Mercurial > repos > iuc > brew3r_r

annotate brew3r_r.xml @ 2:448beaf9deb8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit d287d5688e57f4154d5875789e0cd4d5c87f11ce
author iuc
date Thu, 03 Oct 2024 22:35:41 +0000
parents a0708b9d33be
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9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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1 <tool id="brew3r_r" name="BREW3R.r" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
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2 <description>Extend GTF</description>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0.2</token>
2
448beaf9deb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit d287d5688e57f4154d5875789e0cd4d5c87f11ce
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5 <token name="@VERSION_SUFFIX@">1</token>
0
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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6 </macros>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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7 <xrefs>
1
a0708b9d33be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 934f4b672e4f21e211a530281a973b61c20035c5
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8 <xref type="bio.tools">brew3r.r</xref>
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9 <xref type="bioconductor">BREW3R.r</xref>
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10 </xrefs>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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11 <requirements>
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12 <!-- <requirement type="package" version="@TOOL_VERSION@">bioconductor-brew3r.r</requirement>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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13 <requirement type="package" version="1.64.0">bioconductor-rtracklayer</requirement>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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14 <requirement type="package" version="1.20.4">r-getopt</requirement> -->
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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15 <container type="docker">lldelisle/brew3r:v2</container>
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16 </requirements>
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17 <required_files>
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18 <include path="brew3r.r_script.R" />
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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19 </required_files>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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20 <version_command><![CDATA[
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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21 echo $(R --version | grep version | grep -v GNU)", BREW3R.r version" $(R --vanilla --slave -e "library(BREW3R.r); cat(sessionInfo()\$otherPkgs\$BREW3R.r\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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22 ]]></version_command>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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23 <command detect_errors="exit_code"><![CDATA[
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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24 Rscript '${__tool_directory__}/brew3r.r_script.R'
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25 --gtf_to_extend '$gtf_to_extend'
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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26 --gtf_to_overlap '$gtf_to_overlap'
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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27 #if '$sup_output' == 'true':
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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28 --sup_output '$output_table'
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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29 #end if
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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30 #if str($no_add) != '':
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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31 '$no_add'
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32 #end if
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33 #if str($exclude_pattern) != '':
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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34 --exclude_pattern '$exclude_pattern'
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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35 #end if
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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36 #if str($filter_unstranded) != '':
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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37 '$filter_unstranded'
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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38 #end if
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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39 -o output.gtf
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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40
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41 ]]></command>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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42 <inputs>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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43 <param argument="--gtf_to_extend" type="data" format="gtf" label="Input gtf file to be extended on 3'" help="Usually coming from public resource." />
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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44 <param argument="--gtf_to_overlap" type="data" format="gtf" label="Input gtf file that will be used to extend" help="Coming from StringTie or another public resource." />
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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45 <param argument="--sup_output" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Get a supplementary output table with resolution of overlaps" />
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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46 <param argument="--no_add" type="boolean" truevalue="--no_add" falsevalue="" checked="false" label="Do not add new exons" />
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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47 <param argument="--exclude_pattern" type="text" value="" label="Do not extend genes with names matching this pattern" help="Leave empty if you want to extend all genes.">
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48 <sanitizer>
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49 <valid initial="string.printable">
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50 <remove value="'"/>
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51 <remove value="\"/>
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52 </valid>
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53 </sanitizer>
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54 </param>
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55 <param argument="--filter_unstranded" type="boolean" truevalue="--filter_unstranded" falsevalue="" checked="false" label="Filter unstranded intervals that overlaps genes of both strands" help="Recommanded if you used StringTie on unstranded libraries." />
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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56 </inputs>
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57 <outputs>
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58 <data name="output" format="gtf" from_work_dir="output.gtf" label="${tool.name} on ${gtf_to_extend.name} and ${gtf_to_overlap.name}: GTF" />
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59 <data name="output_table" format="tabular" label="${tool.name} on ${gtf_to_extend.name} and ${gtf_to_overlap.name}: overlap resolution">
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60 <filter>sup_output == True</filter>
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61 </data>
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62 </outputs>
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63 <tests>
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64 <test expect_num_outputs="1">
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65 <param name="gtf_to_extend" value="input.gtf"/>
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66 <param name="gtf_to_overlap" value="second_input.gtf"/>
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67 <output name="output" value="output.gtf" compare="diff" lines_diff="2"/>
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68 </test>
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69 <test expect_num_outputs="1">
2
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70 <param name="gtf_to_extend" value="input_noexonid.gtf"/>
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71 <param name="gtf_to_overlap" value="second_input.gtf"/>
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72 <output name="output">
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73 <assert_contents>
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74 <has_n_lines n="36"/>
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75 <has_text text="BREW3R"/>
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76 </assert_contents>
