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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
author bgruening
date Wed, 09 Nov 2016 14:50:45 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
bgruening
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1 <tool id="sed_stream_editor" name="Manipulation" version="0.0.1">
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
bgruening
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2 <description>utility that parses and transforms text using regular expressions (sed)</description>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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3 <command>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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4 <![CDATA[
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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5 sed -r '$pattern'
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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6 $input > $outfile
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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7 ]]>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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8 </command>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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9 <inputs>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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10 <param format="txt, tabular" name="input" type="data" label="Replace lines from"/>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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11 <param name="pattern" type="text" value="" label="the pattern" help="here you can enter your sed expression (No syntax check or sanitising!)" />
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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12 </inputs>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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13 <outputs>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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14 <data format="input" name="outfile" metadata_source="input"/>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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15 </outputs>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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16 <options sanitize="False"/>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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17 <requirements>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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18 <requirement type="binary">sed</requirement>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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19 </requirements>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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20 <tests>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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21
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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22 </tests>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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23 <help>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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24 <![CDATA[
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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25
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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26 .. class:: warningmark
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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27
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
bgruening
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28 Use with caution! Its a plain wrapper around **sed** and the input is not sanitized.
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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29
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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30
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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31 -----
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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32
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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33 **What it does**
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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34
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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35 Changes every line of a text file according to a given regular expression.
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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36
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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37 -----
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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38
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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39 **Syntax**
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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40
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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41 Use the **sed**-syntax -> **s/find-pattern/replace-pattern/**
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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43 **Example**
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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44
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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45 - **s/x/-/** Replace all **x** with **-**.
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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46
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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47 - **s/_.*//** Splits a string after **_** and replaces the rest with nothing.
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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48 - **s/[^_]*_*//** Splits a string after **_** and replaces the first part with nothing.
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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49
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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50 - **s/\\s.*//** Splits a string after whitespaces and replaces the rest with nothing.
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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51 - **s/\\S*\\s*//** Splits a string after whitespaces and replaces the first part with nothing.
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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52
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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53
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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54 ]]>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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55 </help>
8ae62a63e93d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sed commit cfb00484086246d51865572f004e3140b8bf4852
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56 </tool>