# HG changeset patch
# User galaxyp
# Date 1372193474 14400
# Node ID d3d4e579321bf9b668aeb3d82d7cf6e3d2b0dab1
# Parent fdd81c7b7fd5fd6f0b66014713ba50486545f543
Uploaded
diff -r fdd81c7b7fd5 -r d3d4e579321b LICENSE
--- a/LICENSE Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,202 +0,0 @@
-
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- Version 2.0, January 2004
- http://www.apache.org/licenses/
-
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- the conditions stated in this License.
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- 5. Submission of Contributions. Unless You explicitly state otherwise,
- any Contribution intentionally submitted for inclusion in the Work
- by You to the Licensor shall be under the terms and conditions of
- this License, without any additional terms or conditions.
- Notwithstanding the above, nothing herein shall supersede or modify
- the terms of any separate license agreement you may have executed
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- 7. Disclaimer of Warranty. Unless required by applicable law or
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- Unless required by applicable law or agreed to in writing, software
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diff -r fdd81c7b7fd5 -r d3d4e579321b README.md
--- a/README.md Tue Jun 25 16:31:39 2013 -0400
+++ b/README.md Tue Jun 25 16:51:14 2013 -0400
@@ -1,25 +1,3 @@
-This repository contains tool wrappers for the Tabb lab tools
-idqonvert, myrimatch, and tagrecon. There is also an IDPicker3 tool
-wrapper, but it does not work due to bugs in IDPicker3's file merging
-functionality.# Obtaining Tools
-
-Repositories for all Galaxy-P tools can be found at
-https:/bitbucket.org/galaxyp/.
-
-# Contact
-
-Please send suggestions for improvements and bug reports to
-jmchilton@gmail.com.
-
-# License
-
-All Galaxy-P tools are licensed under the Apache License Version 2.0
-unless otherwise documented.
-
-# Tool Versioning
-
-Galaxy-P tools will have versions of the form X.Y.Z. Versions
-differing only after the second decimal should be completely
-compatible with each other. Breaking changes should result in an
-increment of the number before and/or after the first decimal. All
-tools of version less than 1.0.0 should be considered beta.
+Galaxy tool shed repository for install idpqonvert dependency. This
+repository contains no tools, see the bumbershoot repository for
+actual Galaxy tools.
\ No newline at end of file
diff -r fdd81c7b7fd5 -r d3d4e579321b README_GALAXYP.md
--- a/README_GALAXYP.md Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-# Obtaining Tools
-
-Repositories for all Galaxy-P tools can be found at
-https:/bitbucket.org/galaxyp/.
-
-# Contact
-
-Please send suggestions for improvements and bug reports to
-jmchilton@gmail.com.
-
-# License
-
-All Galaxy-P tools are licensed under the Apache License Version 2.0
-unless otherwise documented.
-
-# Tool Versioning
-
-Galaxy-P tools will have versions of the form X.Y.Z. Versions
-differing only after the second decimal should be completely
-compatible with each other. Breaking changes should result in an
-increment of the number before and/or after the first decimal. All
-tools of version less than 1.0.0 should be considered beta.
diff -r fdd81c7b7fd5 -r d3d4e579321b README_REPO.md
--- a/README_REPO.md Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-This repository contains tool wrappers for the Tabb lab tools
-idqonvert, myrimatch, and tagrecon. There is also an IDPicker3 tool
-wrapper, but it does not work due to bugs in IDPicker3's file merging
-functionality.
\ No newline at end of file
diff -r fdd81c7b7fd5 -r d3d4e579321b bumbershoot.py
--- a/bumbershoot.py Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-from galaxy.datatypes.binary import Binary
-
-class IdpDB(Binary):
- file_ext = "idpDB"
-
-Binary.register_unsniffable_binary_ext('idpDB')
-
diff -r fdd81c7b7fd5 -r d3d4e579321b bumbershoot_types.py
--- a/bumbershoot_types.py Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-from galaxy.datatypes.binary import Binary
-
-class IdpDB(Binary):
- file_ext = "idpDB"
-
-Binary.register_unsniffable_binary_ext('idpDB')
-
diff -r fdd81c7b7fd5 -r d3d4e579321b datatypes_conf.xml
--- a/datatypes_conf.xml Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-
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diff -r fdd81c7b7fd5 -r d3d4e579321b idpicker.xml
--- a/idpicker.xml Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-
-
- Assemble parsimonious protien identifications.
