Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

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author galaxyp
date Wed, 01 Nov 2017 19:33:35 -0400
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1 <tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="1.16.1.0">
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2 <description>builder</description>
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3 <requirements>
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4 <requirement type="package" version="3.3.1">r-base</requirement>
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5 <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>-->
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6 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
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7 <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>
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8 <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement>
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9 <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement>
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10 <requirement type="package" version="1.11.1">r-devtools</requirement>
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11 <requirement type="package" version="3.98_1.4">r-xml</requirement>
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12 <requirement type="package" version="0.10.11">r-rmysql</requirement>
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13 <requirement type="package" version="1.0.2">r-testthat</requirement>
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14 <requirement type="package" version="0.1.0">r-getoptlong</requirement>
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15 <requirement type="package" version="1.1.2">r-stringi</requirement>
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16 <requirement type="package" version="1.1.0">r-stringr</requirement>
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17 <requirement type="package" version="1.10.0">r-data.table</requirement>
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18 <requirement type="package" version="0.4_10">r-sqldf</requirement>
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19 <requirement type="package" version="0.6_6">r-gsubfn</requirement>
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20 <requirement type="package" version="2.3_47">r-chron</requirement>
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21 <requirement type="package" version="0.3_10">r-proto</requirement>
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22 <requirement type="package" version="1.8.4">r-plyr</requirement>
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23 </requirements>
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24 <stdio>
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25 <exit_code range=":-1" />
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26 <exit_code range="1:" />
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27 </stdio>
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28 <command><![CDATA[
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29 Rscript --vanilla '$__tool_directory__/customProDB_annotation.R'
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30 --outputFile '${out_file}'
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31
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32 #if str($transcriptome_annotation.source) == 'refseq':
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33 --dbkey '${transcriptome_annotation.dbkey}'
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34 --dbkey_description '${ transcriptome_annotation.dbkey.get_display_text().strip("\"'") }'
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35 #else:
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36 --ensembl_dataset '${transcriptome_annotation.ensembl_dataset.fields.dataset}'
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37 --ensembl_host '${transcriptome_annotation.ensembl_dataset.fields.host}'
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38 --dbkey_description '${transcriptome_annotation.ensembl_dataset.fields.name}'
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39 #end if
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40
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41 --dbsnp '${dbsnp}'
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42 $cosmic
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43 2>&1
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44 ]]>
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45 </command>
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46 <inputs>
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47 <conditional name="transcriptome_annotation">
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48 <param name="source" type="select" label="What source do you want to use for mapping between genes, transcripts, and proteins?" help="RefSeq transcripts are like NM_xxxx, Ensembl transcripts are like ENSTxxxx">
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49 <option value="refseq">Annotate transcriptome with RefSeq (from NCBI/UCSC)</option>
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50 <option value="ensembl">Annotate transcriptome with Ensembl (from Biomart)</option>
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51 </param>
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52 <when value="refseq">
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53 <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" help="e.g. hg38, hg19, mm10, canFam31" />
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54 </when>
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55 <when value="ensembl">
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56 <param type="select" name="ensembl_dataset" value="" label="Ensembl reference genome identifier">
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57 <options from_file="ensembl_datasets.loc">
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58 <column name="value" index="2" />
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59 <column name="dataset" index="0" />
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60 <column name="host" index="1" />
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61 <validator type="no_options" message="Ensembl dataset list not loaded"/>
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62 </options>
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63 </param>
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64 </when>
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65 </conditional>
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66 <param type="text" name="dbsnp" value="" label="dbSNP identifier (select organisms only, e.g. human, mouse, cow)" help="e.g. snp142" />
10
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67 <param type="boolean" name="cosmic" truevalue="--cosmic true" falsevalue="" label="Annotate somatic SNPs from COSMIC (human only)" />
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68 </inputs>
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69 <outputs>
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70 <data name="out_file" format="data_manager_json"/>
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71 </outputs>
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72 <help>
9
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73
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74 .. class:: infomark
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75
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76 This data manager creates the transcriptome annotation in the RData format needed by customProDB.
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77 Two annotation sources are supported: UCSC and Ensembl.
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78 Note that because UCSC's table browser only provides current gene annotations for a given genome assembly,
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79 only the Ensembl annotation is entirely reproducible, i.e. running again with the same settings next month will create the same annotation.
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80
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81 Ensembl chromosome names (1,2, ...) are converted to UCSC format (chr1,chr2, ...) to ease integration with other Galaxy tools.
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82 </help>
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83 <citations>
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84 <citation type="doi">10.1093/bioinformatics/btt543</citation>
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85 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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86 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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87 </citations>
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88 </tool>