Mercurial > repos > galaxyp > dbbuilder
changeset 5:1d3557cec567 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
| author | galaxyp |
|---|---|
| date | Sat, 29 Apr 2017 09:46:31 -0400 |
| parents | b39347891609 |
| children | 19ee2e85931a |
| files | README.md dbbuilder.xml tool-data/uniprot_taxons.loc.sample tools/dbbuilder.xml |
| diffstat | 4 files changed, 119 insertions(+), 99 deletions(-) [+] |
line wrap: on
line diff
--- a/README.md Fri Sep 26 14:31:06 2014 -0400 +++ b/README.md Sat Apr 29 09:46:31 2017 -0400 @@ -1,7 +1,7 @@ GalaxyP - Protein Database Downloader ===================================== -* Home: <https://bitbucket.org/galaxyp/dbbuilder> +* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> * Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/dbbuilder> * Tool ID: `dbbuilder` @@ -15,9 +15,9 @@ GalaxyP Community ----------------- -Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at: +Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at: -<https://bitbucket.org/galaxyp/galaxyp> +<https://github.com/galaxyproteomics> License @@ -35,7 +35,7 @@ Contributing ------------ -Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out. +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> Authors
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dbbuilder.xml Sat Apr 29 09:46:31 2017 -0400 @@ -0,0 +1,109 @@ +<tool id="dbbuilder" name="Protein Database Downloader" version="0.2.1"> + <description></description> + <requirements> + <requirement type="package">gnu-wget</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error downloading database." /> + <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." /> + </stdio> + <!-- TODO: escape quotes. --> + <!-- Add NCBI and maxquant contaminants. --> + <!-- http://maxquant.org/contaminants.zip --> + <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz--> + <command> +<![CDATA[ + #if $source.from == "uniprot" + #set $url = "http://www.uniprot.org/uniprot/?query=taxonomy%3a%22" + str($source.taxon) + "%22" + str($source.set) + str($source.reviewed) + "&force=yes&format=fasta" + str($source.include_isoform) + #set $type = "direct" + #elif $source.from == "cRAP" + ##set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" + #set $url = "https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta" + #set $type = "direct" + #elif $source.from == "url" + #set $url = $source.url + #set $type = "direct" + #end if + #if $type =="direct" + wget -nv '$url' -O '${output_database}' + #end if +]]> + </command> + <inputs> + <conditional name="source"> + <param name="from" type="select" label="Download from" help="Select database source. cRAP acts as a database for common MS contaminants. UniProtKB is a corss species collection of functional protein databases"> + <option value="uniprot">UniProtKB</option> + <option value="cRAP">cRAP (contaminants)</option> + <option value="url">Custom URL</option> + </param> + <when value="uniprot"> + <param name="taxon" type="select" format="text" help="select species for protein database"> + <label>Taxonomy</label> + <options from_file="uniprot_taxons.loc"> + <column name="name" index="0" /> + <column name="value" index="1" /> + </options> + </param> + <param name="reviewed" type="select" help="UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database- may contain redundant sequences, but there is a higher chance peptides will be identified. UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database- less of a chance peptides will be identified but less sequence redundancy"> + <option value="+">UniProtKB</option> + <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option> + <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option> + <sanitizer> + <valid> + <add value="%"/> + </valid> + </sanitizer> + </param> + <param name="set" type="select" label="Proteome Set"> + <option value="+">Any</option> + <option value="+keyword%3a1185" selected="true">Reference Proteome Set</option> + <option value="+keyword%3a181">Complete Proteome Set</option> + <sanitizer> + <valid> + <add value="%"/> + </valid> + </sanitizer> + </param> + <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" help="several different forms of a given protein are incorporated into database" /> + </when> + <when value="cRAP" /> + <when value="url"> + <param name="url" value="" type="text" label="URL (http, ftp)"> + <sanitizer> + <valid> + <add value="%"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data format="fasta" name="output_database" label="Protein Database" /> + </outputs> + <tests> + <test> + <param name="from" value="cRAP" /> + <output name="output_database"> + <assert_contents> + <has_text text="KKA1_ECOLX" /> + </assert_contents> + </output> + </test> + </tests> + <help> +<![CDATA[ +**Output** + +Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm. + +**External Links** + +_Galaxy-P 101 shows usage Protein Database Downloader tool in the creation of a workflow +.. _Galaxy-P 101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html +_UniProtKB provides additional information about the UniProt Knowledgebase +.. _UniProtKB: http://www.uniprot.org/help/uniprotkb +]]> + </help> +</tool> +
