Mercurial > repos > jmchilton > johnstestrepo
changeset 1:d2e7c70eb815 draft
Deleted selected files
| author | jmchilton |
|---|---|
| date | Wed, 19 Sep 2012 00:12:05 -0400 |
| parents | 942cec8d04c7 |
| children | f3234fa35d1b |
| files | galaxyp-galaxyp-toolshed-msconvert-9663ae998499/LICENSE galaxyp-galaxyp-toolshed-msconvert-9663ae998499/README.md galaxyp-galaxyp-toolshed-msconvert-9663ae998499/README_GALAXYP.md galaxyp-galaxyp-toolshed-msconvert-9663ae998499/README_REPO.md galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert.xml.template galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert2.xml galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert2_raw.xml galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert3.xml galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert3_raw.xml galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert_raw_wrapper.py galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert_subset.xml galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert_wrapper.py galaxyp-galaxyp-toolshed-msconvert-9663ae998499/update.sh galaxyp-galaxyp-toolshed-msconvert-9663ae998499/update_repo.sh galaxyp-galaxyp-toolshed-msconvert-9663ae998499/version |
| diffstat | 15 files changed, 0 insertions(+), 2182 deletions(-) [+] |
line wrap: on
line diff
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/LICENSE Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,202 +0,0 @@ - - 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 2012 University of Minnesota - - 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.
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/README.md Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -Galaxy tool wrappers for msconvert. - -Due to potential difficulties installing ProteoWizard with vendor -library support, tools for interacting with vendor types are seperated -out into their own wrappers. Galaxy is generally deployed under Linux, -but vendor support in ProteoWizard requires .NET 4.0. There are at -least two ways to get this to work: - - * Galaxy jobs may be configured to submit to a Windows host with - ProteoWizard installed using the - LWR. http://wiki.g2.bx.psu.edu/Admin/Config/LWR - - * ProteoWizard can be installed under Wine. Guidance on how to set - this up and package such environments for cloud deployments can be - found here: https://github.com/jmchilton/proteomics-wine-env - -Wrappers for both msconvert version 2 and version 3+ are provided -because version 3+ of msconvert with vendor library support requires -.NET 4.0 and this may difficult or impossible under Wine in Linux with -all but the most recent versions of Wine (1.4+). - - -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 noted. - -Tool Versions: - -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.
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/README_GALAXYP.md Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -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 noted. - -Tool Versions: - -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.
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/README_REPO.md Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -Galaxy tool wrappers for msconvert. - -Due to potential difficulties installing ProteoWizard with vendor -library support, tools for interacting with vendor types are seperated -out into their own wrappers. Galaxy is generally deployed under Linux, -but vendor support in ProteoWizard requires .NET 4.0. There are at -least two ways to get this to work: - - * Galaxy jobs may be configured to submit to a Windows host with - ProteoWizard installed using the - LWR. http://wiki.g2.bx.psu.edu/Admin/Config/LWR - - * ProteoWizard can be installed under Wine. Guidance on how to set - this up and package such environments for cloud deployments can be - found here: https://github.com/jmchilton/proteomics-wine-env - -Wrappers for both msconvert version 2 and version 3+ are provided -because version 3+ of msconvert with vendor library support requires -.NET 4.0 and this may difficult or impossible under Wine in Linux with -all but the most recent versions of Wine (1.4+). - -
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert.xml.template Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,320 +0,0 @@ -<tool id="msconvert$VERSION$DESCRIPTION" name="msconvert$VERSION$DESCRIPTION" version="0.1.0"> - <!-- BEGIN_VERSION_RAW --> - <description>Convert and filter a Thermo Finnigan RAW file</description> - <!-- END_VERSION_RAW --> - <!-- BEGIN_VERSION_DEFAULT --> - <description>Convert and filter a mass spec peak list</description> - <!-- END_VERSION_DEFAULT --> - - <command interpreter="python"> - msconvert_wrapper.py - --input=${input} - --output=${output} - ## BEGIN_VERSION_DEFAULT - --fromextension=${input.ext} - ## END_VERSION_DEFAULT - - ## BEGIN_VERSION_RAW - --fromextension=RAW - ## END_VERSION_RAW - - --toextension=${output_type} - - #if $settings.settingsType == "full" - --binaryencoding=${settings.binary_encoding} - --mzencoding=${settings.mz_encoding} - --intensityencoding=${settings.intensity_encoding} - --zlib=${settings.zlib} - #end if - - #if $filtering.filtering_use - - #if $filtering.precursor_recalculation.value - --filter "precursorRecalculation" - #end if - - #if $filtering.peak_picking.pick_peaks - --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" - #end if - - #if str($filtering.activation) != "false" - --filter "activation $filtering.activation" - #end if - - #if len($filtering.indices) > 0 - --filter "index - #for $index in $filtering.indices - [${index.from},${index.to}] - #end for - " - #end if - - #if len($filtering.scan_numbers) > 0 - --filter "scanNumber - #for $scanNumber in $filtering.scanNumbers - [${scanNumber.from},${scanNumber.to}] - #end for - " - #end if - - #if $filtering.strip_it.value - --filter "stripIT" - #end if - - #if $filtering.filter_mz_windows.do_filter - --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" - #end if - - - #if $filtering.filter_ms_levels.do_filter - --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" - #end if - - #if str($filtering.etd_filtering.do_etd_filtering) == "default" - --filter "ETDFilter" - #end if - - #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" - --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" - #end if - - ## BEGIN_VERSION_3 - #if str($filtering.ms2deisotope) == "true" - --filter "MS2Deisotope" - #end if - - #if str($filtering.polarity) != "false" - --filter "polarity $filtering.polarity" - #end if - - #if str($filtering.analyzer) != "false" - --filter "analyzer $filtering.analyzer" - #end if - - ## END_VERSION_3 - - #end if - - </command> - - <inputs> - <!