| Previous changeset 9:54c7e3593aac (2015-03-29) |
|
Commit message:
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty |
|
modified:
mascot.xml mascot_to_pepxml.xml |
|
added:
tool_dependencies.xml |
|
removed:
repository_dependencies.xml |
| b |
| diff -r 54c7e3593aac -r b3427b77073e mascot.xml --- a/mascot.xml Sun Mar 29 18:17:54 2015 -0400 +++ b/mascot.xml Tue Oct 20 19:50:46 2015 -0400 |
| [ |
| b'@@ -1,249 +1,230 @@\n-<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.0">\n+<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.1">\n+ <description>Mascot MS/MS Search</description>\n+ <requirements>\n+ <container type="docker">iracooke/protk-1.4.3</container>\n+ <requirement type="package" version="1.4.3">protk</requirement>\n+ </requirements>\n+ <command>mascot_search.rb \n+\n+ #if $database.source_select=="built_in":\n+ -d $database.dbkey\n+ #else \n+ -d $database.custom_db\n+ #end if\n+\n+ -f $fragment_ion_tol \n+ -S $server $input_file \n+ -o $output\n+ -r\n+ ## Variable Mods\n+\n+ --var-mods=\'\n+ $variable_mods\n+ \'\n+ --fix-mods=\'\n+ $fixed_mods\n+ \'\n+\n+ --allowed-charges=\'$allowed_charges\'\n+ --enzyme=$enzyme \n+ --instrument=\'$instrument\'\n+ -p $precursor_ion_tol\n+ --precursor-ion-tol-units=$precursor_tolu \n+\n+ #if $email\n+ --email=$email \n+ #end if\n+\n+ -v $missed_cleavages\n+\n+ #if str ( $quant_method ) != \'No Quant\'\n+ --quantitation=\'$quant_method\'\n+ #end if\n+\n+ #if $security.security_use\n+ --use-security\n+ --username $security.username\n+ --password $security.password\n+ #end if\n+\n+ #if $proxy\n+ --proxy $proxy\n+ #end if\n+\n+ --timeout=600\n+\n+ </command>\n+ <inputs>\n+ <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>\n+\n+ <conditional name="database">\n+ <param name="source_select" type="select" label="Database Type">\n+ <option value="built_in">Built-In</option>\n+ <option selected="true" value="custom_defined">Custom</option>\n+ </param>\n+ <when value="built_in">\n+ <param name="dbkey" type="select" format="text" >\n+ <label>Database</label>\n+ <options from_file="mascot_databases.loc">\n+ <column name="name" index="0" />\n+ <column name="value" index="2" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="custom_defined">\n+ <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)"/>\n+ </when>\n+ </conditional>\n \n-\t<requirements>\n- <container type="docker">iracooke/protk-1.4.1</container>\n-\t <requirement type="package" version="1.4">protk</requirement>\n- </requirements>\n+ <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">\n+ <options from_file="mascot_mods.loc">\n+ <column name="name" index="0" />\n+ <column name="value" index="2" />\n+ </options>\n+ </param>\n+\n+ <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">\n+ <options from_file="mascot_mods.loc">\n+ <column name="name" index="0" />\n+ <column name="value" index="2" />\n+ </options>\n+ </param>\n+\n+ <param name="missed_cleavages" type="select" format="text">\n+ <label>Missed Cleavages Allowed</label>\n+ <option value="0">0</option>\n+ <option value="1">1</option>\n+ <option selected="true" value="2">2</option>\n+ </param>\n \n-\t<description>Mascot MS/MS Search</description>\n+ <param name="enzyme" type="select" format="text">\n+ <label>Enzyme</label>\n+ <option selected="true" value="Trypsin">Trypsin</opt'..b']">ICPL quadruplex pre-digest [MD]</option>\n-\t\t<option value="18O corrected [MD]">18O corrected [MD]</option>\n-\t\t<option value="15N Metabolic [MD]">15N Metabolic [MD]</option>\n-\t\t<option value="15N + 13C Metabolic [MD]">15N + 13C Metabolic [MD]</option>\n-\t\t<option value="SILAC K+6 R+10 [MD]">SILAC K+6 R+10 [MD]</option>\n-\t\t<option value="SILAC K+6 R+10 Arg-Pro [MD]">SILAC K+6 R+10 Arg-Pro [MD]</option>\n-\t\t<option value="SILAC K+6 R+6 [MD]">SILAC K+6 R+6 [MD]</option>\n-\t\t<option value="SILAC R+6 R+10 [MD]">SILAC R+6 R+10 [MD]</option>\n-\t\t<option value="SILAC K+8 R+10 [MD]">SILAC K+8 R+10 [MD]</option>\t\t\n-\t\t<option value="SILAC K+4 K+8 R+6 R+10 [MD]">SILAC K+4 K+8 R+6 R+10 [MD]</option>\n-\t\t<option value="ICAT ABI Cleavable [MD]">ICAT ABI Cleavable [MD]</option>\n-\t\t<option value="ICAT D8 [MD]">ICAT D8 [MD]</option>\n-\t\t<option