Mercurial > repos > jjohnson > arriba_download_reference

annotate arriba_download_reference.xml @ 1:55ca46d68a57 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
author jjohnson
date Mon, 13 Jun 2022 12:10:34 +0000
parents 7345cb1bb772
children
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7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
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1 <tool id="arriba_download_reference" name="Arriba Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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2 <description>Download to history</description>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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6 <expand macro="requirements" />
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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7 <expand macro="version_command" />
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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8 <command detect_errors="exit_code"><![CDATA[
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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9 echo $arriba_reference_name > '$star_index' &&
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10 BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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11 REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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12 #if $is_test != 'yes'
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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13 \$REF_SCRIPT '$arriba_reference_name' &&
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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14 cp *.fa* '$genome_fasta' &&
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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15 cp *.gtf* '$genome_gtf' &&
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16 mv STAR_index_* '$star_index.extra_files_path'
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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17 #else
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18 [[ -x \$REF_SCRIPT ]]
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19 #end if
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20 ]]></command>
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21 <inputs>
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22 <param name="is_test" type="hidden" value="no"/>
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23 <param name="arriba_reference_name" type="select" label="Select reference">
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24 <option value="GRCh38+ENSEMBL93">GRCh38+ENSEMBL93</option>
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25 <option value="GRCh38+GENCODE28">GRCh38+GENCODE28</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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26 <option value="GRCh38+RefSeq">GRCh38+RefSeq</option>
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27 <option value="GRCh38viral+ENSEMBL93">GRCh38viral+ENSEMBL93</option>
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28 <option value="GRCh38viral+GENCODE28">GRCh38viral+GENCODE28</option>
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29 <option value="GRCh38viral+RefSeq">GRCh38viral+RefSeq</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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30 <option value="hg38+ENSEMBL93">hg38+ENSEMBL93</option>
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31 <option value="hg38+GENCODE28">hg38+GENCODE28</option>
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32 <option value="hg38+RefSeq">hg38+RefSeq</option>
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33 <option value="hg38viral+ENSEMBL93">hg38viral+ENSEMBL93</option>
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34 <option value="hg38viral+GENCODE28">hg38viral+GENCODE28</option>
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35 <option value="hg38viral+RefSeq">hg38viral+RefSeq</option>
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36 <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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37 <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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38 <option value="GRCh37+RefSeq">GRCh37+RefSeq</option>
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39 <option value="GRCh37viral+ENSEMBL87">GRCh37viral+ENSEMBL87</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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40 <option value="GRCh37viral+GENCODE19">GRCh37viral+GENCODE19</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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41 <option value="GRCh37viral+RefSeq">GRCh37viral+RefSeq</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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42 <option value="hg19+ENSEMBL87">hg19+ENSEMBL87</option>
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43 <option value="hg19+GENCODE19">hg19+GENCODE19</option>
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44 <option value="hg19+RefSeq">hg19+RefSeq</option>
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45 <option value="hg19viral+ENSEMBL87">hg19viral+ENSEMBL87</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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46 <option value="hg19viral+GENCODE19">hg19viral+GENCODE19</option>
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47 <option value="hg19viral+RefSeq">hg19viral+RefSeq</option>
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48 <option value="hs37d5+ENSEMBL87">hs37d5+ENSEMBL87</option>
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49 <option value="hs37d5+GENCODE19">hs37d5+GENCODE19</option>
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50 <option value="hs37d5+RefSeq">hs37d5+RefSeq</option>
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51 <option value="hs37d5viral+ENSEMBL87">hs37d5viral+ENSEMBL87</option>
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52 <option value="hs37d5viral+GENCODE19">hs37d5viral+GENCODE19</option>
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53 <option value="hs37d5viral+RefSeq">hs37d5viral+RefSeq</option>
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54 <option value="GRCm39+GENCODEM26">GRCm39+GENCODEM26</option>
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55 <option value="GRCm39+RefSeq">GRCm39+RefSeq</option>
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56 <option value="GRCm39viral+GENCODEM26">GRCm39viral+GENCODEM26</option>
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57 <option value="GRCm39viral+RefSeq">GRCm39viral+RefSeq</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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58 <option value="GRCm38+GENCODEM25">GRCm38+GENCODEM25</option>
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59 <option value="GRCm38+RefSeq">GRCm38+RefSeq</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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60 <option value="GRCm38viral+GENCODEM25">GRCm38viral+GENCODEM25</option>
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61 <option value="GRCm38viral+RefSeq">GRCm38viral+RefSeq</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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62 <option value="mm39+GENCODEM26">mm39+GENCODEM26</option>
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63 <option value="mm39+RefSeq">mm39+RefSeq</option>
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64 <option value="mm39viral+GENCODEM26">mm39viral+GENCODEM26</option>
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65 <option value="mm39viral+RefSeq">mm39viral+RefSeq</option>
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66 <option value="mm10+GENCODEM25">mm10+GENCODEM25</option>
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67 <option value="mm10+RefSeq">mm10+RefSeq</option>
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68 <option value="mm10viral+GENCODEM25">mm10viral+GENCODEM25</option>
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69 <option value="mm10viral+RefSeq">mm10viral+RefSeq</option>
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70 </param>
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71 </inputs>
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72 <outputs>
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73 <data name="genome_fasta" format="fasta" label="${tool.name} ${arriba_reference_name} fasta"/>
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74 <data name="genome_gtf" format="gtf" label="${tool.name} ${arriba_reference_name} GTF"/>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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75 <data name="star_index" format="txt" label="${tool.name} ${arriba_reference_name} STAR index"/>
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76 </outputs>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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77 <tests>
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78 <!-- Downloading a genome and annotation plus build a STAR index requires too many resources for testing.
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79 Just test that we can locate the script. -->
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80 <test>
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81 <param name="is_test" value="yes"/>
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82 <param name="arriba_reference_name" value="GRCh38+ENSEMBL93"/>
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83 <output name="star_index">
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84 <assert_contents>
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85 <has_text text="GRCh38+ENSEMBL93"/>
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86 </assert_contents>
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87 </output>
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88 </test>
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89 </tests>
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90 <help><![CDATA[
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91 ** Arriba Reference **
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92
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93 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
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94 It is based on chimeric alignments found by the STAR RNA-Seq aligner.
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95
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96 **Arriba Reference** downloads a genome sequence fasta and its related annotation GTF, and then build a STAR index for the RNA STAR aligner.
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97
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98 These datasets will be added to your Galaxy history:
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99
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100 - genome assembly fasta
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101 - genome annotation GTF
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102 - STAR index
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103
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104 See Arriba manual pages:
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105
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106 - https://arriba.readthedocs.io/en/latest/workflow/
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107 - https://arriba.readthedocs.io/en/latest/input-files/
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108
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109
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110 **NOTE:** This is a resource intensive process, so the results should be copied to new histories as needed rather than running this in each workflow.
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111
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112 .. _Arriba: https://arriba.readthedocs.io/en/latest/
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113
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114 ]]></help>
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115 <expand macro="citations" />
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116 </tool>