Mercurial > repos > galaxyp > custom_pro_db
diff customProDB.xml @ 4:bc08158abf77 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 11:06:13 -0400 |
parents | 344f606eeb9a |
children | 2c7df0077d28 |
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--- a/customProDB.xml Thu May 18 12:31:04 2017 -0400 +++ b/customProDB.xml Thu Jun 08 11:06:13 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="custom_pro_db" name="CustomProDB" version="1.16.0.1"> +<tool id="custom_pro_db" name="CustomProDB" version="1.16.1.0"> <description>Generate protein FASTAs from exosome or transcriptome data</description> <requirements> <requirement type="package" version="3.3.1">r-base</requirement> @@ -6,6 +6,7 @@ <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement> <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement> <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement> + <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement> <requirement type="package" version="1.11.1">r-devtools</requirement> <requirement type="package" version="3.98_1.4">r-xml</requirement> <requirement type="package" version="0.10.11">r-rmysql</requirement> @@ -85,8 +86,8 @@ <validator type="unspecified_build" /> <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" /> </param> - <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" /> - <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" /> + <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP" help="The genome annotation must have been prepared with dbSNP." /> + <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" help="The genome annotation must have been prepared with COSMIC." /> </when> <when value="history"> <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" /> @@ -181,7 +182,16 @@ <help> **Description** -Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help> +Generate custom protein FASTAs from exosome or transcriptome data. + +The reference protein set can be filtered by transcript expression level (RPKM calculated from a BAM file), +and variant protein forms can be predicted based on variant calls (SNPs and INDELs reported in a VCF file). + + +**Annotations** +CustomProDB depends on a set of annotation files (in RData format) to create reference and variant protein sequences. +Galaxy administrators can use the customProDB data manager to create these annotations to make them available for users. +</help> <citations> <citation type="doi">10.1093/bioinformatics/btt543</citation> <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},