# HG changeset patch
# User galaxyp
# Date 1372193565 14400
# Node ID 933a77287b5f3bb6b4439d28149e19f270fa7bd6
# Parent d3d4e579321bf9b668aeb3d82d7cf6e3d2b0dab1
Uploaded
diff -r d3d4e579321b -r 933a77287b5f LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,202 @@
+
+ Apache License
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+
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+ Unless required by applicable law or agreed to in writing, software
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diff -r d3d4e579321b -r 933a77287b5f README.md
--- a/README.md Tue Jun 25 16:51:14 2013 -0400
+++ b/README.md Tue Jun 25 16:52:45 2013 -0400
@@ -1,3 +1,25 @@
-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
+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.
diff -r d3d4e579321b -r 933a77287b5f README_GALAXYP.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_GALAXYP.md Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,22 @@
+# 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 d3d4e579321b -r 933a77287b5f README_REPO.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_REPO.md Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,4 @@
+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 d3d4e579321b -r 933a77287b5f bumbershoot.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bumbershoot.py Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,7 @@
+from galaxy.datatypes.binary import Binary
+
+class IdpDB(Binary):
+ file_ext = "idpDB"
+
+Binary.register_unsniffable_binary_ext('idpDB')
+
diff -r d3d4e579321b -r 933a77287b5f bumbershoot_types.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bumbershoot_types.py Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,7 @@
+from galaxy.datatypes.binary import Binary
+
+class IdpDB(Binary):
+ file_ext = "idpDB"
+
+Binary.register_unsniffable_binary_ext('idpDB')
+
diff -r d3d4e579321b -r 933a77287b5f datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,9 @@
+
+
+
+
+
+
+
+
+
diff -r d3d4e579321b -r 933a77287b5f idpicker.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/idpicker.xml Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,56 @@
+
+
+ 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
+
+
+
+
+
+
+
+
+
+
+
+
+ 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 d3d4e579321b -r 933a77287b5f idpicker_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/idpicker_wrapper.py Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,26 @@
+#!/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 d3d4e579321b -r 933a77287b5f idpqonvert.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/idpqonvert.xml Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,217 @@
+
+
+
+ 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
+
+
+**What it does**
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `TODO`
+
+If you use this tool in Galaxy, please cite TODO
+
+
+
diff -r d3d4e579321b -r 933a77287b5f myrimatch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/myrimatch.xml Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,192 @@
+
+
+
+ #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 d3d4e579321b -r 933a77287b5f proteases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/proteases.loc.sample Tue Jun 25 16:52:45 2013 -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
+
diff -r d3d4e579321b -r 933a77287b5f repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,5 @@
+
+
+
+
+
diff -r d3d4e579321b -r 933a77287b5f tagrecon.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tagrecon.xml Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,210 @@
+
+
+
+ #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.
+
+
+
diff -r d3d4e579321b -r 933a77287b5f tool_dependencies.xml
--- a/tool_dependencies.xml Tue Jun 25 16:51:14 2013 -0400
+++ b/tool_dependencies.xml Tue Jun 25 16:52:45 2013 -0400
@@ -1,20 +1,15 @@
-
-
-
- http://getgalaxyp.msi.umn.edu/downloads/idpQonvert_3.0.475
-
- idpQonvert_3.0.475
- $INSTALL_DIR/
-
-
- $INSTALL_DIR
-
-
-
-
- This package downloads and installs idqonvert.
-
-
+
+
+
+
+
+
+
+
+
+
+
+
diff -r d3d4e579321b -r 933a77287b5f update.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/update.sh Tue Jun 25 16:52:45 2013 -0400
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+LICENSE_FILE=LICENSE
+# Ensure repository contains license file.
+if [ ! -e "$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