Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager
comparison data_manager/customProDB_annotation.xml @ 1:9b4ee836e35b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 2174137cf8a15deefed5910ffa152c4ce9c81af6
author | galaxyp |
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date | Thu, 08 Jun 2017 10:55:08 -0400 |
parents | 45755942ae7b |
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0:45755942ae7b | 1:9b4ee836e35b |
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1 <tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1"> | 1 <tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="1.16.1.0"> |
2 <description>builder</description> | 2 <description>builder</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement> | 4 <requirement type="package" version="3.3.1">r-base</requirement> |
5 <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>--> | |
6 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement> | |
7 <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement> | |
8 <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement> | |
9 <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement> | |
10 <requirement type="package" version="1.11.1">r-devtools</requirement> | |
11 <requirement type="package" version="3.98_1.4">r-xml</requirement> | |
12 <requirement type="package" version="0.10.11">r-rmysql</requirement> | |
13 <requirement type="package" version="1.0.2">r-testthat</requirement> | |
14 <requirement type="package" version="0.1.0">r-getoptlong</requirement> | |
15 <requirement type="package" version="1.1.2">r-stringi</requirement> | |
16 <requirement type="package" version="1.1.0">r-stringr</requirement> | |
17 <requirement type="package" version="1.10.0">r-data.table</requirement> | |
18 <requirement type="package" version="0.4_10">r-sqldf</requirement> | |
19 <requirement type="package" version="0.6_6">r-gsubfn</requirement> | |
20 <requirement type="package" version="2.3_47">r-chron</requirement> | |
21 <requirement type="package" version="0.3_10">r-proto</requirement> | |
22 <requirement type="package" version="1.8.4">r-plyr</requirement> | |
5 </requirements> | 23 </requirements> |
6 <stdio> | 24 <stdio> |
7 <exit_code range=":-1" /> | 25 <exit_code range=":-1" /> |
8 <exit_code range="1:" /> | 26 <exit_code range="1:" /> |
9 </stdio> | 27 </stdio> |
10 <command><![CDATA[ | 28 <command><![CDATA[ |
11 Rscript --vanilla '$__tool_directory__/customProDB_annotation.R' | 29 Rscript --vanilla '$__tool_directory__/customProDB_annotation.R' |
12 --outputFile '${out_file}' | 30 --outputFile '${out_file}' |
13 --dbkey '${dbkey}' | 31 |
14 --dbsnp '${dbsnp}' | 32 #if str($transcriptome_annotation.source) == 'refseq': |
15 $cosmic | 33 --dbkey '${transcriptome_annotation.dbkey}' |
16 --dbkey_description '${ dbkey.get_display_text() }' | 34 --dbkey_description '${ transcriptome_annotation.dbkey.get_display_text().strip("\"'") }' |
17 2>1 | 35 #else: |
36 --ensembl_dataset '${transcriptome_annotation.ensembl_dataset.fields.dataset}' | |
37 --ensembl_host '${transcriptome_annotation.ensembl_dataset.fields.host}' | |
38 --dbkey_description '${transcriptome_annotation.ensembl_dataset.fields.name}' | |
39 #end if | |
40 | |
41 --dbsnp '${dbsnp}' | |
42 $cosmic | |
43 2>&1 | |
18 ]]> | 44 ]]> |
19 </command> | 45 </command> |
20 <inputs> | 46 <inputs> |
21 <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" /> | 47 <conditional name="transcriptome_annotation"> |
22 <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" /> | 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"> |
49 <option value="refseq">Annotate transcriptome with RefSeq (from NCBI/UCSC)</option> | |
50 <option value="ensembl">Annotate transcriptome with Ensembl (from Biomart)</option> | |
51 </param> | |
52 <when value="refseq"> | |
53 <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" help="e.g. hg38, hg19, mm10, canFam31" /> | |
54 </when> | |
55 <when value="ensembl"> | |
56 <param type="select" name="ensembl_dataset" value="" label="Ensembl reference genome identifier"> | |
57 <options from_file="ensembl_datasets.loc"> | |
58 <column name="value" index="2" /> | |
59 <column name="dataset" index="0" /> | |
60 <column name="host" index="1" /> | |
61 <validator type="no_options" message="Ensembl dataset list not loaded"/> | |
62 </options> | |
63 </param> | |
64 </when> | |
65 </conditional> | |
66 <param type="text" name="dbsnp" value="" label="dbSNP identifier (select organisms only, e.g. human, mouse, cow)" help="e.g. snp142" /> | |
23 <param type="boolean" name="cosmic" truevalue="--cosmic true" falsevalue="" label="Annotate somatic SNPs from COSMIC (human only)" /> | 67 <param type="boolean" name="cosmic" truevalue="--cosmic true" falsevalue="" label="Annotate somatic SNPs from COSMIC (human only)" /> |
24 </inputs> | 68 </inputs> |
25 <outputs> | 69 <outputs> |
26 <data name="out_file" format="data_manager_json"/> | 70 <data name="out_file" format="data_manager_json"/> |
27 </outputs> | 71 </outputs> |
28 <help> | 72 <help> |
29 | 73 |
30 .. class:: infomark | 74 .. class:: infomark |
31 | 75 |
32 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | 76 This data manager creates the transcriptome annotation in the RData format needed by customProDB. |
77 Two annotation sources are supported: UCSC and Ensembl. | |
78 Note that because UCSC's table browser only provides current gene annotations for a given genome assembly, | |
79 only the Ensembl annotation is entirely reproducible, i.e. running again with the same settings next month will create the same annotation. | |
33 | 80 |
81 Ensembl chromosome names (1,2, ...) are converted to UCSC format (chr1,chr2, ...) to ease integration with other Galaxy tools. | |
34 </help> | 82 </help> |
35 <citations> | 83 <citations> |
36 <citation type="doi">10.1093/bioinformatics/btt543</citation> | 84 <citation type="doi">10.1093/bioinformatics/btt543</citation> |
37 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, | 85 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, |
38 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> | 86 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> |