Mercurial > repos > iracooke > mascot
changeset 8:487533fa6990 draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 18:34:34 -0400 |
| parents | 0ae7738e33e9 |
| children | da575eb4432d |
| files | README README.rst mascot.xml mascot_to_pepxml.xml repository_dependencies.xml tool_dependencies.xml |
| diffstat | 6 files changed, 328 insertions(+), 329 deletions(-) [+] |
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--- a/README Mon Jan 05 17:01:18 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -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 uses protk which must be installed separately. - -For instructions please see: https://github.com/iracooke/protk/#galaxy-integration
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Oct 20 18:34:34 2015 -0400 @@ -0,0 +1,36 @@ +Mascot +====== + +Galaxy wrapper for the Mascot_ tandem ms search tool and a tool to convert results to `pepXML` + +.. _Mascot: http://www.matrixscience.com/ + +Requirements +------------ + +This package uses protk_, and the trans_proteomic_pipeline_ which need to be present in order for the tool to work. In addition, you will need a working installation of Mascot_ which is commercial software. + +.. _protk: https://github.com/iracooke/protk +.. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP + + +There are two ways you can satify these dependencies (choose one): + +1. **Manual Install:** Details on how to install protk_, msgfplus_ and Proteowizard_ manually are available here_. + +2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work. The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed. + +.. _docker: https://www.docker.com/ +.. _here: https://github.com/iracooke/protk/#galaxy-integration +.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker +__ container_ + + +Further Info +------------ + +The source code for this tool and other protk galaxy tools is on github_. Please visit the github page to contribute to the project or to `report an issue`__ + +.. _github: https://github.com/iracooke/protk-galaxytools +.. _issue: https://github.com/iracooke/protk-galaxytools/issues +__ issue_
--- a/mascot.xml Mon Jan 05 17:01:18 2015 -0500 +++ b/mascot.xml Tue Oct 20 18:34:34 2015 -0400 @@ -1,249 +1,230 @@ -<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.3"> +<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.0"> + <description>Mascot MS/MS Search</description> + <requirements> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4.2">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">simonalpha/protk:1.4.0</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 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>
--- a/mascot_to_pepxml.xml Mon Jan 05 17:01:18 2015 -0500 +++ b/mascot_to_pepxml.xml Tue Oct 20 18:34:34 2015 -0400 @@ -1,83 +1,72 @@ -<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.3"> - <requirements> - <container type="docker">simonalpha/protk:1.4.0</container> - <requirement type="package" version="1.4">protk</requirement> - <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> - </requirements> +<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.0"> + <description>Converts a mascot results file to pepXML</description> + <requirements> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4.2">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>
--- a/repository_dependencies.xml Mon Jan 05 17:01:18 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Proteomics datatypes"> - <repository changeset_revision="9cfabf0b942d" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 18:34:34 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="protk" version="1.4.2"> + <repository changeset_revision="226662e0d0d2" name="package_protk_1_4_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>