Mercurial > repos > iuc > obi_grep

annotate obigrep.xml @ 4:63b47deab5ff draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:54:50 +0000
parents 4568c98d1dfe
children 16dc1dbb4cb2
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4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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1 <tool id="obi_grep" name="obigrep" version="@TOOL_VERSION@" profile="@PROFILE@">
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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2 <description>Filters sequence file</description>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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3 <expand macro="bio_tools"/>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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4 <macros>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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5 <import>macros.xml</import>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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6 </macros>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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7 <expand macro="requirements"/>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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8 <expand macro="stdio"/>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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9 <command><![CDATA[
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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10 @GUNZIP_INPUT@
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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11
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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12 obigrep
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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13 --without-progress-bar
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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14 ${v}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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15 #if str($options_grep.options_grep_selector) == 'sequence'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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16 -s ${options_grep.sequence}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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17 #else if str($options_grep.options_grep_selector) == 'definition'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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18 -D ${options_grep.definition}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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19 #else if str($options_grep.options_grep_selector) == 'identifier'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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20 -I ${options_grep.identifier}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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21 #else if str($options_grep.options_grep_selector) == 'idlist'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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22 --id-list '${options_grep.idlist}'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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23 #else if str($options_grep.options_grep_selector) == 'attribute'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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24 -a ${options_grep.attribute}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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25 #else if str($options_grep.options_grep_selector) == 'hasattribute'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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26 -A ${options_grep.attribute}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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27 #else if str($options_grep.options_grep_selector) == 'predicat'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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28 -p ${options_grep.predicat}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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29 #else if str($options_grep.options_grep_selector) == 'lmax'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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30 -L ${options_grep.lmax}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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31 #else if str($options_grep.options_grep_selector) == 'lmin'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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32 -l ${options_grep.lmin}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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33 #end if
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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34 @INPUT_FORMAT@
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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35 @OUT_FORMAT@
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36 input
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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37 @GZIP_OUTPUT@
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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38 > '$output'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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39 @GENERATE_GALAXY_JSON@
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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40 ]]></command>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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41 <inputs>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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42 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" />
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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43 <conditional name="options_grep">
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44 <param name="options_grep_selector" type="select" label="Choose the sequence record selection option" >
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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45 <option value="sequence" selected="true">sequence</option>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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46 <option value="definition">definition</option>
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47 <option value="identifier">identifier</option>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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48 <option value="idlist">idlist</option>
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49 <option value="attribute">attribute</option>
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50 <option value="hasattribute">hasattribute</option>
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51 <option value="predicat">predicat</option>
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52 <option value="lmax">lmax</option>
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53 <option value="lmin">lmin</option>
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54 </param>
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55 <when value="sequence">
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56 <param name="sequence" type="text" label="Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive." >
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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57 <expand macro="sanitizer" />
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58 </param>
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59 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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60 <when value="definition">
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61 <param name="definition" type="text" label="Regular expression pattern to be tested against the definition of the sequence record. The pattern is case sensitive." >
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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62 <expand macro="sanitizer" />
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63 </param>
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64 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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65 <when value="identifier">
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66 <param name="identifier" type="text" label="Regular expression pattern to be tested against the identifier of the sequence record. The pattern is case sensitive." >
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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67 <expand macro="sanitizer" />
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68 </param>
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69 </when>
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70 <when value="idlist">
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71 <param name="idlist" type="data" format="txt,tabular" label="points to a text file containing the list of sequence record identifiers to be selected. The file format consists in a single identifier per line." />
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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72 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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73 <when value="attribute">
