Mercurial > repos > bgruening > text_processing
annotate awk.xml @ 26:f22a309187a3 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
| author | bgruening |
|---|---|
| date | Fri, 16 Aug 2024 10:41:17 +0000 |
| parents | 5fef6d08de83 |
| children | 08cdbfffce67 |
| rev | line source |
|---|---|
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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1 <tool id="tp_awk_tool" name="Text reformatting" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 2 | 2 <description>with awk</description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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6 <expand macro="creator"/> |
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3c685c4106b3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
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7 <requirements> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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8 <requirement type="package" version="5.3.0">gawk</requirement> |
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3c685c4106b3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
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9 </requirements> |
| 4 | 10 <version_command>awk --version | head -n 1</version_command> |
| 0 | 11 <command> |
| 4 | 12 <![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 4f79443517baf378fbfe1f81be361d97f2938601
bgruening
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13 env -i |
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5fef6d08de83
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 5f5d5802a961a77ceb092cbdef90d93e29717029-dirty"
bgruening
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14 \$(which awk) |
| 4 | 15 --sandbox |
| 6 | 16 -v FS=' ' |
| 17 -v OFS=' ' | |
| 4 | 18 --re-interval |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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19 -f '$awk_script' |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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20 '$infile' |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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21 > '$outfile' |
| 4 | 22 ]]> |
| 0 | 23 </command> |
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3c685c4106b3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
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changeset
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24 <configfiles> |
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3c685c4106b3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
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changeset
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25 <configfile name="awk_script">$code</configfile> |
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3c685c4106b3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
parents:
12
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changeset
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26 </configfiles> |
| 0 | 27 <inputs> |
| 6 | 28 <param name="infile" format="txt" type="data" label="File to process" /> |
| 29 <param name="code" type="text" area="true" size="5x35" label="AWK Program" help=""> | |
| 0 | 30 <sanitizer> |
| 31 <valid initial="string.printable"> | |
| 32 <remove value="'"/> | |
| 33 </valid> | |
| 34 </sanitizer> | |
| 35 </param> | |
| 4 | 36 </inputs> |
| 37 <outputs> | |
| 6 | 38 <data name="outfile" format_source="infile" metadata_source="infile"/> |
| 4 | 39 </outputs> |
| 40 <tests> | |
| 6 | 41 <test> |
| 42 <param name="infile" value="awk1.txt" /> | |
| 43 <!-- commas are not allowed in a value field. Values with comma will be splitted --> | |
| 44 <param name="code" value='$2>0.5 { print $2*9"\t"$1 }' /> | |
| 45 <output name="outfile" file="awk_results1.txt" /> | |
| 46 </test> | |
| 4 | 47 </tests> |
| 48 <help> | |
| 49 <![CDATA[ | |
| 0 | 50 **What it does** |
| 51 | |
| 52 This tool runs the unix **awk** command on the selected data file. | |
| 53 | |
| 54 .. class:: infomark | |
| 55 | |
| 7 | 56 **TIP:** |
| 1 | 57 |
| 7 | 58 This tool uses the **extended regular** expression syntax (not the perl syntax). |
| 1 | 59 **\\d**, **\\w**, **\\s** etc. are **not** supported. |
| 0 | 60 |
| 61 | |
| 62 **Further reading** | |
| 63 | |
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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64 - Awk by Example (http://www.ibm.com/developerworks/linux/library/l-awk1/index.html) |
| 0 | 65 - Long AWK tutorial (http://www.grymoire.com/Unix/Awk.html) |
| 66 | |
| 67 ----- | |
| 68 | |
| 69 **AWK programs** | |
| 70 | |
| 71 Most AWK programs consist of **patterns** (i.e. rules that match lines of text) and **actions** (i.e. commands to execute when a pattern matches a line). | |
| 72 | |
| 73 The basic form of AWK program is:: | |
| 74 | |
| 75 pattern { action 1; action 2; action 3; } | |
| 76 | |
| 77 | |
| 78 **Pattern Examples** | |
| 79 | |
| 80 - **$2 == "chr3"** will match lines whose second column is the string 'chr3' | |
| 81 - **$5-$4>23** will match lines that after subtracting the value of the fourth column from the value of the fifth column, gives value alrger than 23. | |
| 82 - **/AG..AG/** will match lines that contain the regular expression **AG..AG** (meaning the characeters AG followed by any two characeters followed by AG). (This is the way to specify regular expressions on the entire line, similar to GREP.) | |
| 83 - **$7 ~ /A{4}U/** will match lines whose seventh column contains 4 consecutive A's followed by a U. (This is the way to specify regular expressions on a specific field.) | |
| 6 | 84 - **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000 |
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1e974b82380d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
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85 - **BEGIN** will be executed once only, before the first input record is read. |
| 0 | 86 - If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines). |
| 87 | |
| 88 | |
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74aae7d6cb09
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
bgruening
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89 |
| 0 | 90 **Action Examples** |
| 91 | |
| 92 - **{ print }** or **{ print $0 }** will print the entire input line (the line that matched in **pattern**). **$0** is a special marker meaning 'the entire line'. | |
| 93 - **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line. | |
| 94 - **{ print $4, $5-$4 }** will print the fourth column and the difference between the fifth and fourth column. (If the fourth column was start-position in the input file, and the fifth column was end-position - the output file will contain the start-position, and the length). | |
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74aae7d6cb09
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
bgruening
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95 - **{ FS = "," }** can be used to change the field separator (delimeter) for parsing the input file. |
| 0 | 96 - If no action part is specified (not even the curly brackets) - the default action is to print the entire line. |
| 97 | |
| 98 | |
| 99 **AWK's Regular Expression Syntax** | |
| 100 | |
| 7 | 101 The select 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. |
| 0 | 102 |
| 103 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. | |
| 104 - **^** matches the beginning of a string(but not an internal line). | |
| 105 - **(** .. **)** groups a particular pattern. | |
| 106 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. | |
| 107 | |
| 108 - **{n}** The preceding item is matched exactly n times. | |
| 7 | 109 - **{n,}** The preceding item ismatched n or more times. |
| 110 - **{n,m}** The preceding item is matched at least n times but not more than m times. | |
| 0 | 111 |
| 112 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. | |
| 113 - **.** Matches any single character except a newline. | |
| 114 - ***** The preceding item will be matched zero or more times. | |
| 115 - **?** The preceding item is optional and matched at most once. | |
| 116 - **+** The preceding item will be matched one or more times. | |
| 117 - **^** has two meaning: | |
| 7 | 118 - matches the beginning of a line or string. |
| 0 | 119 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. |
| 120 - **$** matches the end of a line or string. | |
| 7 | 121 - **\|** Separates alternate possibilities. |
| 0 | 122 |
| 4 | 123 ]]> |
| 1 | 124 </help> |
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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125 <expand macro="citations" /> |
| 0 | 126 </tool> |