--- a/tool-data/uniprot_taxons.loc.sample Fri Sep 26 14:31:06 2014 -0400 +++ b/tool-data/uniprot_taxons.loc.sample Sat Apr 29 09:46:31 2017 -0400 @@ -12,3 +12,9 @@ Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 64091 Apis mellifera (Honeybee) 7460 Mycobacterium tuberculosis H37Rv (MTB) [Not complete proteome] 83332 +Mycoplasma orale [Not complete proteome] 2121 +Mycoplasma hyorhinis 2100 +Mycoplasma arginini 2094 +Mycoplasma fermentans 2115 +Mycoplasma hominis 2098 +Acholeplasma laidlawii 2148
--- a/tools/dbbuilder.xml Fri Sep 26 14:31:06 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,95 +0,0 @@ -<tool id="dbbuilder" version="0.2.0" name="Protein Database Downloader"> - <description> - </description> - <requirements> - <requirement type="binary">wget</requirement> - </requirements> - <stdio> - <exit_code range="1:" level="fatal" description="Error downloading database." /> - <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." /> - </stdio> - <!-- TODO: escape quotes. --> - <!-- Add NCBI and maxquant contaminants. --> - <!-- http://maxquant.org/contaminants.zip --> - <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz--> - <command> - #if $source.from == "uniprot" - #set $url = "http://www.uniprot.org/uniprot/?query=taxonomy%3a%22" + str($source.taxon) + "%22" + str($source.set) + str($source.reviewed) + "&force=yes&format=fasta" + str($source.include_isoform) - #set $type = "direct" - #elif $source.from == "cRAP" - #set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" - #set $type = "direct" - #elif $source.from == "url" - #set $url = $source.url - #set $type = "direct" - #end if - #if $type =="direct" - wget -nv '$url' -O '${output_database}' - #end if - </command> - <inputs> - <conditional name="source"> - <param name="from" type="select" label="Download from" help="select database source. cRAP acts as a database for common MS contaminants. UniProtKB is a corss species collection of functional protein databases"> - <option value="uniprot">UniProtKB</option> - <option value="cRAP">cRAP (contaminants)</option> - <option value="url">Custom URL</option> - </param> - <when value="uniprot"> - <param name="taxon" type="select" format="text" help="select species for protein database"> - <label>Taxonomy</label> - <options from_file="uniprot_taxons.loc"> - <column name="name" index="0" /> - <column name="value" index="1" /> - </options> - </param> - <param name="reviewed" type="select" help="UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database- may contain redundant sequences, but there is a higher chance peptides will be identified. UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database- less of a chance peptides will be identified but less sequence redundancy"> - <option value="+">UniProtKB</option> - <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option> - <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option> - <sanitizer> - <valid> - <add value="%"/> - </valid> - </sanitizer> - </param> - <param name="set" type="select" label="Proteome Set"> - <option value="+">Any</option> - <option value="+keyword%3a1185" selected="true">Reference Proteome Set</option> - <option value="+keyword%3a181">Complete Proteome Set</option> - <sanitizer> - <valid> - <add value="%"/> - </valid> - </sanitizer> - </param> - <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" help="several different forms of a given protein are incorporated into database" /> - </when> - <when value="cRAP" /> - <when value="url"> - <param name="url" value="" type="text" label="URL (http, ftp)"> - <sanitizer> - <valid> - <add value="%"/> - </valid> - </sanitizer> - </param> - </when> - </conditional> - </inputs> - <outputs> - <data format="fasta" name="output_database" label="Protein Database" /> - </outputs> - <help> -**Output** - -Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm. - -**External Links** - -_Galaxy-P 101 shows usage Protein Database Downloader tool in the creation of a workflow -.. _Galaxy-P 101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html -_UniProtKB provides additional information about the UniProt Knowledgebase -.. _UniProtKB: http://www.uniprot.org/help/uniprotkb - </help> -</tool> -