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77 </output>
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78 </test>
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79 <test expect_num_outputs="1">
0
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80 <param name="gtf_to_extend" value="input.gtf"/>
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81 <param name="gtf_to_overlap" value="second_input.gtf"/>
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82 <param name="no_add" value="true"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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83 <output name="output">
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84 <assert_contents>
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iuc
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diff changeset
85 <has_n_lines n="31"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
iuc
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86 <not_has_text text="BREW3R"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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87 </assert_contents>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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88 </output>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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89 </test>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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90 <test expect_num_outputs="1">
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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91 <param name="gtf_to_extend" value="input.gtf"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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92 <param name="gtf_to_overlap" value="second_input.gtf"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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93 <param name="exclude_pattern" value="^Gm"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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94 <output name="output">
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95 <assert_contents>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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96 <has_n_lines n="34"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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97 <not_has_text text="exon111.ext"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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98 </assert_contents>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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99 </output>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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100 </test>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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101 <test expect_num_outputs="1">
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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102 <param name="gtf_to_extend" value="input.gtf"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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103 <param name="gtf_to_overlap" value="second_input.gtf"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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104 <param name="exclude_pattern" value="Gm$"/>
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105 <output name="output" value="output.gtf" compare="diff" lines_diff="2"/>
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106 <assert_command>
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107 <has_text text="--exclude_pattern 'Gm$'"/>
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108 </assert_command>
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109 </test>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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110 <test expect_num_outputs="1">
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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111 <param name="gtf_to_extend" value="input.gtf"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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112 <param name="gtf_to_overlap" value="second_input.gtf"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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113 <param name="filter_unstranded" value="true"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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114 <output name="output">
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115 <assert_contents>
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116 <has_n_lines n="36"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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117 <not_has_text text="exon121.ext"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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118 </assert_contents>
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119 </output>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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120 </test>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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121 <test expect_num_outputs="1">
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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122 <param name="gtf_to_extend" value="input2.gtf"/>
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123 <param name="gtf_to_overlap" value="second_input2.gtf"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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124 <param name="filter_unstranded" value="true"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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125 <output name="output" value="output2.gtf" compare="diff" lines_diff="2"/>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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126 </test>
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127 </tests>
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128 <help><![CDATA[
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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129
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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130 .. class:: infomark
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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131
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132 **What it does**
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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133
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134 This tool extend the annotations existing in an input GTF file in the 3' end using annotations from another input GTF. During the process, it makes sure that there will not be new overlaps between different genes.
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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135
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136 Usage
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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137 .....
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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138
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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139
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140 **Input**
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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141
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142 2 GTF files:
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143 - First one to extend usually comes from a public resource.
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144 - Second one that is used as template may come from a public resource or from StringTie.
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145
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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146
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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147 **Output**
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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148
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149 1 GTF file with all exons from the input GTF where some of them have been extended (the exon_id ends with '.ext') and potentially new exons (the exon_id contains BREW3R).
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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150
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151 ]]></help>
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152 <citations>
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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153 <citation type="bibtex">
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154 @unpublished{None,
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155 author = {Lucille Lopez-Delisle},
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156 title = {None},
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157 year = {None},
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158 eprint = {None},
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159 url = {https://github.com/lldelisle/BREW3R.r}
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160 }</citation>
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161 </citations>
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162 </tool>