Mercurial > repos > bgruening > text_processing
comparison grep.xml @ 20:fbf99087e067 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c4f50d1ee81c1618344ede1f04a46a28d8068bcc
author | bgruening |
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date | Thu, 28 Mar 2024 13:20:16 +0000 |
parents | 12615d397df7 |
children |
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19:12615d397df7 | 20:fbf99087e067 |
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6 <expand macro="creator"/> | 6 <expand macro="creator"/> |
7 <requirements> | 7 <requirements> |
8 <requirement type="package" version="3.11">grep</requirement> | 8 <requirement type="package" version="3.11">grep</requirement> |
9 <requirement type="package" version="4.8">sed</requirement><!-- for ansi2html.sh --> | 9 <requirement type="package" version="4.8">sed</requirement><!-- for ansi2html.sh --> |
10 </requirements> | 10 </requirements> |
11 <stdio> | |
12 <exit_code range="2:" level="fatal" description="grep failed" /> | |
13 </stdio> | |
11 <version_command>grep --version | head -n 1</version_command> | 14 <version_command>grep --version | head -n 1</version_command> |
12 <command> | 15 <command> |
13 <![CDATA[ | 16 <![CDATA[ |
14 #if str($color) == "COLOR": | 17 #if str($color) == "COLOR": |
15 GREP_COLOR='1;34' | 18 GREP_COLOR='1;34' |
25 #else: | 28 #else: |
26 grep | 29 grep |
27 $regex_type | 30 $regex_type |
28 -A $lines_after | 31 -A $lines_after |
29 -B $lines_before | 32 -B $lines_before |
33 --no-group-separator | |
30 $invert | 34 $invert |
31 $case_sensitive | 35 $case_sensitive |
32 -- '${url_paste}' | 36 -- '${url_paste}' |
33 '${infile}' | grep -v "^--$" > '${output}' | 37 '${infile}' > '${output}' |
34 #end if | 38 #end if |
35 ]]> | 39 ]]> |
36 </command> | 40 </command> |
37 <inputs> | 41 <inputs> |
38 <param name="infile" format="txt" type="data" label="Select lines from" /> | 42 <param name="infile" format="txt" type="data" label="Select lines from" /> |
76 <when input="color" value="COLOR" format="html"/> | 80 <when input="color" value="COLOR" format="html"/> |
77 </change_format> | 81 </change_format> |
78 </data> | 82 </data> |
79 </outputs> | 83 </outputs> |
80 <tests> | 84 <tests> |
81 <test> | 85 <!-- grep a FASTA file for sequences with specific motif --> |
82 <!-- grep a FASTA file for sequences with specific motif --> | 86 <test> |
83 <param name="infile" value="grep1.txt" /> | 87 <param name="infile" value="grep1.txt" /> |
84 <param name="case_sensitive" value="case sensitive" /> | 88 <param name="case_sensitive" value="case sensitive" /> |
85 <param name="regex_type" value="-P" /> | 89 <param name="regex_type" value="-P" /> |
86 <param name="invert" value="" /> | 90 <param name="invert" value="" /> |
87 <param name="url_paste" value="AA.{2}GT" /> | 91 <param name="url_paste" value="AA.{2}GT" /> |
88 <param name="lines_before" value="1" /> | 92 <param name="lines_before" value="1" /> |
89 <param name="lines_after" value="0" /> | 93 <param name="lines_after" value="0" /> |
90 <param name="color" value="NOCOLOR" /> | 94 <param name="color" value="NOCOLOR" /> |
91 <output name="output" file="grep_results1.txt" /> | 95 <output name="output" file="grep_results1.txt" /> |
92 </test> | 96 </test> |
93 <test> | 97 <!-- grep a FASTA file for sequences with specific motif - |
94 <!-- grep a FASTA file for sequences with specific motif - | |
95 show highlighed output --> | 98 show highlighed output --> |
99 <test> | |
96 <param name="infile" value="grep1.txt" /> | 100 <param name="infile" value="grep1.txt" /> |
97 <param name="case_sensitive" value="case sensitive" /> | 101 <param name="case_sensitive" value="case sensitive" /> |
98 <param name="regex_type" value="-P" /> | 102 <param name="regex_type" value="-P" /> |
99 <param name="invert" value="" /> | 103 <param name="invert" value="" /> |