-- BEGIN_VERSION_RAW --> - <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/> - <!-- END_VERSION_RAW --> - - <!-- BEGIN_VERSION_DEFAULT --> - <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> - <!-- END_VERSION_DEFAULT --> - <param name="output_type" type="select" label="Output Type"> - <option value="mzML">mzML (indexed)</option> - <option value="unindexed_mzML">mzML (unindexed)</option> - <option value="mzXML">mzXML (indexed)</option> - <option value="unindexed_mzXML">mzXML (unindexed)</option> - <option value="mgf">mgf</option> - <option value="ms2">ms2</option> - </param> - <conditional name="filtering"> - <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> - - <conditional name="peak_picking"> - <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> - <option value="1">MS1 Only (1)</option> - <option value="2">MS2 Only (2)</option> - <option value="2-">MS2 and on (2-)</option> - <option value="1-">All Levels (1-)</option> - </param> - <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> - </when> - </conditional> - - - <param name="activation" type="select" label="Filter by Activation"> - <option value="false" selected="true">no</option> - <option value="ETD">ETD</option> - <option value="CID">CID</option> - <option value="SA">SA</option> - <option value="HCD">HCD</option> - <!-- BEGIN_VERSION_3 --> - <option>BIRD</option> - <option>ECD</option> - <option>IRMPD</option> - <option>PD</option> - <option>PSD</option> - <option>PQD</option> - <option>SID</option> - <option>SORI</option> - <!-- END_VERSION_3 --> - </param> - - <repeat name="indices" title="Filter Scan Indices"> - <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> - </repeat> - - <repeat name="scan_numbers" title="Filter Scan Numbers"> - <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> - </repeat> - - <conditional name="filter_mz_windows"> - <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> - <when value="false" /> - <when value="true"> - <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> - <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> - </when> - </conditional> - - - <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> - - <conditional name="filter_ms_levels"> - <param name="do_filter" type="boolean" label="Filter MS Levels" /> - <when value="false" /> - <when value="true"> - <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> - </when> - </conditional> - - <conditional name="etd_filtering"> - <param name="do_etd_filtering" type="select" label="ETD Filtering"> - <option value="none" selected="true">none</option> - <option value="default">yes (with default options)</option> - <option value="advanced">yes (show advanced options) </option> - </param> - <when value="none" /> - <when value="default" /> - <when value="advanced"> - <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> - </param> - <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> - <option value="MZ" selected="true">mz</option> - <option value="PPM">ppm</option> - </param> - <param name="remove_precursor" type="select" label="ETD Remove Precursor"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="blanket_removal" type="select" label="ETD Blanket Removal"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - </when> - </conditional> - - - <!-- BEGIN_VERSION_3 --> - <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" /> - - <param name="polarity" type="select" label="Filter by Polarity"> - <option value="false" selected="true">no</option> - <option value="positive">positive</option> - <option value="negative">negative</option> - </param> - - <param name="analyzer" type="select" label="Filter by Analyzer"> - <option value="false" selected="true">no</option> - <option value="quad">quad</option> - <option value="orbi">orbi</option> - <option value="FT">FT</option> - <option value="IT">IT</option> - <option value="TOF">TOF</option> - </param> - <!-- END_VERSION_3 --> - </when> - </conditional> - - <conditional name="settings"> - <param name="settingsType" type="select" label="Advanced Settings" help=""> - <option value="default">Use Defaults</option> - <option value="full">Full Parameter List</option> - </param> - <when value="default" /> - <when value="full"> - <param type="select" name="binary_encoding" label="Binary Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="mz_encoding" label="m/z Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> - <option value="64">64</option> - <option value="32" selected="true">32</option> - </param> - <param type="boolean" name="zlib" label="Use zlib"> - </param> - </when> - </conditional> - - - </inputs> - <outputs> - <data format="mzml" name="output"> - <change_format> - <when input="output_type" value="mzxml" format="mzxml" /> - <when input="output_type" value="unindexed_mzxml" format="mzxml" /> - <when input="output_type" value="ms2" format="ms2" /> - <when input="output_type" value="mgf" format="mgf" /> - </change_format> - </data> - </outputs> - - <requirements> - <requirement type="package">proteowizard</requirement> - </requirements> - - <help> -**What it does** - -Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. - -You can view the original documentation here_. - -.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html - ------- - -**Citation** - -For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert - - </help> -</tool>
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert2.xml Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,269 +0,0 @@ -<tool id="msconvert2" name="msconvert2" version="0.2.0"> - <!-- BEGIN_VERSION_DEFAULT --> - <description>Convert and filter a mass spec peak list</description> - <!-- END_VERSION_DEFAULT --> - - <command interpreter="python"> - msconvert_wrapper.py - --input=${input} - --output=${output} - ## BEGIN_VERSION_DEFAULT - --fromextension=${input.ext} - ## END_VERSION_DEFAULT - - - --toextension=${output_type} - - #if $settings.settingsType == "full" - --binaryencoding=${settings.binary_encoding} - --mzencoding=${settings.mz_encoding} - --intensityencoding=${settings.intensity_encoding} - --zlib=${settings.zlib} - #end if - - #if $filtering.filtering_use - - #if $filtering.precursor_recalculation.value - --filter "precursorRecalculation" - #end if - - #if $filtering.peak_picking.pick_peaks - --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" - #end if - - #if str($filtering.activation) != "false" - --filter "activation $filtering.activation" - #end if - - #if len($filtering.indices) > 0 - --filter "index - #for $index in $filtering.indices - [${index.from},${index.to}] - #end for - " - #end if - - #if len($filtering.scan_numbers) > 0 - --filter "scanNumber - #for $scanNumber in $filtering.scanNumbers - [${scanNumber.from},${scanNumber.to}] - #end for - " - #end if - - #if $filtering.strip_it.value - --filter "stripIT" - #end if - - #if $filtering.filter_mz_windows.do_filter - --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" - #end if - - - #if $filtering.filter_ms_levels.do_filter - --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" - #end if - - #if str($filtering.etd_filtering.do_etd_filtering) == "default" - --filter "ETDFilter" - #end if - - #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" - --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" - #end if - - - #end if - - </command> - - <inputs> - - <!