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74 <param name="attribute" type="text" label="Regular expression pattern matched against the attributes of the sequence record. the value of this attribute is of the form : key:regular_pattern. The pattern is case sensitive." >
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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75 <expand macro="sanitizer" />
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76 </param>
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77 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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78 <when value="hasattribute">
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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79 <param name="hasattribute" type="text" label="Selects sequence records having an attribute who is key." >
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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80 <expand macro="sanitizer" />
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81 </param>
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82 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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83 <when value="predicat">
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84 <param name="predicat" type="text" label="Python boolean expression to be evaluated for each sequence record." help="The attribute keys defined for each sequence record can be used in the expression as variable names. An extra variable named sequenceefers to the sequence record itself." >
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85 <expand macro="sanitizer" />
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86 </param>
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87 </when>
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88 <when value="lmax">
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89 <param name="lmax" type="text" label="lmax" help="Keeps sequence records whose sequence length is equal or shorter than lmax" />
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90 </when>
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91 <when value="lmin">
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92 <param name="lmin" type="text" label="lmin" help="Keeps sequence records whose sequence length is equal or longer than lmin"/>
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93 </when>
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94 </conditional>
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95
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96 <param name="v" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Invert the sequence record selection (option -v)" />
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97 <expand macro="input_format_options_macro"/>
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98 <expand macro="out_format_macro"/>
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99 </inputs>
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100 <outputs>
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101 <data format="auto" name="output"/>
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102 </outputs>
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103 <tests>
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104 <test>
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105 <param name="input" value="illuminapairedend.output.fastq" />
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106 <conditional name="options_grep">
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107 <param name="options_grep_selector" value="lmin"/>
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108 <param name="lmin" value="80"/>
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109 </conditional>
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110 <param name="v" value="true" />
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111 <param name="out_format" value="fastq" />
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112 <output name="output" file="output_obigrep_lmin.fastq" ftype="fastqsanger"/>
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113 </test>
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114 <test>
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115 <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastq.gz" />
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116 <conditional name="options_grep">
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117 <param name="options_grep_selector" value="predicat"/>
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118 <param name="predicat" value='mode!="joined"'/>
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119 </conditional>
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120 <param name="v" value="false" />
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121 <param name="out_format" value="fasta" />
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122 <output name="output" file="output_obigrep_predicat.fasta.gz" ftype="fasta.gz" decompress="true"/>
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123 </test>
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124 </tests>
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125 <help><![CDATA[
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126
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127 .. class:: infomark
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128
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129 **What it does**
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130
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131 The obigrep command is in some way analog to the standard Unix grep command. It selects a subset of sequence records from a sequence file.
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132
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133 A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself.
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134
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135 Instead of working text line by text line as the standard Unix tool, selection is done sequence record by sequence record. A large set of options allows refining selection on any of the sequence record elements.
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136
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137 Moreover obigrep allows specifying simultaneously several conditions (that take the value TRUE or FALSE) and only the sequence records that fulfill all the conditions (all conditions are TRUE) are selected.
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138
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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139 Sequence record selection options :
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140 * sequence : Regular expression pattern to be tested against the sequence itself. ex: GAATTC
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141
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142 * definition : Regular expression pattern to be tested against the definition of the sequence record. ex: [Cc]hloroplast
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143
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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144 * identifier : Regular expression pattern to be tested against the identifier of the sequence record. ex: ^GH
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145
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146 * idlist : points to a text file containing the list of sequence record identifiers to be selected.
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147
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148 * attribute : Regular expression pattern matched against the attributes of the sequence record. the value of this attribute is of the form : key:regular_pattern. ex:'family_name:Asteraceae'
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149
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150 * hasattribute : Selects sequence records having an attribute whose key = KEY.
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151
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152 * predicat : Python boolean expression to be evaluated for each sequence record. The attribute keys defined for each sequence record can be used in the expression as variable names. An extra variable named ‘sequence’ refers to the sequence record itself. ex: mode!="joined"
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153
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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154 * lmax : Keeps sequence records whose sequence length is equal or shorter than lmax. ex : 100
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155
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156 * lmin : Selects sequence records whose sequence length is equal or longer than lmin. ex : 100
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157
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158 @OBITOOLS_LINK@
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159
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160 ]]>
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161
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162 </help>
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163 <expand macro="citation" />
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164
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165 </tool>