Mercurial > repos > iracooke > mascot
diff mascot.xml @ 10:b3427b77073e draft default tip
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 19:50:46 -0400 |
| parents | 54c7e3593aac |
| children |
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--- a/mascot.xml Sun Mar 29 18:17:54 2015 -0400 +++ b/mascot.xml Tue Oct 20 19:50:46 2015 -0400 @@ -1,249 +1,230 @@ -<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.0"> +<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.1"> + <description>Mascot MS/MS Search</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + </requirements> + <command>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=' + $variable_mods + ' + --fix-mods=' + $fixed_mods + ' + + --allowed-charges='$allowed_charges' + --enzyme=$enzyme + --instrument='$instrument' + -p $precursor_ion_tol + --precursor-ion-tol-units=$precursor_tolu + + #if $email + --email=$email + #end if + + -v $missed_cleavages + + #if str ( $quant_method ) != 'No Quant' + --quantitation='$quant_method' + #end if + + #if $security.security_use + --use-security + --username $security.username + --password $security.password + #end if + + #if $proxy + --proxy $proxy + #end if + + --timeout=600 + + </command> + <inputs> + <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/> + + <conditional name="database"> + <param name="source_select" type="select" label="Database Type"> + <option value="built_in">Built-In</option> + <option selected="true" 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> - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - </requirements> + <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="Multiple values allowed"> + <options from_file="mascot_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="2" /> + </options> + </param> + + <param name="missed_cleavages" type="select" format="text"> + <label>Missed Cleavages Allowed</label> + <option value="0">0</option> + <option value="1">1</option> + <option selected="true" value="2">2</option> + </param> - <description>Mascot MS/MS Search</description> + <param name="enzyme" type="select" format="text"> + <label>Enzyme</label> + <option selected="true" value="Trypsin">Trypsin</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="Arg-C">Arg-C</option> + <option value="Asp-N">Asp-N</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="CNBr">CNBr</option> + <option value="CNBr+Trypsin">CNBr+Trypsin</option> + <option value="Formic_acid">Formic_acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="LysC+AspN">LysC+AspN</option> + <option value="Lys-N">Lys-N</option> + <option value="PepsinA">PepsinA</option> + <option value="semiTrypsin">semiTrypsin</option> + <option value="TrypChymo">TrypChymo</option> + <option value="TrypsinMSIPI">TrypsinMSIPI</option> + <option value="TrypsinMSIPI/P">TrypsinMSIPI/P</option> + <option value="V8-DE">V8-DE</option> + <option value="V8-E">V8-E</option> + <option value="none">none</option> + </param> + + <param name="allowed_charges" type="select" format="text"> + <label>Peptide Charge</label> + <option value="8-">8-</option> + <option value="7-">7-</option> + <option value="6-">6-</option> + <option value="5-">5-</option> + <option value="4-">4-</option> + <option value="3-">3-</option> + <option value="2-,3- and 4-">2-,3- and 4-</option> + <option value="2- and 3-">2- and 3-</option> + <option value="2-">2-</option> + <option value="1-,2- and 3-">1-,2- and 3-</option> + <option value="1-">1-</option> + <option value="Mr">Mr</option> + <option value="1+">1+</option> + <option value="1+, 2+ and 3+">1+,2+ and 3+</option> + <option value="2+">2+</option> + <option value="2+ and 3+">2+ and 3+</option> + <option selected="true" value="2+,3+ and 4+">2+,3+ and 4+</option> + <option value="3+">3+</option> + <option value="4+">4+</option> + <option value="5+">5+</option> + <option value="6+">6+</option> + <option value="7+">7+</option> + <option value="8+">8+</option> + </param> + + <param name="instrument" type="select" format="text"> + <label>Instrument</label> + <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option> + <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option> + <option selected="true" value="ESI-TRAP">ESI-TRAP</option> + <option value="ESI-QUAD">ESI-QUAD</option> + <option value="ESI-FTICR">ESI-FTICR</option> + <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option> + <option value="ESI-4SECTOR">ESI-4SECTOR</option> + <option value="FTMS-ECD">FTMS-ECD</option> + <option value="ETD-TRAP">ETD-TRAP</option> + <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option> + <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option> + <option