Mercurial > repos > iuc > obi_grep

annotate obigrep.xml @ 1:71cb8b117c05 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
author iuc
date Fri, 12 Oct 2018 06:25:55 -0400
parents 1aa790551187
children fe7ec8a3d35e
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1
71cb8b117c05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
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1 <tool id="obi_grep" name="obigrep" version="@TOOL_VERSION@">
0
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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2 <description>Filters sequence file</description>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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3 <macros>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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4 <import>macros.xml</import>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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5 </macros>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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6 <expand macro="requirements"/>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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7 <expand macro="stdio"/>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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8
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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9 <command>
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10
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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11 <![CDATA[
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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12 obigrep
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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13 ${v}
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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14 #if str($options_grep.options_grep_selector) == 'sequence'
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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15 -s ${options_grep.sequence}
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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16 #else if str($options_grep.options_grep_selector) == 'definition'
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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17 -D ${options_grep.definition}
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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18 #else if str($options_grep.options_grep_selector) == 'identifier'
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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19 -I ${options_grep.identifier}
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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20 #else if str($options_grep.options_grep_selector) == 'idlist'
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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21 --id-list '$options_grep.idlist}
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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22 #else if str($options_grep.options_grep_selector) == 'attribute'
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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23 -a ${options_grep.attribute}
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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24 #else if str($options_grep.options_grep_selector) == 'hasattribute'
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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25 -A ${options_grep.attribute}
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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26 #else if str($options_grep.options_grep_selector) == 'predicat'
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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27 -p ${options_grep.predicat}
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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28 #else if str($options_grep.options_grep_selector) == 'lmax'
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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29 -L ${options_grep.lmax}
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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30 #else if str($options_grep.options_grep_selector) == 'lmin'
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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31 -l ${options_grep.lmin}
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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32 #end if
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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33 '$input' > '$output'
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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34 ]]>
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35
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36 </command>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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37
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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38 <inputs>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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39 <param name="input" type="data" format="fasta,fastq" label="Input sequences file" />
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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40 <conditional name="options_grep">
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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41 <param name="options_grep_selector" type="select" label="Choose the sequence record selection option" >
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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42 <option value="sequence" selected="true">sequence</option>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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43 <option value="definition">definition</option>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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44 <option value="identifier">identifier</option>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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45 <option value="idlist">idlist</option>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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46 <option value="attribute">attribute</option>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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47 <option value="hasattribute">hasattribute</option>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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48 <option value="predicat">predicat</option>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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49 <option value="lmax">lmax</option>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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50 <option value="lmin">lmin</option>
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51 </param>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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52 <when value="sequence">
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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53 <param name="sequence" type="text" label="Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive." >
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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54 <expand macro="sanitizer" />
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55 </param>
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56 </when>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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57 <when value="definition">
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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58 <param name="definition" type="text" label="Regular expression pattern to be tested against the definition of the sequence record. The pattern is case sensitive." >
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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59 <expand macro="sanitizer" />
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60 </param>
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61 </when>
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62 <when value="identifier">
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63 <param name="identifier" type="text" label="Regular expression pattern to be tested against the identifier of the sequence record. The pattern is case sensitive." >
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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64 <expand macro="sanitizer" />
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65 </param>
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66 </when>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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67 <when value="idlist">
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68 <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." />
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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69 </when>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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70 <when value="attribute">
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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71 <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." >
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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72 <expand macro="sanitizer" />
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73 </param>
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74 </when>
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75 <when value="hasattribute">
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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76 <param name="hasattribute" type="text" label="Selects sequence records having an attribute who is key." >
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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77 <expand macro="sanitizer" />
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78 </param>
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79 </when>
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80 <when value="predicat">
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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81 <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." >
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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82 <expand macro="sanitizer" />
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83 </param>
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84 </when>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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85 <when value="lmax">
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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86 <param name="lmax" type="text" label="lmax" help="Keeps sequence records whose sequence length is equal or shorter than lmax" />
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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87 </when>
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88 <when value="lmin">
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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89 <param name="lmin" type="text" label="lmin" help="Keeps sequence records whose sequence length is equal or longer than lmin"/>
1aa790551187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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90 </when>
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91 </conditional>
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92
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93 <param name="v" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Invert the sequence record selection (option -v)" />
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94 <param name="out_format" type="select" label="Output data type">
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95 <option value="fasta">fasta</option>
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96 <option value="fastq">fastq</option>
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97 </param>
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98
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99 </inputs>
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100 <outputs>
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101 <data format="fastq" name="output" label="output with ${tool.name} on ${on_string}" >
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102 <change_format>
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103 <when input="out_format" value="fasta" format="fasta" />
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104 </change_format>
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105 </data>
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106 </outputs>
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107 <tests>
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108 <test>
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109 <param name="input" value="illuminapairedend.output.fastq" />
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110 <conditional name="options_grep">
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111 <param name="options_grep_selector" value="lmin"/>
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112 <param name="lmin" value="80"/>
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113 </conditional>
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114 <param name="v" value="true" />
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115 <param name="out_format" value="fastq" />
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116 <output name="output" file="output_obigrep_lmin.fastq" ftype="fastq"/>
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117 </test>
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118 <test>
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119 <param name="input" value="illuminapairedend.output.fastq" />
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120 <conditional name="options_grep">
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121 <param name="options_grep_selector" value="predicat"/>
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122 <param name="predicat" value='mode!="joined"'/>
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123 </conditional>
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124 <param name="v" value="false" />
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125 <param name="out_format" value="fasta" />
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126 <output name="output" file="output_obigrep_predicat.fasta" ftype="fasta"/>
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127 </test>
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128 </tests>
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129 <help><![CDATA[
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130
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131 .. class:: infomark
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132
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133 **What it does**
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134
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135 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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136
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137 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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138
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139 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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140
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141 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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142
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143 Sequence record selection options :
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144 * sequence : Regular expression pattern to be tested against the sequence itself. ex: GAATTC
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145
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146 * definition : Regular expression pattern to be tested against the definition of the sequence record. ex: [Cc]hloroplast
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147
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148 * identifier : Regular expression pattern to be tested against the identifier of the sequence record. ex: ^GH
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149
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150 * idlist : points to a text file containing the list of sequence record identifiers to be selected.
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151
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152 * 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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153
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154 * hasattribute : Selects sequence records having an attribute whose key = KEY.
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155
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156 * 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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157
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158 * lmax : Keeps sequence records whose sequence length is equal or shorter than lmax. ex : 100
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159
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160 * lmin : Selects sequence records whose sequence length is equal or longer than lmin. ex : 100
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161
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162 @OBITOOLS_LINK@
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163
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164 ]]>
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165
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166 </help>
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167 <expand macro="citation" />
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168
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169 </tool>