-
-
- # Simple format group:group_name followed by pairs of name:name and path:path lines
-#for $group in $groups:
-group:$group.group_name
-#for $idpdb_input in $group.idpdb_inputs:
-name:${idpdb_input.display_name}
-path:${idpdb_input}
-#end for
-#end for
-
-
-
- idpicker_wrapper.py --input $group_config --output $output
-
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-
-
-
-
- idpicker
-
-
-**WARNING**
-
-This tool does not current work.
-
-**What it does**
-
-
-
-** Building Groups **
-
-Build arbitrary hierarchy by nesting groups with colon (e.g. control:666Gx6).
-
-http://fenchurch.mc.vanderbilt.edu/bumbershoot/idpicker/index_files/image003.gif
-
-------
-
-
-**Citation**
-
-For the underlying tool, please cite `TODO`
-
-If you use this tool in Galaxy, please cite TODO
-
-
\ No newline at end of file
diff -r fdd81c7b7fd5 -r d3d4e579321b idpicker_wrapper.py
--- a/idpicker_wrapper.py Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-#!/usr/bin/env python
-import optparse
-import sys
-import os
-
-
-def stop_err(msg):
- sys.stderr.write("%s\n" % msg)
- sys.exit(-1)
-
-
-def build_groups(input):
- os.makedir("input_directory")
-
-
-def main():
- parser = optparse.OptionParser()
- parser.add_option('--input')
- parser.add_option('--output')
- (options, args) = parser.parse_args()
- if not len(options.input):
- stop_err("No input file found")
- build_groups(options.input)
-
-if __name__ == '__main__':
- main()
diff -r fdd81c7b7fd5 -r d3d4e579321b idpqonvert.xml
--- a/idpqonvert.xml Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,217 +0,0 @@
-
-
-
- Prepare identification results for IDPicker.
-
-
- #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
- #set $input_name = $input.display_name
- #set $output_name = $input_name.split(".")[0] + ".idpDB"
- ln -s '$input' '${input_name}';
- ln -s '$input_database' '${db_name}';
- idpQonvert -DecoyPrefix '${decoy_prefix}' \
- -WriteQonversionDetails true \
- -ProteinDatabase '${db_name}' \
- -MaxFDR $max_fdr \
- -EmbedSpectrumScanTimes false \
- -EmbedSpectrumSources false \
- #if $scoring.override_scoring
- #set $score_info = []
- #for $engine in ["myrimatch:mvh", "xcorr", "sequest:xcorr", "sequest:deltacn", "mascot:score", "x!tandem:expect", "x!tandem:hyperscore", "ms-gf:spacevalue"]
- #set $weight = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_weight.value")
- #set $type = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_type.value")
- #set $score_info = $score_info + [str($weight) + " " + $type + " " + $engine]
- #continue
- #end for
- #set $score_str = "; ".join($score_info)
- -ScoreInfo '$score_str' \
- #end if
- #if $advanced_options.use_advanced_options
- -MaxImportFDR $advanced_options.max_import_fdr \
- -MaxResultRank $advanced_options.max_result_rank \
- -RerankMatches $advanced_options.rerank_matches \
- -Gamma $advanced_options.gamma \
- -Nu $advanced_options.nu \
- -PolynomialDegree $advanced_options.polynomial_degree \
- -TruePositiveThreshold $advanced_options.true_positive_threshold \
- -MaxTrainingRank $advanced_options.max_training_rank \
- -SVMType $advanced_options.svm_type \
- -Kernel $advanced_options.kernel \
- -ChargeStateHandling $advanced_options.charge_state_handling \
- -QonverterMethod $advanced_options.qonverter_method \
- -MinPartitionSize $advanced_options.min_partition_size \
- #end if
- '${input_name}';
- mv '$output_name' output
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- idpQonvert
-
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-**What it does**
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `TODO`
-
-If you use this tool in Galaxy, please cite TODO
-
-
-
diff -r fdd81c7b7fd5 -r d3d4e579321b myrimatch.xml
--- a/myrimatch.xml Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,192 +0,0 @@
-
-
-
- #set $mod_rep_chars = "*$^@.%!"