value="MALDI-ISD">MALDI-ISD</option> + <option value="CID+ETD">CID+ETD</option> + </param> - <command>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=' - $variable_mods - ' - - --fix-mods=' - $fixed_mods - ' - - --allowed-charges='$allowed_charges' - - --enzyme=$enzyme - - --instrument='$instrument' - - -p $precursor_ion_tol - - --precursor-ion-tol-units=$precursor_tolu - - #if $email - --email=$email - #end if - - -v $missed_cleavages - - --quantitation='$quant_method' - - #if $security.security_use - --use-security - --username $security.username - --password $security.password - #end if - - #if $proxy - --proxy $proxy - #end if - - --timeout=600 - - </command> - - <inputs> - - <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/> - - <conditional name="database"> - <param name="source_select" type="select" label="Database Type"> - <option value="built_in">Built-In</option> - <option selected="true" 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="Multiple values allowed"> - <options from_file="mascot_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> + <param name="quant_method" type="select" format="text"> + <label>Quantitation</label> + <option selected="true" value="No Quant">No Quant</option> + <option value="iTRAQ 4plex">iTRAQ 4plex</option> + <option value="iTRAQ 4plex (protein)">iTRAQ 4plex (protein)</option> + <option value="iTRAQ 8plex">iTRAQ 8plex</option> + <option value="TMT 6plex">TMT 6plex</option> + <option value="TMT 2plex">TMT 2plex</option> + <option value="DiLeu 4plex">DiLeu 4plex</option> + <option value="18O multiplex">18O multiplex</option> + <option value="SILAC K+6 R+6 multiplex">SILAC K+6 R+6 multiplex</option> + <option value="IPTL (Succinyl and IMID) multiplex">IPTL (Succinyl and IMID) multiplex</option> + <option value="ICPL duplex pre-digest [MD]">ICPL duplex pre-digest [MD]</option> + <option value="ICPL duplex post-digest [MD]">ICPL duplex post-digest [MD]</option> + <option value="ICPL triplex pre-digest [MD]">ICPL triplex pre-digest [MD]</option> + <option value="ICPL quadruplex pre-digest [MD]">ICPL quadruplex pre-digest [MD]</option> + <option value="18O corrected [MD]">18O corrected [MD]</option> + <option value="15N Metabolic [MD]">15N Metabolic [MD]</option> + <option value="15N + 13C Metabolic [MD]">15N + 13C Metabolic [MD]</option> + <option value="SILAC K+6 R+10 [MD]">SILAC K+6 R+10 [MD]</option> + <option value="SILAC K+6 R+10 Arg-Pro [MD]">SILAC K+6 R+10 Arg-Pro [MD]</option> + <option value="SILAC K+6 R+6 [MD]">SILAC K+6 R+6 [MD]</option> + <option value="SILAC R+6 R+10 [MD]">SILAC R+6 R+10 [MD]</option> + <option value="SILAC K+8 R+10 [MD]">SILAC K+8 R+10 [MD]</option> + <option value="SILAC K+4 K+8 R+6 R+10 [MD]">SILAC K+4 K+8 R+6 R+10 [MD]</option> + <option value="ICAT ABI Cleavable [MD]">ICAT ABI Cleavable [MD]</option> + <option value="ICAT D8 [MD]">ICAT D8 [MD]</option> + <option value="Dimethylation [MD]">Dimethylation [MD]</option> + <option value="NBS Shimadzu [MD]">NBS Shimadzu [MD]</option> + <option value="Acetylation [MD]">Acetylation [MD]</option> + <option value="Label-free [MD]">Label-free [MD]</option> + </param> + <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.5" min="0" max="10000" help="Fragment ion tolerance in Daltons"/> - <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" /> - </options> - </param> - - <param name="missed_cleavages" type="select" format="text"> - <label>Missed Cleavages Allowed</label> - <option value="0">0</option> - <option value="1">1</option> - <option selected="true" value="2">2</option> - </param> - - <param name="enzyme" type="select" format="text"> - <label>Enzyme</label> - <option selected="true" value="Trypsin">Trypsin</option> - <option value="Trypsin/P">Trypsin/P</option> - <option value="Arg-C">Arg-C</option> - <option value="Asp-N">Asp-N</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> - <option value="Chymotrypsin">Chymotrypsin</option> - <option value="CNBr">CNBr</option> - <option value="CNBr+Trypsin">CNBr+Trypsin</option> - <option value="Formic_acid">Formic_acid</option> - <option value="Lys-C">Lys-C</option> - <option value="Lys-C/P">Lys-C/P</option> - <option value="LysC+AspN">LysC+AspN</option> - <option value="Lys-N">Lys-N</option> - <option value="PepsinA">PepsinA</option> - <option value="semiTrypsin">semiTrypsin</option> - <option value="TrypChymo">TrypChymo</option> - <option value="TrypsinMSIPI">TrypsinMSIPI</option> - <option value="TrypsinMSIPI/P">TrypsinMSIPI/P</option> - <option value="V8-DE">V8-DE</option> - <option value="V8-E">V8-E</option> - <option