| Previous changeset 4:d9564913a944 (2013-03-05) Next changeset 6:f36b84d1ac09 (2014-06-13) |
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Commit message:
Update |
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modified:
README mascot.xml mascot_to_pepxml.xml repository_dependencies.xml tool-data/mascot_databases.loc.sample tool-data/pepxml_databases.loc.sample tool_dependencies.xml |
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| diff -r d9564913a944 -r 327b2d99d4c5 README --- a/README Tue Mar 05 00:18:41 2013 -0500 +++ b/README Sun Jun 09 08:17:38 2013 -0500 |
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| @@ -1,8 +1,10 @@ -This package installs wrapper scripts for running Mascot MS/MS searches +This includes tools for running Mascot MS/MS searches Running this tool requires a working installation of Mascot (commercial software). Mascot is available from http://www.matrixscience.com/ Requirements: This package depends on the galaxy_protk and protk_trans_proteomic_pipeline packages -Please see instructions for those packages before installing +Please see instructions for those packages before installing. In particular +you will need to install system package requirements for galaxy_protk and protk_trans_proteomic_pipeline +using your package manager |
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| diff -r d9564913a944 -r 327b2d99d4c5 mascot.xml --- a/mascot.xml Tue Mar 05 00:18:41 2013 -0500 +++ b/mascot.xml Sun Jun 09 08:17:38 2013 -0500 |
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| @@ -2,13 +2,28 @@ <requirements> - <requirement type="package" version="1.2.0">galaxy_protk</requirement> + <requirement type="package" version="1.2.2">galaxy_protk</requirement> </requirements> <description>Mascot MS/MS Search</description> - <command>rvm 1.9.3@protk-1.2.0 do mascot_search.rb -d $database -f $fragment_ion_tol -S $server $input_file -o $output -r + <command>rvm 1.9.3@protk-1.2.2 do mascot_search.rb + + #if $database.source_select=="built_in": + -d $database.dbkey + #else + -d $database.custom_db + #end if + + -f $fragment_ion_tol + + -S $server $input_file + + -o $output + + -r + ## Variable Mods --var-mods=' @@ -18,34 +33,61 @@ --fix-mods=' $fixed_mods ' - --allowed-charges=$allowed_charges --enzyme=$enzyme --instrument=$instrument --precursor-ion-tol-units=$precursor_tolu --email=$email --username=$username -v $missed_cleavages - + --allowed-charges=$allowed_charges + + --enzyme=$enzyme + + --instrument=$instrument + + --precursor-ion-tol-units=$precursor_tolu + + --email=$email + + -v $missed_cleavages + + #if $security.security_use + --use-security + --username $security.username + --password $security.password + #end if + + #if $proxy + --proxy $proxy + #end if + </command> <inputs> <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/> - <param name="database" type="select" format="text" > - <label>Database</label> - <options from_file="mascot_databases.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> + <conditional name="database"> + <param name="source_select" type="select" label="Database Type"> + <option value="built_in">Built-In</option> + <option value="custom_defined">Custom</option> + </param> + <when value="built_in"> + <param name="dbkey" type="select" format="text" > + <label>Database</label> + <options from_file="mascot_databases.loc"> + <column name="name" index="0" /> + <column name="value" index="2" /> + </options> + </param> + </when> + <when value="custom_defined"> + <param name="custom_db" type="text" size="80" value="SwissProt" label="Database Name" help="Exact name of a database defined on the Mascot server (case-sensitive)"/> + </when> + </conditional> - - - <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while - clicking to select multiple items"> + <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed"> <options from_file="mascot_mods.loc"> <column name="name" index="0" /> <column name="value" index="2" /> </options> </param> - <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while - clicking to select multiple items"> + <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed"> <options from_file="mascot_mods.loc"> <column name="name" index="0" /> <column name="value" index="2" /> @@ -108,24 +150,33 @@ <option value="CID+ETD">CID+ETD</option> </param> - <param name="fragment_ion_tol" label="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/> + <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/> - <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Precursor ion tolerance"/> + <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/> <param name="precursor_tolu" type="select" format="text"> <label>Precursor Ion Tolerance Units</label> <option value="ppm">ppm</option> <option value="Da">Da</option> </param> - <param name="server" type="text" label="URL to Mascot Server cgi " size="60" value="http://www.exampleserver.com/mascot/cgi/"/> + <param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/> + <param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/> + + <conditional name="security"> + <param name="security_use" type="boolean" label="Use Mascot Security?" help="Select this if you need to enter a username and password" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/> + <param name="password" type="text" label="Password" size="60" value="" help="Mascot Password. Password is encrypted when over the internet but is stored in clear-text on the Galaxy server"/> + </when> + </conditional> + <param name="email" type="text" label="Email " size="60" value="" help=""/> - <param name="email" type="text" label="Email " size="60" value="" help="Not Supported Yet."/> - <param name="username" type="text" label="Username" size="60" value="" help="Not Supported Yet."/> </inputs> <outputs> - <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database}.${input_file.display_name}.mascotdat"/> + <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database.dbkey if $database.has_key('dbkey') else $database.custom_db}.${input_file.display_name}.mascotdat"/> </outputs> <help> |