-- BEGIN_VERSION_DEFAULT --> - <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> - <!-- END_VERSION_DEFAULT --> - <param name="output_type" type="select" label="Output Type"> - <option value="mzML">mzML (indexed)</option> - <option value="unindexed_mzML">mzML (unindexed)</option> - <option value="mzXML">mzXML (indexed)</option> - <option value="unindexed_mzXML">mzXML (unindexed)</option> - <option value="mgf">mgf</option> - <option value="ms2">ms2</option> - </param> - <conditional name="filtering"> - <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> - - <conditional name="peak_picking"> - <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> - <option value="1">MS1 Only (1)</option> - <option value="2">MS2 Only (2)</option> - <option value="2-">MS2 and on (2-)</option> - <option value="1-">All Levels (1-)</option> - </param> - <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> - </when> - </conditional> - - - <param name="activation" type="select" label="Filter by Activation"> - <option value="false" selected="true">no</option> - <option value="ETD">ETD</option> - <option value="CID">CID</option> - <option value="SA">SA</option> - <option value="HCD">HCD</option> - </param> - - <repeat name="indices" title="Filter Scan Indices"> - <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> - </repeat> - - <repeat name="scan_numbers" title="Filter Scan Numbers"> - <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> - </repeat> - - <conditional name="filter_mz_windows"> - <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> - <when value="false" /> - <when value="true"> - <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> - <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> - </when> - </conditional> - - - <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> - - <conditional name="filter_ms_levels"> - <param name="do_filter" type="boolean" label="Filter MS Levels" /> - <when value="false" /> - <when value="true"> - <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> - </when> - </conditional> - - <conditional name="etd_filtering"> - <param name="do_etd_filtering" type="select" label="ETD Filtering"> - <option value="none" selected="true">none</option> - <option value="default">yes (with default options)</option> - <option value="advanced">yes (show advanced options) </option> - </param> - <when value="none" /> - <when value="default" /> - <when value="advanced"> - <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> - </param> - <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> - <option value="MZ" selected="true">mz</option> - <option value="PPM">ppm</option> - </param> - <param name="remove_precursor" type="select" label="ETD Remove Precursor"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="blanket_removal" type="select" label="ETD Blanket Removal"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - </when> - </conditional> - - - </when> - </conditional> - - <conditional name="settings"> - <param name="settingsType" type="select" label="Advanced Settings" help=""> - <option value="default">Use Defaults</option> - <option value="full">Full Parameter List</option> - </param> - <when value="default" /> - <when value="full"> - <param type="select" name="binary_encoding" label="Binary Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="mz_encoding" label="m/z Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> - <option value="64">64</option> - <option value="32" selected="true">32</option> - </param> - <param type="boolean" name="zlib" label="Use zlib"> - </param> - </when> - </conditional> - - - </inputs> - <outputs> - <data format="mzml" name="output"> - <change_format> - <when input="output_type" value="mzxml" format="mzxml" /> - <when input="output_type" value="unindexed_mzxml" format="mzxml" /> - <when input="output_type" value="ms2" format="ms2" /> - <when input="output_type" value="mgf" format="mgf" /> - </change_format> - </data> - </outputs> - - <requirements> - <requirement type="package">proteowizard</requirement> - </requirements> - - <help> -**What it does** - -Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. - -You can view the original documentation here_. - -.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html - ------- - -**Citation** - -For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert - - </help> -</tool>
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert2_raw.xml Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,250 +0,0 @@ -<tool id="msconvert2_raw" name="msconvert2_raw" version="0.2.0"> - <!-- BEGIN_VERSION_RAW --> - <description>Convert and filter a Thermo Finnigan RAW file</description> - <!-- END_VERSION_RAW --> - - <command interpreter="python"> - msconvert_wrapper.py - --input=${input} - --output=${output} - - ## BEGIN_VERSION_RAW - --fromextension=RAW - ## END_VERSION_RAW - - --toextension=${output_type} - - #if $settings.settingsType == "full" - --binaryencoding=${settings.binary_encoding} - --mzencoding=${settings.mz_encoding} - --intensityencoding=${settings.intensity_encoding} - --zlib=${settings.zlib} - #end if - - #if $filtering.filtering_use - - #if $filtering.precursor_recalculation.value - --filter "precursorRecalculation" - #end if - - #if $filtering.peak_picking.pick_peaks - --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" - #end if - - #if str($filtering.activation) != "false" - --filter "activation $filtering.activation" - #end if - - #if len($filtering.indices) > 0 - --filter "index - #for $index in $filtering.indices - [${index.from},${index.to}] - #end for - " - #end if - - #if len($filtering.scan_numbers) > 0 - --filter "scanNumber - #for $scanNumber in $filtering.scanNumbers - [${scanNumber.from},${scanNumber.to}] - #end for - " - #end if - - #if $filtering.strip_it.value - --filter "stripIT" - #end if - - #if $filtering.filter_mz_windows.do_filter - --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" - #end if - - - #if $filtering.filter_ms_levels.do_filter - --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" - #end if - - #if str($filtering.etd_filtering.do_etd_filtering) == "default" - --filter "ETDFilter" - #end if - - #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" - --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" - #end if - - - #end if - - </command> - - <inputs> - <!