines_after" value="0" />
148 </output> 148 </output>
149 </test> 149 </test>
150 <!-- tests invalid regex; i.e. that we still get exit code 2 --> 150 <!-- tests invalid regex; i.e. that we still get exit code 2 -->
151 <test expect_failure="true" expect_exit_code="2"> 151 <test expect_failure="true" expect_exit_code="2">
152 <param name="infile" value="egrep1.txt" /> 152 <param name="infile" value="egrep1.txt" />
153 <param name="case_sensitive" value="case sensitive" /> 153 <param name="case_sensitive" value="-i" />
154 <param name="regex_type" value="-G" /> 154 <param name="regex_type" value="-G" />
155 <param name="invert" value="" /> 155 <param name="invert" value="" />
156 <param name="url_paste" value="\(" /> 156 <param name="url_paste" value="\(" />
157 <param name="lines_before" value="0" /> 157 <param name="lines_before" value="0" />
158 <param name="lines_after" value="0" /> 158 <param name="lines_after" value="0" />