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| diff -r d9564913a944 -r 327b2d99d4c5 mascot_to_pepxml.xml --- a/mascot_to_pepxml.xml Tue Mar 05 00:18:41 2013 -0500 +++ b/mascot_to_pepxml.xml Sun Jun 09 08:17:38 2013 -0500 |
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| @@ -1,29 +1,80 @@ <tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.1"> <requirements> - <requirement type="package" version="1.2.0">galaxy_protk</requirement> + <requirement type="package" version="1.2.2">galaxy_protk</requirement> <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> </requirements> <description>Converts a mascot results file to pepXML</description> -<command>rvm 1.9.3@protk-1.2.0 do mascot_to_pepxml.rb $input_file -o $output -d $database</command> +<command>rvm 1.9.3@protk-1.2.2 do mascot_to_pepxml.rb + $input_file + + -o $output + + #if $database.source_select=="built_in": + -d $database.dbkey + #else + -d $database.fasta_file + #end if + + #if $explicit_enzyme.explicit_enzyme_use + --enzyme $explicit_enzyme.enzyme + #end if + + $shortid + +</command> <inputs> + <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/> - <param name="database" type="select" format="text" > - <label>Database</label> - <options from_file="pepxml_databases.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - + + <conditional name="database"> + <param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search"> + <option value="built_in">Built-In</option> + <option value="input_ref">Uploaded fasta file</option> + </param> + <when value="built_in"> + <param name="dbkey" type="select" format="text" > + <label>Database</label> + <options from_file="pepxml_databases.loc"> + <column name="name" index="0" /> + <column name="value" index="2" /> + </options> + </param> + </when> + <when value="input_ref"> + <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> + </when> + </conditional> + + <param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" /> + + <conditional name="explicit_enzyme"> + <param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/> + </when> + </conditional> + + </inputs> <outputs> <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" /> </outputs> + <tests> + <test> + <param name="source_select" value="input_ref"/> + <param name="fasta_file" value="bsa.fasta"/> + <param name="input_file" value="F002832.dat"/> + <output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" /> + </test> + + </tests> + <help> Convert mascot results from mascotdat to pepXML </help> |
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| diff -r d9564913a944 -r 327b2d99d4c5 repository_dependencies.xml --- a/repository_dependencies.xml Tue Mar 05 00:18:41 2013 -0500 +++ b/repository_dependencies.xml Sun Jun 09 08:17:38 2013 -0500 |
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| @@ -1,10 +1,6 @@ <?xml version="1.0"?> -<repositories description="Proteomics datatypes and mascot2xml from the TPP"> - - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="463328a6967f"/> +<repositories description="Requires the Proteomics Datatypes package"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349"/> - - </repositories> +</repositories> |
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| diff -r d9564913a944 -r 327b2d99d4c5 tool-data/mascot_databases.loc.sample --- a/tool-data/mascot_databases.loc.sample Tue Mar 05 00:18:41 2013 -0500 +++ b/tool-data/mascot_databases.loc.sample Sun Jun 09 08:17:38 2013 -0500 |
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| @@ -9,5 +9,5 @@ # Entries should follow the be structured as follows # Display_name dbkey dbNameOnMascot dbkey # -Swissprot spall_ SPAll spall_ +Swissprot spall_ SwissProt spall_ Swissprot Human sphuman_ SPHuman sphuman_ \ No newline at end of file |
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| diff -r d9564913a944 -r 327b2d99d4c5 tool-data/pepxml_databases.loc.sample --- a/tool-data/pepxml_databases.loc.sample Tue Mar 05 00:18:41 2013 -0500 +++ b/tool-data/pepxml_databases.loc.sample Sun Jun 09 08:17:38 2013 -0500 |
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| @@ -6,7 +6,7 @@ # Display_name omssa_tandem_dbname dbkey # # -Swissprot spall_ spall spall_ +Swissprot spall_ SwissProt spall_ Combined PlasmboDB (falciparum) and Swissprot Human plasmodb_pfalciparum_sphuman_ plasmodb_pfalciparum_sphuman plasmodb_pfalciparum_sphuman_ Swissprot Human sphuman_ sphuman sphuman_ Combined Swissprot/TRembl Human sptrhuman_ sptrhuman sptrhuman_ |
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| diff -r d9564913a944 -r 327b2d99d4c5 tool_dependencies.xml --- a/tool_dependencies.xml Tue Mar 05 00:18:41 2013 -0500 +++ b/tool_dependencies.xml Sun Jun 09 08:17:38 2013 -0500 |
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| @@ -1,12 +1,12 @@ <?xml version="1.0"?> <tool_dependency> - <package name="galaxy_protk" version="1.2.0"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/> + <package name="galaxy_protk" version="1.2.2"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/> </package> <package name="trans_proteomic_pipeline" version="4.6.1"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/> </package> -</tool_dependency> \ No newline at end of file +</tool_dependency> |