-- BEGIN_VERSION_RAW --> - <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/> - <!-- END_VERSION_RAW --> - - <param name="output_type" type="select" label="Output Type"> - <option value="mzML">mzML (indexed)</option> - <option value="unindexed_mzML">mzML (unindexed)</option> - <option value="mzXML">mzXML (indexed)</option> - <option value="unindexed_mzXML">mzXML (unindexed)</option> - <option value="mgf">mgf</option> - <option value="ms2">ms2</option> - </param> - <conditional name="filtering"> - <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> - - <conditional name="peak_picking"> - <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> - <option value="1">MS1 Only (1)</option> - <option value="2">MS2 Only (2)</option> - <option value="2-">MS2 and on (2-)</option> - <option value="1-">All Levels (1-)</option> - </param> - <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> - </when> - </conditional> - - - <param name="activation" type="select" label="Filter by Activation"> - <option value="false" selected="true">no</option> - <option value="ETD">ETD</option> - <option value="CID">CID</option> - <option value="SA">SA</option> - <option value="HCD">HCD</option> - </param> - - <repeat name="indices" title="Filter Scan Indices"> - <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> - </repeat> - - <repeat name="scan_numbers" title="Filter Scan Numbers"> - <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> - </repeat> - - <conditional name="filter_mz_windows"> - <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> - <when value="false" /> - <when value="true"> - <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> - <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> - </when> - </conditional> - - - <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> - - <conditional name="filter_ms_levels"> - <param name="do_filter" type="boolean" label="Filter MS Levels" /> - <when value="false" /> - <when value="true"> - <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> - </when> - </conditional> - - <conditional name="etd_filtering"> - <param name="do_etd_filtering" type="select" label="ETD Filtering"> - <option value="none" selected="true">none</option> - <option value="default">yes (with default options)</option> - <option value="advanced">yes (show advanced options) </option> - </param> - <when value="none" /> - <when value="default" /> - <when value="advanced"> - <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> - </param> - <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> - <option value="MZ" selected="true">mz</option> - <option value="PPM">ppm</option> - </param> - <param name="remove_precursor" type="select" label="ETD Remove Precursor"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="blanket_removal" type="select" label="ETD Blanket Removal"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - </when> - </conditional> - - - </when> - </conditional> - - <conditional name="settings"> - <param name="settingsType" type="select" label="Advanced Settings" help=""> - <option value="default">Use Defaults</option> - <option value="full">Full Parameter List</option> - </param> - <when value="default" /> - <when value="full"> - <param type="select" name="binary_encoding" label="Binary Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="mz_encoding" label="m/z Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> - <option value="64">64</option> - <option value="32" selected="true">32</option> - </param> - <param type="boolean" name="zlib" label="Use zlib"> - </param> - </when> - </conditional> - - - </inputs> - <outputs> - <data format="mzml" name="output"> - <change_format> - <when input="output_type" value="mzxml" format="mzxml" /> - <when input="output_type" value="unindexed_mzxml" format="mzxml" /> - <when input="output_type" value="ms2" format="ms2" /> - <when input="output_type" value="mgf" format="mgf" /> - </change_format> - </data> - </outputs> - - <requirements> - <requirement type="package">proteowizard</requirement> - </requirements> - - <help> -**What it does** - -Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. - -You can view the original documentation here_. - -.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html - ------- - -**Citation** - -For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert - - </help> -</tool>
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert3.xml Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,311 +0,0 @@ -<tool id="msconvert3" name="msconvert3" version="0.2.0"> - <!-- BEGIN_VERSION_DEFAULT --> - <description>Convert and filter a mass spec peak list</description> - <!-- END_VERSION_DEFAULT --> - - <command interpreter="python"> - msconvert_wrapper.py - --input=${input} - --output=${output} - ## BEGIN_VERSION_DEFAULT - --fromextension=${input.ext} - ## END_VERSION_DEFAULT - - - --toextension=${output_type} - - #if $settings.settingsType == "full" - --binaryencoding=${settings.binary_encoding} - --mzencoding=${settings.mz_encoding} - --intensityencoding=${settings.intensity_encoding} - --zlib=${settings.zlib} - #end if - - #if $filtering.filtering_use - - #if $filtering.precursor_recalculation.value - --filter "precursorRecalculation" - #end if - - #if $filtering.peak_picking.pick_peaks - --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" - #end if - - #if str($filtering.activation) != "false" - --filter "activation $filtering.activation" - #end if - - #if len($filtering.indices) > 0 - --filter "index - #for $index in $filtering.indices - [${index.from},${index.to}] - #end for - " - #end if - - #if len($filtering.scan_numbers) > 0 - --filter "scanNumber - #for $scanNumber in $filtering.scanNumbers - [${scanNumber.from},${scanNumber.to}] - #end for - " - #end if - - #if $filtering.strip_it.value - --filter "stripIT" - #end if - - #if $filtering.filter_mz_windows.do_filter - --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" - #end if - - - #if $filtering.filter_ms_levels.do_filter - --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" - #end if - - #if str($filtering.etd_filtering.do_etd_filtering) == "default" - --filter "ETDFilter" - #end if - - #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" - --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" - #end if - - ## BEGIN_VERSION_3 - #if str($filtering.ms2deisotope) == "true" - --filter "MS2Deisotope" - #end if - - #if str($filtering.polarity) != "false" - --filter "polarity $filtering.polarity" - #end if - - #if str($filtering.analyzer) != "false" - --filter "analyzer $filtering.analyzer" - #end if - - ## END_VERSION_3 - - #end if - - </command> - - <inputs> - - <!