Mercurial > repos > galaxyp > directag_and_tagrecon
changeset 0:45b68db74563 draft default tip
Uploaded
| author | galaxyp |
|---|---|
| date | Fri, 26 Sep 2014 18:49:37 -0400 |
| parents | |
| children | |
| files | COPYING README.md test-data/.gitkeep tool-data/.gitkeep tool-data/proteases.loc.sample tools/directag_and_tagrecon.xml tools/repository_dependencies.xml tools/tool_dependencies.xml |
| diffstat | 6 files changed, 410 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Fri Sep 26 18:49:37 2014 -0400 @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN + ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS + INFORMATION ON AN "AS-IS" BASIS. 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Sep 26 18:49:37 2014 -0400 @@ -0,0 +1,52 @@ +GalaxyP - DirecTag and TagRecon +=============================== + +* Home: <https://bitbucket.org/galaxyp/directag_and_tagrecon> +* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/directag_and_tagrecon> +* Tool ID: `directag_and_tagrecon` + + +Description +----------- + +Bumbershoot DirecTag and TagRecon. + +See: + +* <http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag/> +* <http://fenchurch.mc.vanderbilt.edu/bumbershoot/tagrecon/> + + +GalaxyP Community +----------------- + +Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at: + +<https://bitbucket.org/galaxyp/galaxyp> + + +License +------- + +Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. + +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. + +You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. + + +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. + + +Authors +------- + +Authors and contributors: + +* John Chilton <jmchilton@gmail.com> +* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/proteases.loc.sample Fri Sep 26 18:49:37 2014 -0400 @@ -0,0 +1,22 @@ +Trypsin Trypsin +Trypsin/P Trypsin/P +2-iodobenzoate 2-iodobenzoate +Arg-C Arg-C +Asp-N Asp-N +Asp-N_ambic Asp-N_ambic +CNBr CNBr +Chymotrypsin Chymotrypsin +Formic_acid Formic_acid +Lys-C Lys-C +Lys-C/P Lys-C/P +NoEnzyme NoEnzyme +PepsinA PepsinA +TrypChymo TrypChymo +V8-DE V8-DE +V8-E V8-E +glutamyl endopeptidase glutamyl endopeptidase +leukocyte elastase leukocyte elastase +no cleavage no cleavage +proline endopeptidase proline endopeptidase +unspecific cleavage unspecific cleavage +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/directag_and_tagrecon.xml Fri Sep 26 18:49:37 2014 -0400 @@ -0,0 +1,202 @@ +<tool id="directag_and_tagrecon" version="0.1.0" name="DirecTag and TagRecon"> + <requirements> + <requirement type="package" version="333">binaries_for_package_directag</requirement> + <requirement type="package" version="444">binaries_for_package_tagrecon</requirement> + </requirements> + + <description></description> + <command> + #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta" + #if $output_type.value == "mzid" + #set $output_ext="mzid" + #set $output_format="mzIdentML" + #else + #set $output_ext="pepXML" + #set $output_format="pepXML" + #end if + #set $input_name = $input.display_name + #set $tags_name = $input_name.split(".")[0] + ".tags" + #set $output_name = $input_name.split(".")[0] + "." + $output_ext + #set $static_mods_str = "" + #for $static_mod in $static_mods + #set $static_mods_str = $static_mods_str + "" + str($static_mod.aa) + " " + str($static_mod.mass) + #end for + #set $dynamic_mods_str = "" + #set $dynamic_mod_index = 0 + #for $dynamic_mod in $dynamic_mods + #set $dynamic_mods_str = $dynamic_mods_str + "" + str($dynamic_mod.motif) + " " + $mod_rep_chars[$dynamic_mod_index] + " " + str($dynamic_mod.mass) + #set $dynamic_mod_index = $dynamic_mod_index + 1 + #end for + ln -s '$input' '${input_name}'; + ln -s '$input_database' '${db_name}'; + cp \${TAGRECON_UNIMOD_PATH:-${GALAXY_DATA_INDEX_DIR}/unimod.xml} .; + cp \${TAGRECON_BLOSUM_PATH:-${GALAXY_DATA_INDEX_DIR}/blosum62.fas} .; + directag '${input_name}' \ + -StaticMods '${static_mods_str}' \ + -DynamicMods '${dynamic_mods_str}' \ + -MaxDynamicMods '$max_dynamic_mods' \ + -MaxResults ${max_tags} \ + -FragmentMzTolerance ${tag_mz_tolerance} \ + #if $advanced_charge_options.specify + -UseChargeStateFromMS $advanced_charge_options.use_ms_charge_state \ + #end if + #if $tag_weights.specify + -IntensityScoreWeight $tag_weights.intensity \ + -MzFidelityScoreWeight $tag_weights.mz \ + -ComplementScoreWeight $tag_weights.complement \ + #end if + ; + tagrecon -DecoyPrefix '${decoy_prefix}' \ + -ProteinDatabase '${db_name}' \ + -OutputFormat '${$output_format}' \ + -StaticMods '${static_mods_str}' \ + -DynamicMods '${dynamic_mods_str}' \ + -MaxDynamicMods '$max_dynamic_mods' \ + -CleavageRules '${protease}' \ + -MaxMissedCleavages ${max_missed_cleavages} \ + #if $advanced_cleavage_options.specify + -MinTerminiCleavages $advanced_cleavage_options.min_termini_cleavages \ + -UseNETAdjustment $advanced_cleavage_options.use_net_adjustment \ + #end if + #if $advanced_charge_options.specify + -UseChargeStateFromMS $advanced_charge_options.use_ms_charge_state \ + #end if + #if $search_untagged.search + -SearchUntaggedSpectra true \ + -UntaggedSpectraPrecMZTol $search_untagged.precursor_mz_tolerance + #end if + '${tags_name}'; + mv '$output_name' output + </command> + <stdio> + <exit_code range="1:" level="fatal" description="Job Failed" /> + <regex match="^Could not find the default configuration file.*$" + source="both" + level="warning" /> + </stdio> + <inputs> + <conditional name="type"> + <param name="input_type" type="select" label="Input Type"> + <option value="mzml">mzML</option> + <option value="mzxml">mzXML</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <when value="mzml"> + <param format="mzml" name="input" type="data" label="Input mzML"/> + </when> + <when value="mzxml"> + <param format="mzxml" name="input" type="data" label="Input mzXML"/> + </when> + <when value="mgf"> + <param format="mgf" name="input" type="data" label="Input mgf"/> + </when> + <when value="ms2"> + <param format="ms2" name="input" type="data" label="Input ms2"/> + </when> + </conditional> + <param name="output_type" type="select" label="Output Type"> + <option value="raw_pepxml">pepXML</option> + <option value="mzid">mzIdentML</option> + </param> + <param format="fasta" name="input_database" type="data" label="Protein Database"/> + <param name="decoy_prefix" type="text" label="Decoy Prefix"/> + <repeat name="static_mods" title="Static Modifications (used by both directag and tagrecon) "> + <param name="aa" type="text" label="Amino Acid" /> + <param name="mass" type="float" label="Mass" value="0" /> + </repeat> + <repeat name="dynamic_mods" title="Dynamic Modifications (used by both directag and tagrecon)" max="7"> + <param name="motif" type="text" label="Amino Acid Motif" /> + <param name="mass" type="float" label="Mass" value="0" /> + </repeat> + <param name="max_dynamic_mods" type="integer" label="Maximum Dynamic Mods per Sequence" value="2" /> + <param name="tag_length" type="integer" label="Tag Length" value="3" help="A sequence tag is generated from the gaps between a number of peaks equal to this parameter plus one. Longer tag lengths are more specific, but harder to find because many consecutive ion fragments are rare." /> + <param name="max_tags" type="integer" label="Maximum Number of Tags per Spectrum" value="20" /> + <param name="tag_mz_tolerance" type="float" label="Fragment m/z Tolerance during Tag Generation (Da/z)" value=".5" /> + <param name="protease" type="select" label="Protease"> + <options from_file="proteases.loc"> + <column name="name" index="0" /> + <column name="value" index="1" /> + </options> + </param> + <param name="max_missed_cleavages" label="Maximum Number of Missed Cleavages" type="integer" value="-1" /> + <conditional name="advanced_cleavage_options"> + <param name="specify" type="boolean" label="Specify advanced cleavage options" help="" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="min_termini_cleavages" type="select" label="Minimum Termini Cleavages" value="2" help="A peptide must start after a cleavage and end before a cleavage. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified above."> + <option value="2">2</option> + <option value="1">1</option> + <option value="0">0</option> + </param> + <param name="use_net_adjustment" type="boolean" label="Use NET Adjustment" help="When enabled, TagRecon adds a probabilistic bonus to peptide scores depending on whether the peptides are fully-enzymatic, semi-enzymatic, or non-enzymatic." truevalue="true" falsevalue="false" /> + </when> + </conditional> + <conditional name="advanced_charge_options"> + <param name="specify" type="boolean" label="Specify Advanced Charge State Handling Options" help="" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="use_ms_charge_state" type="boolean" label="Use Charge State from MS" truevalue="true" falsevalue="false" help="When enabled, DirecTag and TagRecon will not use their internal algorithm to determine charge state of a spectrum when it is available in the input file." /> + <!-- TODO: Add DuplicateSpectra, NumChargeStates --> + </when> + </conditional> + <!-- TODO: Advanced Peptide Filtering: Min/Max Peptide Mass/Length --> + <conditional name="tag_weights"> + <param name="specify" type="boolean" label="Override Default Tag Weighting" help="By default equal weights are assigned to intensity, m/z fidelity, and complement scores." truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="intensity" type="float" label="Intensity Score Weight" help="" value="1.0" /> + <param name="mz" type="float" label="m/z Fidelity Score Weight" help="" value="1.0" /> + <param name="complement" type="float" label="Complement Score Weight" help="" value="1.0" /> + </when> + </conditional> + <conditional name="search_untagged"> + <param name="search" type="boolean" label="Search Untagged Spectra" help="Search untagged spectra like a database search." truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="precursor_mz_tolerance" type="float" label="Untagged Spectra Precursor m/z Tolerance" value="1.25" /> + </when> + </conditional> + <conditional name="unknown_mass_shifts"> + <param name="how" type="select" label="Explaination for Unknown Mass Shifts"> + <option value="">None, disable delta mass interpretation by TagRecon</option> + <option value="blindptms">Blind PTMs</option> + <option value="mutations">Mutations</option> + <!-- TODO: Add preferredptms --> + </param> + <when value="blindptms"> + <!-- BlindPTMResidues ??? --> + </when> + <when value="mutations"> + <!-- BlosumScoreThreshold ??? BlosumThreshold ???--> + </when> + <when value="" /> + </conditional> + </inputs> +<!-- + Both: + AdjustPrecursorMass (defaults to false) + + TagRecon: + Skip for now: ComputeXCorr + Skip forever: ProteinSampleSize + + TO ADD: + + Both: Advanced, ClassSizeMultiplier, float 2.0. +--> + <outputs> + <data format="raw_pepxml" name="output" from_work_dir="output"> + <change_format> + <when input="output_type" value="mzid" format="mzid" /> + </change_format> + </data> + </outputs> + + <help> +**What it does** + +Performs protein identification via Directag and TagRecon. + </help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/repository_dependencies.xml Fri Sep 26 18:49:37 2014 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories> + <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/tool_dependencies.xml Fri Sep 26 18:49:37 2014 -0400 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="binaries_for_package_directag" version="333"> + <repository changeset_revision="3897712f4b92" name="package_directag" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="binaries_for_package_tagrecon" version="444"> + <repository changeset_revision="3682c9938aca" name="package_tagrecon" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>