# HG changeset patch # User jmchilton # Date 1348027925 14400 # Node ID d2e7c70eb815c14c0845e68f40d5baa764daef02 # Parent 942cec8d04c709410cc19336cbcc6de0db36a0f5 Deleted selected files diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/LICENSE --- 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. 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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. diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/README.md --- 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. diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/README_GALAXYP.md --- 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. diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/README_REPO.md --- 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+). - - diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert.xml.template --- 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 @@ - - - Convert and filter a Thermo Finnigan RAW file - - - Convert and filter a mass spec peak list - - - - 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 $filtering.analyzer" - #end if - - ## END_VERSION_3 - - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - proteowizard - - - -**What it does** - -Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. - -You can view the original documentation here_. - -.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html - ------- - -**Citation** - -For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert - - - diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert2.xml --- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert2.xml Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,269 +0,0 @@ - - - Convert and filter a mass spec peak list - - - - msconvert_wrapper.py - --input=${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 $filtering.etd_filtering.matching_tolerance_units" - #end if - - - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - proteowizard - - - -**What it does** - -Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. - -You can view the original documentation here_. - -.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html - ------- - -**Citation** - -For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert - - - diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert2_raw.xml --- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert2_raw.xml Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,250 +0,0 @@ - - - Convert and filter a Thermo Finnigan RAW file - - - - msconvert_wrapper.py - --input=${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 $filtering.etd_filtering.matching_tolerance_units" - #end if - - - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - proteowizard - - - -**What it does** - -Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. - -You can view the original documentation here_. - -.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html - ------- - -**Citation** - -For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert - - - diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert3.xml --- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert3.xml Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,311 +0,0 @@ - - - Convert and filter a mass spec peak list - - - - msconvert_wrapper.py - --input=${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 $filtering.analyzer" - #end if - - ## END_VERSION_3 - - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - proteowizard - - - -**What it does** - -Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. - -You can view the original documentation here_. - -.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html - ------- - -**Citation** - -For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert - - - diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert3_raw.xml --- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert3_raw.xml Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,292 +0,0 @@ - - - Convert and filter a Thermo Finnigan RAW file - - - - msconvert_wrapper.py - --input=${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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - proteowizard - - - -**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 - - - diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert_raw_wrapper.py --- 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__() diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert_subset.xml --- 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 @@ - - against list of scan numbers or indices. - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - proteowizard - - - - - diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert_wrapper.py --- 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__() diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/update.sh --- 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 diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/update_repo.sh --- 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 - diff -r 942cec8d04c7 -r d2e7c70eb815 galaxyp-galaxyp-toolshed-msconvert-9663ae998499/version --- a/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/version Wed Sep 19 00:07:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -0.2.0 \ No newline at end of file