-- BEGIN_VERSION_DEFAULT --> - <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> - <!-- END_VERSION_DEFAULT --> - <param name="output_type" type="select" label="Output Type"> - <option value="mzML">mzML (indexed)</option> - <option value="unindexed_mzML">mzML (unindexed)</option> - <option value="mzXML">mzXML (indexed)</option> - <option value="unindexed_mzXML">mzXML (unindexed)</option> - <option value="mgf">mgf</option> - <option value="ms2">ms2</option> - </param> - <conditional name="filtering"> - <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> - - <conditional name="peak_picking"> - <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> - <option value="1">MS1 Only (1)</option> - <option value="2">MS2 Only (2)</option> - <option value="2-">MS2 and on (2-)</option> - <option value="1-">All Levels (1-)</option> - </param> - <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> - </when> - </conditional> - - - <param name="activation" type="select" label="Filter by Activation"> - <option value="false" selected="true">no</option> - <option value="ETD">ETD</option> - <option value="CID">CID</option> - <option value="SA">SA</option> - <option value="HCD">HCD</option> - <!-- BEGIN_VERSION_3 --> - <option>BIRD</option> - <option>ECD</option> - <option>IRMPD</option> - <option>PD</option> - <option>PSD</option> - <option>PQD</option> - <option>SID</option> - <option>SORI</option> - <!-- END_VERSION_3 --> - </param> - - <repeat name="indices" title="Filter Scan Indices"> - <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> - </repeat> - - <repeat name="scan_numbers" title="Filter Scan Numbers"> - <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> - </repeat> - - <conditional name="filter_mz_windows"> - <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> - <when value="false" /> - <when value="true"> - <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> - <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> - </when> - </conditional> - - - <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> - - <conditional name="filter_ms_levels"> - <param name="do_filter" type="boolean" label="Filter MS Levels" /> - <when value="false" /> - <when value="true"> - <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> - </when> - </conditional> - - <conditional name="etd_filtering"> - <param name="do_etd_filtering" type="select" label="ETD Filtering"> - <option value="none" selected="true">none</option> - <option value="default">yes (with default options)</option> - <option value="advanced">yes (show advanced options) </option> - </param> - <when value="none" /> - <when value="default" /> - <when value="advanced"> - <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> - </param> - <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> - <option value="MZ" selected="true">mz</option> - <option value="PPM">ppm</option> - </param> - <param name="remove_precursor" type="select" label="ETD Remove Precursor"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="blanket_removal" type="select" label="ETD Blanket Removal"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - </when> - </conditional> - - - <!-- BEGIN_VERSION_3 --> - <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" /> - - <param name="polarity" type="select" label="Filter by Polarity"> - <option value="false" selected="true">no</option> - <option value="positive">positive</option> - <option value="negative">negative</option> - </param> - - <param name="analyzer" type="select" label="Filter by Analyzer"> - <option value="false" selected="true">no</option> - <option value="quad">quad</option> - <option value="orbi">orbi</option> - <option value="FT">FT</option> - <option value="IT">IT</option> - <option value="TOF">TOF</option> - </param> - <!-- END_VERSION_3 --> - </when> - </conditional> - - <conditional name="settings"> - <param name="settingsType" type="select" label="Advanced Settings" help=""> - <option value="default">Use Defaults</option> - <option value="full">Full Parameter List</option> - </param> - <when value="default" /> - <when value="full"> - <param type="select" name="binary_encoding" label="Binary Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="mz_encoding" label="m/z Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> - <option value="64">64</option> - <option value="32" selected="true">32</option> - </param> - <param type="boolean" name="zlib" label="Use zlib"> - </param> - </when> - </conditional> - - - </inputs> - <outputs> - <data format="mzml" name="output"> - <change_format> - <when input="output_type" value="mzxml" format="mzxml" /> - <when input="output_type" value="unindexed_mzxml" format="mzxml" /> - <when input="output_type" value="ms2" format="ms2" /> - <when input="output_type" value="mgf" format="mgf" /> - </change_format> - </data> - </outputs> - - <requirements> - <requirement type="package">proteowizard</requirement> - </requirements> - - <help> -**What it does** - -Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. - -You can view the original documentation here_. - -.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html - ------- - -**Citation** - -For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert - - </help> -</tool>
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert3_raw.xml Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,292 +0,0 @@ -<tool id="msconvert3_raw" name="msconvert3_raw" version="0.2.0"> - <!-- BEGIN_VERSION_RAW --> - <description>Convert and filter a Thermo Finnigan RAW file</description> - <!-- END_VERSION_RAW --> - - <command interpreter="python"> - msconvert_wrapper.py - --input=${input} - --output=${output} - - ## BEGIN_VERSION_RAW - --fromextension=RAW - ## END_VERSION_RAW - - --toextension=${output_type} - - #if $settings.settingsType == "full" - --binaryencoding=${settings.binary_encoding} - --mzencoding=${settings.mz_encoding} - --intensityencoding=${settings.intensity_encoding} - --zlib=${settings.zlib} - #end if - - #if $filtering.filtering_use - - #if $filtering.precursor_recalculation.value - --filter "precursorRecalculation" - #end if - - #if $filtering.peak_picking.pick_peaks - --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" - #end if - - #if str($filtering.activation) != "false" - --filter "activation $filtering.activation" - #end if - - #if len($filtering.indices) > 0 - --filter "index - #for $index in $filtering.indices - [${index.from},${index.to}] - #end for - " - #end if - - #if len($filtering.scan_numbers) > 0 - --filter "scanNumber - #for $scanNumber in $filtering.scanNumbers - [${scanNumber.from},${scanNumber.to}] - #end for - " - #end if - - #if $filtering.strip_it.value - --filter "stripIT" - #end if - - #if $filtering.filter_mz_windows.do_filter - --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" - #end if - - - #if $filtering.filter_ms_levels.do_filter - --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" - #end if - - #if str($filtering.etd_filtering.do_etd_filtering) == "default" - --filter "ETDFilter" - #end if - - #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" - --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" - #end if - - ## BEGIN_VERSION_3 - #if str($filtering.ms2deisotope) == "true" - --filter "MS2Deisotope" - #end if - - #if str($filtering.polarity) != "false" - --filter "polarity $filtering.polarity" - #end if - - #if str($filtering.analyzer) != "false" - --filter "analyzer $filtering.analyzer" - #end if - - ## END_VERSION_3 - - #end if - - </command> - - <inputs> - <!-- BEGIN_VERSION_RAW --> - <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/> - <!-- END_VERSION_RAW --> - - <param name="output_type" type="select" label="Output Type"> - <option value="mzML">mzML (indexed)</option> - <option value="unindexed_mzML">mzML (unindexed)</option> - <option value="mzXML">mzXML (indexed)</option> - <option value="unindexed_mzXML">mzXML (unindexed)</option> - <option value="mgf">mgf</option> - <option value="ms2">ms2</option> - </param> - <conditional name="filtering"> - <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> - - <conditional name="peak_picking"> - <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> - <when value="false" /> - <when value="true"> - <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> - <option value="1">MS1 Only (1)</option> - <option value="2">MS2 Only (2)</option> - <option value="2-">MS2 and on (2-)</option> - <option value="1-">All Levels (1-)</option> - </param> - <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> - </when> - </conditional> - - - <param name="activation" type="select" label="Filter by Activation"> - <option value="false" selected="true">no</option> - <option value="ETD">ETD</option> - <option value="CID">CID</option> - <option value="SA">SA</option> - <option value="HCD">HCD</option> - <!-- BEGIN_VERSION_3 --> - <option>BIRD</option> - <option>ECD</option> - <option>IRMPD</option> - <option>PD</option> - <option>PSD</option> - <option>PQD</option> - <option>SID</option> - <option>SORI</option> - <!-- END_VERSION_3 --> - </param> - - <repeat name="indices" title="Filter Scan Indices"> - <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> - </repeat> - - <repeat name="scan_numbers" title="Filter Scan Numbers"> - <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> - </repeat> - - <conditional name="filter_mz_windows"> - <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> - <when value="false" /> - <when value="true"> - <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> - <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> - </when> - </conditional> - - - <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> - - <conditional name="filter_ms_levels"> - <param name="do_filter" type="boolean" label="Filter MS Levels" /> - <when value="false" /> - <when value="true"> - <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> - <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> - </when> - </conditional> - - <conditional name="etd_filtering"> - <param name="do_etd_filtering" type="select" label="ETD Filtering"> - <option value="none" selected="true">none</option> - <option value="default">yes (with default options)</option> - <option value="advanced">yes (show advanced options) </option> - </param> - <when value="none" /> - <when value="default" /> - <when value="advanced"> - <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> - </param> - <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> - <option value="MZ" selected="true">mz</option> - <option value="PPM">ppm</option> - </param> - <param name="remove_precursor" type="select" label="ETD Remove Precursor"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - <param name="blanket_removal" type="select" label="ETD Blanket Removal"> - <option value="true" selected="true">yes</option> - <option value="false">no</option> - </param> - </when> - </conditional> - - - <!-- BEGIN_VERSION_3 --> - <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" /> - - <param name="polarity" type="select" label="Filter by Polarity"> - <option value="false" selected="true">no</option> - <option value="positive">positive</option> - <option value="negative">negative</option> - </param> - - <param name="analyzer" type="select" label="Filter by Analyzer"> - <option value="false" selected="true">no</option> - <option value="quad">quad</option> - <option value="orbi">orbi</option> - <option value="FT">FT</option> - <option value="IT">IT</option> - <option value="TOF">TOF</option> - </param> - <!-- END_VERSION_3 --> - </when> - </conditional> - - <conditional name="settings"> - <param name="settingsType" type="select" label="Advanced Settings" help=""> - <option value="default">Use Defaults</option> - <option value="full">Full Parameter List</option> - </param> - <when value="default" /> - <when value="full"> - <param type="select" name="binary_encoding" label="Binary Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="mz_encoding" label="m/z Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> - <option value="64">64</option> - <option value="32" selected="true">32</option> - </param> - <param type="boolean" name="zlib" label="Use zlib"> - </param> - </when> - </conditional> - - - </inputs> - <outputs> - <data format="mzml" name="output"> - <change_format> - <when input="output_type" value="mzxml" format="mzxml" /> - <when input="output_type" value="unindexed_mzxml" format="mzxml" /> - <when input="output_type" value="ms2" format="ms2" /> - <when input="output_type" value="mgf" format="mgf" /> - </change_format> - </data> - </outputs> - - <requirements> - <requirement type="package">proteowizard</requirement> - </requirements> - - <help> -**What it does** - -Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. - -You can view the original documentation here_. - -.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html - ------- - -**Citation** - -For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert - - </help> -</tool>