value="Dimethylation [MD]">Dimethylation [MD]</option>\n-\t\t<option value="NBS Shimadzu [MD]">NBS Shimadzu [MD]</option>\n-\t\t<option value="Acetylation [MD]">Acetylation [MD]</option>\n-\t\t<option value="Label-free [MD]">Label-free [MD]</option>\n-\t</param>\t\n-\t\n-\t<param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.5" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>\n-\n-\t<param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>\n-\t<param name="precursor_tolu" type="select" format="text">\n-\t <label>Precursor Ion Tolerance Units</label>\n-\t <option value="ppm">ppm</option>\t\t\n-\t\t<option value="Da">Da</option>\n-\t</param>\n-\n-\t<param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>\n-\t<param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/>\n-\n-\t<conditional name="security">\n-\t\t<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" />\n-\t\t<when value="false" />\n-\t\t<when value="true">\n-\t\t\t<param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>\n-\t\t\t<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"/>\n-\t\t</when>\n-\t</conditional>\n-\t<param name="email" type="text" label="Email " size="60" value="" help=""/>\n-\t\n-\t\n-\n- </inputs>\n- <outputs>\n- <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"/>\n- </outputs>\n-\n- <help>\n-\tRun a Mascot MS/MS Ion Search\n- </help>\n-\n+ <conditional name="security">\n+ <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" />\n+ <when value="false" />\n+ <when value="true">\n+ <param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>\n+ <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"/>\n+ </when>\n+ </conditional>\n+ <param name="email" type="text" label="Email " size="60" value="" help=""/>\n+ </inputs>\n+ <outputs>\n+ <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"/>\n+ </outputs>\n+ <help>\n+ Run a Mascot MS/MS Ion Search\n+ </help>\n </tool>\n' |
| b |
| diff -r 54c7e3593aac -r b3427b77073e mascot_to_pepxml.xml --- a/mascot_to_pepxml.xml Sun Mar 29 18:17:54 2015 -0400 +++ b/mascot_to_pepxml.xml Tue Oct 20 19:50:46 2015 -0400 |
| b |
| @@ -1,83 +1,72 @@ -<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.0"> - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> - </requirements> +<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.1"> + <description>Converts a mascot results file to pepXML</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> + </requirements> + <command>mascot_to_pepxml.rb + $input_file - <description>Converts a mascot results file to pepXML</description> - -<command>mascot_to_pepxml.rb - $input_file - - -o $output + -o $output - #if $database.source_select=="built_in": - -d $database.dbkey - #else - -d $database.fasta_file - #end if + #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 + #if $explicit_enzyme.explicit_enzyme_use + --enzyme $explicit_enzyme.enzyme + #end if -</command> -<inputs> - - - <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/> + $shortid + </command> + <inputs> + <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/> - <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> + <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="" /> + <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> + <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> - <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> - + </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> </tool> |
| b |
| diff -r 54c7e3593aac -r b3427b77073e repository_dependencies.xml --- a/repository_dependencies.xml Sun Mar 29 18:17:54 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Proteomics datatypes"> - <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> - </repositories> |
| b |
| diff -r 54c7e3593aac -r b3427b77073e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 19:50:46 2015 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="protk" version="1.4.3"> + <repository changeset_revision="74bf855be117" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="trans_proteomic_pipeline" version="4.8.0"> + <repository changeset_revision="a7273394d858" name="package_tpp_4_8_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |