Mercurial > repos > brinkmanlab > awkscript

annotate awkscript.xml @ 0:7222917a3948 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
author brinkmanlab
date Fri, 24 Jan 2020 17:30:15 -0500
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children 87c5033654a6
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7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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1 <tool id="awkscript" name="AWK Script" version="1.0">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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2 <description>Transform, modify, or generate data</description>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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3 <edam_topics>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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4 <edam_topic>topic_0769</edam_topic>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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5 </edam_topics>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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6 <edam_operations>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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7 <edam_operation>operation_3429</edam_operation>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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8 <edam_operation>operation_3778</edam_operation>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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9 <edam_operation>operation_3434</edam_operation>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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10 <edam_operation>operation_2409</edam_operation>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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11 </edam_operations>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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12 <requirements>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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13 <requirement type="package" version="5.0.1">gawk</requirement>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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14 </requirements>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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15 <version_command>awk --version | head -n 1</version_command>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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16 <command><![CDATA[
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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17 #set $tool_input = 0
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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18 env -i
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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19 #for env in $envs
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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20 '$env.name'='$env.val'
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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21 #end for
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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22 awk
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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23 --sandbox
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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24 -v FS=' '
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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25 -v OFS=' '
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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26 -f '$awk_script'
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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27 #for group in $infiles
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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28 tool_input=$tool_input
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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29 #set $tool_input+=1
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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30 #if $group.input_type_selection.multiple
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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31 #set $inputs = $group.input_type_selection.infile
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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32 ## Allow capturing the collection id in the program
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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33 ## tool_input_id='$inputs.element_identifier' FIXME collections dont expose their label to tools.
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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34 #else
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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35 #set $inputs = [$group.input_type_selection.infile]
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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36 #end if
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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37 #for file in $inputs
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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38 tool_input_id='$file.element_identifier'
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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39 '$file'
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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40 #end for
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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41 #end for
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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42 > '$outfile'
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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43 ]]></command>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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44 <configfiles>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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45 <configfile name="awk_script">$code</configfile>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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46 </configfiles>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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47 <inputs>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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48 <repeat name="infiles" title="Inputs">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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49 <conditional name="input_type_selection">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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50 <param name="multiple" type="boolean" checked="false" label="Accept multiple" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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51 <when value="false">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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52 <param name="infile" format="txt" type="data" label="Single file to process" help="A separate execution will occur for each provided file"/>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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53 </when>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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54 <when value="true">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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55 <param name="infile" format="txt" type="data" multiple="true" label="File or collection to process" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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56 </when>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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57 </conditional>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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58 </repeat>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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59 <param name="code" type="text" area="true" size="5x35" label="AWK Program" help="">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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60 <sanitizer sanitize="false" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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61 </param>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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62 <repeat name="envs" title="Environment Variables">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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63 <param name="name" type="text" label="Name">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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64 <sanitizer>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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65 <valid initial="string.printable">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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66 <remove value="&apos;" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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67 </valid>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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68 </sanitizer>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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69 </param>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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70 <param name="val" type="text" label="Value">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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71 <sanitizer>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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72 <valid initial="string.printable">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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73 <remove value="&apos;" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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74 </valid>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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75 </sanitizer>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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76 </param>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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77 </repeat>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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78 </inputs>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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79 <outputs>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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80 <data name="outfile" format="txt" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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81 </outputs>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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82 <tests>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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83 <test>
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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84 <repeat name="envs">
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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85 <param name="name" value="message" />
7222917a3948 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/awkscript commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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86 <param name="val" value="Success!" />
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87 </repeat>
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88 <param name="code" value="BEGIN { print ENVIRON[&quot;message&quot;]; }" />
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89 <output name="outfile">
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90 <assert_contents>
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91 <has_text text="Success!" />
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92 </assert_contents>
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93 </output>
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94 </test>
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95 </tests>
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96 <help><![CDATA[
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97 GNU AWK Script
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98
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99 Several kinds of tasks occur repeatedly when working with text files.
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100 You might want to extract certain lines and discard the rest. Or you may need to make changes wherever
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101 certain patterns appear, but leave the rest of the file alone. Such jobs are often easy with awk.
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102 The awk utility interprets a special-purpose programming language that makes it easy to handle simple data-reformatting jobs.
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103
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104 Each input can be set to single, causing any input collections to map over the tool running, a new instance for each.
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105 Setting the input to multiple will pass the entire collection to a single instance of the tool, allowing aggregation of the input data.
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106 A mixture of single and multiple inputs is allowed, the single inputs being mapped over and the multiple inputs passed to each instance.
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107 This tool is also able to operate with no inputs, generating data for whatever purpose.
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108
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109 See [GNU AWK Users Guide](https://www.gnu.org/software/gawk/manual/gawk.html) for more information.
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110
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111 A variable 'tool_input' will be set to the index of the inputs, in order.
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112 You can combine this with ARGIND to determine which file you are currently operating on and its position in any possible input collection.
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113 A variable 'tool_input_id' is also set specifying the current inputs dataset name or collection id.
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114 Beware that ARGIND will increment 3 between inputs as one is consumed setting tool_input and another setting tool_input_id.
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115
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116 The environment inputs allow you to generalise your scripts, specifying constants with the tool invocation, or allow attaching simple workflow inputs.
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117 Environment variables are accessible via [ENVIRON](https://www.gnu.org/software/gawk/manual/gawk.html#index-environment-variables_002c-in-ENVIRON-array).
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118
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119 Due to a limitation in Galaxy, all output is assigned the 'txt' type. This can be changed in the tool settings in a workflow or modifying the dataset after invocation.
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120
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121 gawk is run with the [sandbox](https://www.gnu.org/software/gawk/manual/gawk.html#index-sandbox-mode) argument, disabling some functionality.
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122 ]]></help>
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123 <citations>
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124 <citation type="doi">10.5281/zenodo.3364789</citation>
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125 </citations>
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126 </tool>