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert_raw_wrapper.py Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,124 +0,0 @@ -#!/usr/bin/env python -import optparse -import os -import sys -import tempfile -import shutil -import subprocess -import re -from os.path import basename -import logging - -assert sys.version_info[:2] >= ( 2, 6 ) - -log = logging.getLogger(__name__) -working_directory = os.getcwd() -tmp_stderr_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stderr').name -tmp_stdout_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stdout').name - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - -def read_stderr(): - stderr = '' - if(os.path.exists(tmp_stderr_name)): - with open(tmp_stderr_name, 'rb') as tmp_stderr: - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read(buffsize) - if not stderr or len(stderr) % buffsize != 0: - break - except OverflowError: - pass - return stderr - -def execute(command, stdin=None): - with open(tmp_stderr_name, 'wb') as tmp_stderr: - with open(tmp_stdout_name, 'wb') as tmp_stdout: - proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) - returncode = proc.wait() - if returncode != 0: - raise Exception, "Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()) - -def delete_file(path): - if os.path.exists(path): - try: - os.remove(path) - except: - pass - -def delete_directory(directory): - if os.path.exists(directory): - try: - shutil.rmtree(directory) - except: - pass - -def symlink(source, link_name): - import platform - if platform.system() == 'Windows': - import win32file - win32file.CreateSymbolicLink(source, link_name, 1) - else: - os.symlink(source, link_name) - - -def copy_to_working_directory(data_file, relative_path): - if os.path.abspath(data_file) != os.path.abspath(relative_path): - shutil.copy(data_file, relative_path) - return relative_path - -def __main__(): - run_script() - -#ENDTEMPLATE - -to_extensions = ['mzML', 'mzXML', 'mgf', 'txt', 'ms2', 'cms2'] - -def str_to_bool(v): - """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """ - return v.lower() in ["yes", "true", "t", "1"] - - -def run_script(): - parser = optparse.OptionParser() - parser.add_option('--input', dest='input') - parser.add_option('--output', dest='output') - parser.add_option('--fromextension', dest='fromextension') - parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions) - parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64']) - parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64']) - parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64']) - parser.add_option('--noindex', dest='noindex') - parser.add_option('--zlib', dest='zlib') - parser.add_option('--filter', dest='filter', action='append', default=[]) - - (options, args) = parser.parse_args() - - filter_commands = '' - for filter in options.filter: - filter_commands = "%s --filter \"%s\"" % (filter_commands, filter) - - input_file = 'input.%s' % options.fromextension - copy_to_working_directory(options.input, input_file) - os.mkdir('output') - cmd = "msconvert --%s -o output" % (options.toextension) - if str_to_bool(options.noindex): - cmd = "%s %s" % (cmd, "--noindex") - if str_to_bool(options.zlib): - cmd = "%s %s" % (cmd, "--zlib") - cmd = "%s --%s" % (cmd, options.binaryencoding) - cmd = "%s --mz%s" % (cmd, options.mzencoding) - cmd = "%s --inten%s" % (cmd, options.intensityencoding) - cmd = "%s %s" % (cmd, input_file) - cmd = "%s %s" % (cmd, filter_commands) - print cmd - execute(cmd) - output_files = os.listdir('output') - assert len(output_files) == 1 - output_file = output_files[0] - shutil.copy(os.path.join('output', output_file), options.output) - -if __name__ == '__main__': __main__()
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert_subset.xml Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,105 +0,0 @@ -<tool id="msconvert_subset" name="Subset Peak List" version="0.2.0"> - <description>against list of scan numbers or indices.</description> - <command interpreter="python"> - msconvert_wrapper.py - --input=${input} - --output=${output} - --fromextension=${input.ext} - --toextension=${output_type} - #if $settings.settingsType == "full" - --binaryencoding=${settings.binary_encoding} - --mzencoding=${settings.mz_encoding} - --intensityencoding=${settings.intensity_encoding} - --zlib=${settings.zlib} - #end if - #if $filter.filterType == "scan_number" - --filter_numbers_table="$filter.filterList" - #end if - #if $filter.filterType == "scan_indices" - --filter_indices_table="$filter.filterList" - #end if - </command> - - <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="mzML">mzML (indexed)</option> - <option value="unindexed_mzML">mzML (unindexed)</option> - <option value="mzXML">mzXML (indexed)</option> - <option value="unindexed_mzXML">mzXML (unindexed)</option> - <option value="mgf">mgf</option> - <option value="ms2">ms2</option> - </param> - <conditional name="filter"> - <param name="filterType" type="select" label="Filter by" help=""> - <option value="scan_number" selected="true">Scan Number</option> - <option value="scan_index">Scan Index</option> - </param> - <when value="scan_number"> - <param format="text" name="filterList" type="data" label="Scan Numbers"/> - </when> - <when value="scan_index"> - <param format="text" name="filterList" type="data" label="Scan Indices"/> - </when> - </conditional> - <conditional name="settings"> - <param name="settingsType" type="select" label="Advanced msconvert Settings" help=""> - <option value="default">Use Defaults</option> - <option value="full">Full Parameter List</option> - </param> - <when value="default" /> - <when value="full"> - <param type="select" name="binary_encoding" label="Binary Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="mz_encoding" label="m/z Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> - <option value="64">64</option> - <option value="32" selected="true">32</option> - </param> - <param type="boolean" name="zlib" label="Use zlib"> - </param> - </when> - </conditional> - </inputs> - <outputs> - <data format="mzml" name="output"> - <change_format> - <when input="output_type" value="mzxml" format="mzxml" /> - <when input="output_type" value="unindexed_mzxml" format="mzxml" /> - <when input="output_type" value="ms2" format="ms2" /> - <when input="output_type" value="mgf" format="mgf" /> - </change_format> - </data> - </outputs> - - <requirements> - <requirement type="package">proteowizard</requirement> - </requirements> - - <help> - </help> -</tool>
