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comparison customProDB.xml @ 4:bc08158abf77 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 2174137cf8a15deefed5910ffa152c4ce9c81af6
author galaxyp
date Thu, 08 Jun 2017 11:06:13 -0400
parents 344f606eeb9a
children 2c7df0077d28
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3:344f606eeb9a 4:bc08158abf77
1 <tool id="custom_pro_db" name="CustomProDB" version="1.16.0.1"> 1 <tool id="custom_pro_db" name="CustomProDB" version="1.16.1.0">
2 <description>Generate protein FASTAs from exosome or transcriptome data</description> 2 <description>Generate protein FASTAs from exosome or transcriptome data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.3.1">r-base</requirement> 4 <requirement type="package" version="3.3.1">r-base</requirement>
5 <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>--> 5 <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>-->
6 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement> 6 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
7 <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement> 7 <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>
8 <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement> 8 <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement>
9 <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement>
9 <requirement type="package" version="1.11.1">r-devtools</requirement> 10 <requirement type="package" version="1.11.1">r-devtools</requirement>
10 <requirement type="package" version="3.98_1.4">r-xml</requirement> 11 <requirement type="package" version="3.98_1.4">r-xml</requirement>
11 <requirement type="package" version="0.10.11">r-rmysql</requirement> 12 <requirement type="package" version="0.10.11">r-rmysql</requirement>
12 <requirement type="package" version="1.0.2">r-testthat</requirement> 13 <requirement type="package" version="1.0.2">r-testthat</requirement>
13 <requirement type="package" version="0.1.0">r-getoptlong</requirement> 14 <requirement type="package" version="0.1.0">r-getoptlong</requirement>
83 </param>--> 84 </param>-->
84 <param name="vcfInput" type="data" format="vcf" label="VCF file"> 85 <param name="vcfInput" type="data" format="vcf" label="VCF file">
85 <validator type="unspecified_build" /> 86 <validator type="unspecified_build" />
86 <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" /> 87 <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" />
87 </param> 88 </param>
88 <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" /> 89 <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP" help="The genome annotation must have been prepared with dbSNP." />
89 <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" /> 90 <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" help="The genome annotation must have been prepared with COSMIC." />
90 </when> 91 </when>
91 <when value="history"> 92 <when value="history">
92 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" /> 93 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
93 <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" /> 94 <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
94 <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" /> 95 <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
179 </test> 180 </test>
180 </tests> 181 </tests>
181 <help> 182 <help>
182 **Description** 183 **Description**
183 184
184 Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help> 185 Generate custom protein FASTAs from exosome or transcriptome data.
186
187 The reference protein set can be filtered by transcript expression level (RPKM calculated from a BAM file),
188 and variant protein forms can be predicted based on variant calls (SNPs and INDELs reported in a VCF file).
189
190
191 **Annotations**
192 CustomProDB depends on a set of annotation files (in RData format) to create reference and variant protein sequences.
193 Galaxy administrators can use the customProDB data manager to create these annotations to make them available for users.
194 </help>
185 <citations> 195 <citations>
186 <citation type="doi">10.1093/bioinformatics/btt543</citation> 196 <citation type="doi">10.1093/bioinformatics/btt543</citation>
187 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, 197 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
188 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = 198 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit =
189 {$sha1$}" --> 199 {$sha1$}" -->