# HG changeset patch
# User galaxyp
# Date 1368219974 14400
# Node ID 35cf23cd8c3d16285bbdfa1497653347f7f36597
Initial commit.
diff -r 000000000000 -r 35cf23cd8c3d LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,202 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
+ and distribution as defined by Sections 1 through 9 of this document.
+
+ "Licensor" shall mean the copyright owner or entity authorized by
+ the copyright owner that is granting the License.
+
+ "Legal Entity" shall mean the union of the acting entity and all
+ other entities that control, are controlled by, or are under common
+ control with that entity. For the purposes of this definition,
+ "control" means (i) the power, direct or indirect, to cause the
+ direction or management of such entity, whether by contract or
+ otherwise, or (ii) ownership of fifty percent (50%) or more of the
+ outstanding shares, or (iii) beneficial ownership of such entity.
+
+ "You" (or "Your") shall mean an individual or Legal Entity
+ exercising permissions granted by this License.
+
+ "Source" form shall mean the preferred form for making modifications,
+ including but not limited to software source code, documentation
+ source, and configuration files.
+
+ "Object" form shall mean any form resulting from mechanical
+ transformation or translation of a Source form, including but
+ not limited to compiled object code, generated documentation,
+ and conversions to other media types.
+
+ "Work" shall mean the work of authorship, whether in Source or
+ Object form, made available under the License, as indicated by a
+ copyright notice that is included in or attached to the work
+ (an example is provided in the Appendix below).
+
+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
+ separable from, or merely link (or bind by name) to the interfaces of,
+ the Work and Derivative Works thereof.
+
+ "Contribution" shall mean any work of authorship, including
+ the original version of the Work and any modifications or additions
+ to that Work or Derivative Works thereof, that is intentionally
+ submitted to Licensor for inclusion in the Work by the copyright owner
+ or by an individual or Legal Entity authorized to submit on behalf of
+ the copyright owner. For the purposes of this definition, "submitted"
+ means any form of electronic, verbal, or written communication sent
+ to the Licensor or its representatives, including but not limited to
+ communication on electronic mailing lists, source code control systems,
+ and issue tracking systems that are managed by, or on behalf of, the
+ Licensor for the purpose of discussing and improving the Work, but
+ excluding communication that is conspicuously marked or otherwise
+ designated in writing by the copyright owner as "Not a Contribution."
+
+ "Contributor" shall mean Licensor and any individual or Legal Entity
+ on behalf of whom a Contribution has been received by Licensor and
+ subsequently incorporated within the Work.
+
+ 2. Grant of Copyright License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ copyright license to reproduce, prepare Derivative Works of,
+ publicly display, publicly perform, sublicense, and distribute the
+ Work and such Derivative Works in Source or Object form.
+
+ 3. Grant of Patent License. Subject to the terms and conditions of
+ this License, each Contributor hereby grants to You a perpetual,
+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ (except as stated in this section) patent license to make, have made,
+ use, offer to sell, sell, import, and otherwise transfer the Work,
+ where such license applies only to those patent claims licensable
+ by such Contributor that are necessarily infringed by their
+ Contribution(s) alone or by combination of their Contribution(s)
+ with the Work to which such Contribution(s) was submitted. If You
+ institute patent litigation against any entity (including a
+ cross-claim or counterclaim in a lawsuit) alleging that the Work
+ or a Contribution incorporated within the Work constitutes direct
+ or contributory patent infringement, then any patent licenses
+ granted to You under this License for that Work shall terminate
+ as of the date such litigation is filed.
+
+ 4. Redistribution. You may reproduce and distribute copies of the
+ Work or Derivative Works thereof in any medium, with or without
+ modifications, and in Source or Object form, provided that You
+ meet the following conditions:
+
+ (a) You must give any other recipients of the Work or
+ Derivative Works a copy of this License; and
+
+ (b) You must cause any modified files to carry prominent notices
+ stating that You changed the files; and
+
+ (c) You must retain, in the Source form of any Derivative Works
+ that You distribute, all copyright, patent, trademark, and
+ attribution notices from the Source form of the Work,
+ excluding those notices that do not pertain to any part of
+ the Derivative Works; and
+
+ (d) If the Work includes a "NOTICE" text file as part of its
+ distribution, then any Derivative Works that You distribute must
+ include a readable copy of the attribution notices contained
+ within such NOTICE file, excluding those notices that do not
+ pertain to any part of the Derivative Works, in at least one
+ of the following places: within a NOTICE text file distributed
+ as part of the Derivative Works; within the Source form or
+ documentation, if provided along with the Derivative Works; or,
+ within a display generated by the Derivative Works, if and
+ wherever such third-party notices normally appear. The contents
+ of the NOTICE file are for informational purposes only and
+ do not modify the License. You may add Your own attribution
+ notices within Derivative Works that You distribute, alongside
+ or as an addendum to the NOTICE text from the Work, provided
+ that such additional attribution notices cannot be construed
+ as modifying the License.
+
+ You may add Your own copyright statement to Your modifications and
+ may provide additional or different license terms and conditions
+ for use, reproduction, or distribution of Your modifications, or
+ for any such Derivative Works as a whole, provided Your use,
+ reproduction, and distribution of the Work otherwise complies with
+ the conditions stated in this License.
+
+ 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
+ with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
+ the Work or Derivative Works thereof, You may choose to offer,
+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
+ identification within third-party archives.
+
+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
diff -r 000000000000 -r 35cf23cd8c3d README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,25 @@
+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 000000000000 -r 35cf23cd8c3d README_GALAXYP.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_GALAXYP.md Fri May 10 17:06:14 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 000000000000 -r 35cf23cd8c3d README_REPO.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_REPO.md Fri May 10 17:06:14 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 000000000000 -r 35cf23cd8c3d idpicker.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/idpicker.xml Fri May 10 17:06:14 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 000000000000 -r 35cf23cd8c3d idpicker_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/idpicker_wrapper.py Fri May 10 17:06:14 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 000000000000 -r 35cf23cd8c3d idpqonvert.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/idpqonvert.xml Fri May 10 17:06:14 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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ idpqonvert
+
+
+**What it does**
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `TODO`
+
+If you use this tool in Galaxy, please cite TODO
+
+
+
diff -r 000000000000 -r 35cf23cd8c3d myrimatch.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/myrimatch.xml Fri May 10 17:06:14 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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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 000000000000 -r 35cf23cd8c3d tagrecon.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tagrecon.xml Fri May 10 17:06:14 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 '$output_name' output
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ directag
+ tagrecon
+
+
+
+**What it does**
+
+Performs protein identification via Directag and TagRecon.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `TODO`.
+
+If you use this tool in Galaxy, please cite TODO.
+
+
+
diff -r 000000000000 -r 35cf23cd8c3d update.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/update.sh Fri May 10 17:06:14 2013 -0400
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+LICENSE_FILE=LICENSE
+# Ensure repository contains license file.
+if [ ! -e "$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