100 <param name="url_paste" value="AA.{2}GT" /> | 104 <param name="url_paste" value="AA.{2}GT" /> |
101 <param name="lines_before" value="0" /> | 105 <param name="lines_before" value="0" /> |
102 <param name="lines_after" value="0" /> | 106 <param name="lines_after" value="0" /> |
103 <param name="color" value="COLOR" /> | 107 <param name="color" value="COLOR" /> |
104 <output name="output" file="grep_results2.html" /> | 108 <output name="output" file="grep_results2.html" /> |
105 </test> | 109 </test> |
106 <test><!-- tests egrep --> | 110 <!-- tests egrep --> |
111 <test> | |
107 <param name="infile" value="egrep1.txt" /> | 112 <param name="infile" value="egrep1.txt" /> |
108 <param name="case_sensitive" value="case sensitive" /> | 113 <param name="case_sensitive" value="case sensitive" /> |
109 <param name="regex_type" value="-E" /> | 114 <param name="regex_type" value="-E" /> |
110 <param name="invert" value="" /> | 115 <param name="invert" value="" /> |
111 <param name="url_paste" value="[^ ]+" /> | 116 <param name="url_paste" value="[^ ]+" /> |
112 <param name="lines_before" value="0" /> | 117 <param name="lines_before" value="0" /> |
113 <param name="lines_after" value="0" /> | 118 <param name="lines_after" value="0" /> |
114 <param name="color" value="NOCOLOR" /> | 119 <param name="color" value="NOCOLOR" /> |
115 <output name="output" file="egrep_results1.txt" /> | 120 <output name="output" file="egrep_results1.txt" /> |
116 </test> | 121 </test> |
117 <test><!-- tests basic regex; + must be backslashed to match --> | 122 <!-- tests basic regex; + must be backslashed to match --> |
123 <test> | |
118 <param name="infile" value="egrep1.txt" /> | 124 <param name="infile" value="egrep1.txt" /> |
119 <param name="case_sensitive" value="case sensitive" /> | 125 <param name="case_sensitive" value="case sensitive" /> |
120 <param name="regex_type" value="-G" /> | 126 <param name="regex_type" value="-G" /> |
121 <param name="invert" value="" /> | 127 <param name="invert" value="" /> |
122 <param name="url_paste" value="[^ ]\+" /> | 128 <param name="url_paste" value="[^ ]\+" /> |
123 <param name="lines_before" value="0" /> | 129 <param name="lines_before" value="0" /> |
124 <param name="lines_after" value="0" /> | 130 <param name="lines_after" value="0" /> |
125 <param name="color" value="NOCOLOR" /> | 131 <param name="color" value="NOCOLOR" /> |
126 <output name="output" file="egrep_results1.txt" /> | 132 <output name="output" file="egrep_results1.txt" /> |
133 </test> | |
134 <!-- tests regex;matching nothing --> | |
135 <test> | |
136 <param name="infile" value="egrep1.txt" /> | |
137 <param name="case_sensitive" value="case sensitive" /> | |
138 <param name="regex_type" value="-G" /> | |
139 <param name="invert" value="" /> | |
140 <param name="url_paste" value="not existent pattern" /> | |
141 <param name="lines_before" value="0" /> | |
142 <param name="lines_after" value="0" /> | |
143 <param name="color" value="NOCOLOR" /> | |
144 <output name="output"> | |
145 <assert_contents> | |
146 <has_size value="0"/> | |
147 </assert_contents> | |
148 </output> | |
149 </test> | |
150 <!-- tests invalid regex; i.e. that we still get exit code 2 --> | |
151 <test expect_failure="true" expect_exit_code="2"> | |
152 <param name="infile" value="egrep1.txt" /> | |
153 <param name="case_sensitive" value="case sensitive" /> | |
154 <param name="regex_type" value="-G" /> | |
155 <param name="invert" value="" /> | |
156 <param name="url_paste" value="\(" /> | |
157 <param name="lines_before" value="0" /> | |
158 <param name="lines_after" value="0" /> | |
159 <param name="color" value="NOCOLOR" /> | |
127 </test> | 160 </test> |
128 </tests> | 161 </tests> |
129 <help> | 162 <help> |
130 <![CDATA[ | 163 <![CDATA[ |
131 **What it does** | 164 **What it does** |