- #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 $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' '${db_name}';
- myrimatch -DecoyPrefix '${decoy_prefix}' \
- -ProteinDatabase '${db_name}' \
- -OutputFormat '${$output_format}' \
- '${input_name}' \
- -StaticMods '${static_mods_str}' \
- -DynamicMods '${dynamic_mods_str}' \
- -CleavageRules '${protease}' \
- #set $percursor_type = $percursor_tolerance.percursor_type
- -PrecursorMzToleranceRule '${percursor_type}' \
- #if $percursor_type == "auto" or $percursor_type == "mono"
- -MonoPrecursorMzTolerance '${percursor_tolerance.mono_precursor_mz_tolerance}${percursor_tolerance.mono_precursor_mz_tolerance_units}' \
- #end if
- #if $percursor_type == "auto" or $percursor_type == "avg"
- -AvgPrecursorMzTolerance '${percursor_tolerance.avg_precursor_mz_tolerance}${percursor_tolerance.avg_precursor_mz_tolerance_units}' \
- #end if
- -FragmentMzTolerance '${fragment_mz_tolerance}${fragment_mz_tolerance_units}' \
- #if $advanced.use_advanced
- -UseSmartPlusThreeModel $advanced.use_smart_plus_three_model \
- -MinPeptideLength $advanced.min_peptide_length \
- -MaxPeptideLength $advanced.max_peptide_length \
- #if $advanced.max_peak_count
- -MaxPeakCount $advanced.max_peak_count \
- #end if
- #if $advanced.fragmentation_rule.override
- -FragmentationAutoRule false -FragmentationRule 'manual:${advanced.fragmentation_rule.fragmentation_rule}' \
- #end if
- #end if
- ;
- mv '$output_name' output
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- myrimatch
-
-
-
-**What it does**
-
-Performs protein identification via database search using MyriMatch.
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. Tabb DL, Fernando CG, Chambers MC. J Proteome Res. 6(2) 654-61. 2007 Feb. PMCID PMC2525619`
-
-If you use this tool in Galaxy, please cite TODO
-
-
diff -r fdd81c7b7fd5 -r d3d4e579321b proteases.loc.sample
--- a/proteases.loc.sample Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-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
-
diff -r fdd81c7b7fd5 -r d3d4e579321b repository_dependencies.xml
--- a/repository_dependencies.xml Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
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diff -r fdd81c7b7fd5 -r d3d4e579321b tagrecon.xml
--- a/tagrecon.xml Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,210 +0,0 @@
-
-
-
- #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
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- directag
- tagrecon
-
-
-
-**What it does**
-
-Performs protein identification via Directag and TagRecon.
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `TODO`.
-
-If you use this tool in Galaxy, please cite TODO.
-
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diff -r fdd81c7b7fd5 -r d3d4e579321b tool_dependencies.xml
--- a/tool_dependencies.xml Tue Jun 25 16:31:39 2013 -0400
+++ b/tool_dependencies.xml Tue Jun 25 16:51:14 2013 -0400
@@ -1,15 +1,20 @@
-
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+
+
+
+ http://getgalaxyp.msi.umn.edu/downloads/idpQonvert_3.0.475
+
+ idpQonvert_3.0.475
+ $INSTALL_DIR/
+
+
+ $INSTALL_DIR
+
+
+
+
+ This package downloads and installs idqonvert.
+
+
diff -r fdd81c7b7fd5 -r d3d4e579321b update.sh
--- a/update.sh Tue Jun 25 16:31:39 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-#!/bin/bash
-
-LICENSE_FILE=LICENSE
-# Ensure repository contains license file.
-if [ ! -e "$LICENSE_FILE" ];
-then
- wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE"
-fi
-
-# Run repository specific update actions.
-if [ -f update_repo.sh ];
-then
- ./update_repo.sh
-fi
-
-wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md
-
-# Create repository README
-if [ ! -e README_REPO.md ];
-then
- echo "TODO: Document this tool repository." > README_REPO.md
-fi
-cat README_REPO.md README_GALAXYP.md > README.md
-
-
-# If version file exists, update all tools to this version
-VERSION_FILE=version
-if [ -e "$VERSION_FILE" ];
-then
- VERSION=`cat $VERSION_FILE`
-
- # Replace tool version in each tool XML file `
- find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \;
-
-fi