value="none">none</option> - </param> - - <param name="allowed_charges" type="select" format="text"> - <label>Peptide Charge</label> - <option value="8-">8-</option> - <option value="7-">7-</option> - <option value="6-">6-</option> - <option value="5-">5-</option> - <option value="4-">4-</option> - <option value="3-">3-</option> - <option value="2-,3- and 4-">2-,3- and 4-</option> - <option value="2- and 3-">2- and 3-</option> - <option value="2-">2-</option> - <option value="1-,2- and 3-">1-,2- and 3-</option> - <option value="1-">1-</option> - <option value="Mr">Mr</option> - <option value="1+">1+</option> - <option value="1+, 2+ and 3+">1+,2+ and 3+</option> - <option value="2+">2+</option> - <option value="2+ and 3+">2+ and 3+</option> - <option selected="true" value="2+,3+ and 4+">2+,3+ and 4+</option> - <option value="3+">3+</option> - <option value="4+">4+</option> - <option value="5+">5+</option> - <option value="6+">6+</option> - <option value="7+">7+</option> - <option value="8+">8+</option> - </param> - - <param name="instrument" type="select" format="text"> - <label>Instrument</label> - <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option> - <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option> - <option selected="true" value="ESI-TRAP">ESI-TRAP</option> - <option value="ESI-QUAD">ESI-QUAD</option> - <option value="ESI-FTICR">ESI-FTICR</option> - <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option> - <option value="ESI-4SECTOR">ESI-4SECTOR</option> - <option value="FTMS-ECD">FTMS-ECD</option> - <option value="ETD-TRAP">ETD-TRAP</option> - <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option> - <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option> - <option value="MALDI-ISD">MALDI-ISD</option> - <option value="CID+ETD">CID+ETD</option> - </param> + <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"/> + <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 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"/> - - <param name="quant_method" type="select" format="text"> - <label>Quantitation</label> - <option selected="true" value="None">None</option> - <option value="iTRAQ 4plex">iTRAQ 4plex</option> - <option value="iTRAQ 4plex (protein)">iTRAQ 4plex (protein)</option> - <option value="iTRAQ 8plex">iTRAQ 8plex</option> - <option value="TMT 6plex">TMT 6plex</option> - <option value="TMT 2plex">TMT 2plex</option> - <option value="DiLeu 4plex">DiLeu 4plex</option> - <option value="18O multiplex">18O multiplex</option> - <option value="SILAC K+6 R+6 multiplex">SILAC K+6 R+6 multiplex</option> - <option value="IPTL (Succinyl and IMID) multiplex">IPTL (Succinyl and IMID) multiplex</option> - <option value="ICPL duplex pre-digest [MD]">ICPL duplex pre-digest [MD]</option> - <option value="ICPL duplex post-digest [MD]">ICPL duplex post-digest [MD]</option> - <option value="ICPL triplex pre-digest [MD]">ICPL triplex pre-digest [MD]</option> - <option value="ICPL quadruplex pre-digest [MD]">ICPL quadruplex pre-digest [MD]</option> - <option value="18O corrected [MD]">18O corrected [MD]</option> - <option value="15N Metabolic [MD]">15N Metabolic [MD]</option> - <option value="15N + 13C Metabolic [MD]">15N + 13C Metabolic [MD]</option> - <option value="SILAC K+6 R+10 [MD]">SILAC K+6 R+10 [MD]</option> - <option value="SILAC K+6 R+10 Arg-Pro [MD]">SILAC K+6 R+10 Arg-Pro [MD]</option> - <option value="SILAC K+6 R+6 [MD]">SILAC K+6 R+6 [MD]</option> - <option value="SILAC R+6 R+10 [MD]">SILAC R+6 R+10 [MD]</option> - <option value="SILAC K+8 R+10 [MD]">SILAC K+8 R+10 [MD]</option> - <option value="SILAC K+4 K+8 R+6 R+10 [MD]">SILAC K+4 K+8 R+6 R+10 [MD]</option> - <option value="ICAT ABI Cleavable [MD]">ICAT ABI Cleavable [MD]</option> - <option value="ICAT D8 [MD]">ICAT D8 [MD]</option> - <option value="Dimethylation [MD]">Dimethylation [MD]</option> - <option value="NBS Shimadzu [MD]">NBS Shimadzu [MD]</option> - <option value="Acetylation [MD]">Acetylation [MD]</option> - <option value="Label-free [MD]">Label-free [MD]</option> - </param> - - <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.5" 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="10" 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 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=""/> - - - - </inputs> - <outputs> - <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> - Run a Mascot MS/MS Ion Search - </help> - + <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=""/> + </inputs> + <outputs> + <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> + Run a Mascot MS/MS Ion Search + </help> </tool>