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1 <tool id="cshl_sed_tool" name="sed">
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2 <description></description>
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3 <!-- NOTE
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4 'sandbox' is a patched SED program,
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5 which blocks executing shell commands and file reading/writing.
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6
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7 Hopefully, it is safe enough to allow users to execute their own SED commands
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8 -->
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9 <command interpreter="sh">sed_wrapper.sh $silent $input $output '$url_paste'</command>
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10 <inputs>
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11 <param format="txt" name="input" type="data" label="File to process" />
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12
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13 <!-- Note: the parameter ane MUST BE 'url_paste' -
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14 This is a hack in the galaxy library (see ./lib/galaxy/util/__init__.py line 142)
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15 If the name is 'url_paste' the string won't be sanitized, and all the non-alphanumeric characters
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16 will be passed to the shell script -->
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17 <param name="url_paste" type="text" area="true" size="5x35" label="SED Program" help="">
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18 <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator>
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19 </param>
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20
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21 <param name="silent" type="select" label="operation mode" help="(Same as 'sed -n', leave at 'normal' unless you know what you're doing)" >
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22 <option value="">normal</option>
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23 <option value="-n">silent</option>
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24 </param>
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25
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26 </inputs>
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27 <outputs>
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28 <data format="input" name="output" metadata_source="input" />
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29 </outputs>
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30 <help>
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31
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32 **What it does**
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33
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34 This tool runs the unix **sed** command on the selected data file.
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35
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36 .. class:: infomark
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37
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38 **TIP:** This tool uses the **extended regular** expression syntax (same as running 'sed -r').
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39
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40
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41
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42 **Further reading**
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43
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44 - Short sed tutorial (http://www.linuxhowtos.org/System/sed_tutorial.htm)
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45 - Long sed tutorial (http://www.grymoire.com/Unix/Sed.html)
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46 - sed faq with good examples (http://sed.sourceforge.net/sedfaq.html)
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47 - sed cheat-sheet (http://www.catonmat.net/download/sed.stream.editor.cheat.sheet.pdf)
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48 - Collection of useful sed one-liners (http://student.northpark.edu/pemente/sed/sed1line.txt)
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49
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50 -----
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51
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52 **Sed commands**
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53
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54 The most useful sed command is **s** (substitute).
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55
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56 **Examples**
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57
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58 - **s/hsa//** will remove the first instance of 'hsa' in every line.
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59 - **s/hsa//g** will remove all instances (beacuse of the **g**) of 'hsa' in every line.
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60 - **s/A{4,}/--&--/g** will find sequences of 4 or more consecutive A's, and once found, will surround them with two dashes from each side. The **&** marker is a place holder for 'whatever matched the regular expression'.
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61 - **s/hsa-mir-([^ ]+)/short name: \\1 full name: &/** will find strings such as 'hsa-mir-43a' (the regular expression is 'hsa-mir-' followed by non-space characters) and will replace it will string such as 'short name: 43a full name: hsa-mir-43a'. The **\\1** marker is a place holder for 'whatever matched the first parenthesis' (similar to perl's **$1**) .
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62
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63
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64 **sed's Regular Expression Syntax**
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65
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66 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.
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67
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68 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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69 - **^** matches the beginning of a string(but not an internal line).
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70 - **(** .. **)** groups a particular pattern.
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71 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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72
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73 - **{n}** The preceding item is matched exactly n times.
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74 - **{n,}** The preceding item ismatched n or more times.
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75 - **{n,m}** The preceding item is matched at least n times but not more than m times.
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76
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77 - **[** ... **]** 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**.
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78 - **.** Matches any single character except a newline.
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79 - ***** The preceding item will be matched zero or more times.
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80 - **?** The preceding item is optional and matched at most once.
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81 - **+** The preceding item will be matched one or more times.
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82 - **^** has two meaning:
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83 - matches the beginning of a line or string.
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84 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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85 - **$** matches the end of a line or string.
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86 - **\|** Separates alternate possibilities.
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87
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88
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89 **Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
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90
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91 </help>
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92 </tool>
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