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert_wrapper.py Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,182 +0,0 @@ -#!/usr/bin/env python -import optparse -import os -import sys -import tempfile -import shutil -import subprocess -import re -from os.path import basename -import logging - -assert sys.version_info[:2] >= ( 2, 6 ) - -log = logging.getLogger(__name__) -working_directory = os.getcwd() -tmp_stderr_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stderr').name -tmp_stdout_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stdout').name - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - -def read_stderr(): - stderr = '' - if(os.path.exists(tmp_stderr_name)): - with open(tmp_stderr_name, 'rb') as tmp_stderr: - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read(buffsize) - if not stderr or len(stderr) % buffsize != 0: - break - except OverflowError: - pass - return stderr - -def execute(command, stdin=None): - try: - with open(tmp_stderr_name, 'wb') as tmp_stderr: - with open(tmp_stdout_name, 'wb') as tmp_stdout: - proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) - returncode = proc.wait() - if returncode != 0: - raise Exception, "Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()) - finally: - print open(tmp_stderr_name, "r").read() - print open(tmp_stdout_name, "r").read() - - -def delete_file(path): - if os.path.exists(path): - try: - os.remove(path) - except: - pass - -def delete_directory(directory): - if os.path.exists(directory): - try: - shutil.rmtree(directory) - except: - pass - -def symlink(source, link_name): - import platform - if platform.system() == 'Windows': - import win32file - win32file.CreateSymbolicLink(source, link_name, 1) - else: - os.symlink(source, link_name) - - -def copy_to_working_directory(data_file, relative_path): - if os.path.abspath(data_file) != os.path.abspath(relative_path): - shutil.copy(data_file, relative_path) - return relative_path - -def __main__(): - run_script() - -#ENDTEMPLATE - -to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'txt', 'ms2', 'cms2'] - - -def str_to_bool(v): - """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """ - return v.lower() in ["yes", "true", "t", "1"] - - -def _add_filter(filters_file, contents): - filters_file.write("filter=\"%s\"\n" % contents) - - -def _read_table_numbers(path): - unique_numbers = set([]) - input = open(path, "r") - first_line = True - for line in input: - if not line: - continue - line = line.strip() - if line.startswith("#"): - first_line = False - continue - match = re.match("\d+", line) - if match: - unique_numbers.add(int(match.group())) - first_line = False - return unique_numbers - - -def _add_filter_line_from_file(file, filter_file, filter_prefix): - if not file: - return - numbers = _read_table_numbers(file) - msconvert_int_set = " ".join([str(number) for number in numbers]) - _add_filter(filter_file, "%s %s" % (filter_prefix, msconvert_int_set)) - - -def _create_filters_file(options): - filters_file_path = "filters" - filters_file = open(filters_file_path, "w") - if options.filters_file: - filters_file.write(open(options.filters_file, "r").read()) - for filter in options.filter: - _add_filter(filters_file, filter) - _add_filter_line_from_file(options.filter_indices_table, filters_file, "index") - _add_filter_line_from_file(options.filter_numbers_table, filters_file, "scanNumber") - - filters_file.close() - print open(filters_file_path, "r").read() - return filters_file_path - - -def run_script(): - parser = optparse.OptionParser() - parser.add_option('--input', dest='input') - parser.add_option('--output', dest='output') - parser.add_option('--fromextension', dest='fromextension') - parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions) - parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64']) - parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64']) - parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64']) - parser.add_option('--zlib', dest='zlib', default="false") - parser.add_option('--filter', dest='filter', action='append', default=[]) - parser.add_option('--filters_file', dest='filters_file', default=None) - parser.add_option('--filter_indices_table', default=None) - parser.add_option('--filter_numbers_table', default=None) - - (options, args) = parser.parse_args() - - input_file = 'input.%s' % options.fromextension - copy_to_working_directory(options.input, input_file) - os.mkdir('output') - to_extension = options.toextension - if to_extension.startswith("unindexed_"): - to_extension = to_extension[len("unindexed_"):] - to_params = "--noindex" - else: - to_params = "" - cmd = "msconvert --%s %s -o output" % (to_extension, to_params) - if str_to_bool(options.zlib): - cmd = "%s %s" % (cmd, "--zlib") - if options.binaryencoding: - cmd = "%s --%s" % (cmd, options.binaryencoding) - if options.mzencoding: - cmd = "%s --mz%s" % (cmd, options.mzencoding) - if options.intensityencoding: - cmd = "%s --inten%s" % (cmd, options.intensityencoding) - cmd = "%s %s" % (cmd, input_file) - filters_file_path = _create_filters_file(options) - cmd = "%s -c %s" % (cmd, filters_file_path) - print cmd - execute(cmd) - output_files = os.listdir('output') - assert len(output_files) == 1 - output_file = output_files[0] - shutil.copy(os.path.join('output', output_file), options.output) - - -if __name__ == '__main__': __main__()
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/update.sh Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +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 - -# 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
--- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/update_repo.sh Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -#!/bin/bash - -sed -e '/BEGIN_VERSION_RAW/,/END_VERSION_RAW/d' -e '/BEGIN_VERSION_3/,/END_VERSION_3/d' -e 's/\$VERSION/2/g' -e 's/\$DESCRIPTION//g' msconvert.xml.template > msconvert2.xml -sed -e '/BEGIN_VERSION_DEFAULT/,/END_VERSION_DEFAULT/d' -e '/BEGIN_VERSION_3/,/END_VERSION_3/d' -e 's/\$VERSION/2/g' -e 's/\$DESCRIPTION/_raw/g' msconvert.xml.template > msconvert2_raw.xml - - -sed -e '/BEGIN_VERSION_RAW/,/END_VERSION_RAW/d' -e 's/\$VERSION/3/g' -e 's/\$DESCRIPTION//g' msconvert.xml.template > msconvert3.xml -sed -e '/BEGIN_VERSION_DEFAULT/,/END_VERSION_DEFAULT/d' -e 's/\$VERSION/3/g' -e 's/\$DESCRIPTION/_raw/g' msconvert.xml.template > msconvert3_raw.xml -