| Next changeset 1:861e3f0c2bb6 (2013-02-14) |
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LICENSE README.md README_GALAXYP.md README_REPO.md msconvert.xml.template msconvert2.xml msconvert2_raw.xml msconvert3.xml msconvert3_raw.xml msconvert_raw_wrapper.py msconvert_subset.xml msconvert_wrapper.py update.sh update_repo.sh version |
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| diff -r 000000000000 -r 10f4a0356342 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Wed Dec 19 00:10:08 2012 -0500 |
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| b'@@ -0,0 +1,202 @@\n+\n+ Apache License\n+ Version 2.0, January 2004\n+ http://www.apache.org/licenses/\n+\n+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n+\n+ 1. Definitions.\n+\n+ "License" shall mean the terms and conditions for use, reproduction,\n+ and distribution as defined by Sections 1 through 9 of this document.\n+\n+ "Licensor" shall mean the copyright owner or entity authorized by\n+ the copyright owner that is granting the License.\n+\n+ "Legal Entity" shall mean the union of the acting entity and all\n+ other entities that control, are controlled by, or are under common\n+ control with that entity. 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Subject to the terms and conditions of\n+ this License, each Contributor hereby grants to You a perpetual,\n+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable\n+ copyright license to reproduce, prepare Derivative Works of,\n+ publicly display, publicly perform, sublicense, and distribute the\n+ Work and such Derivative Works in Source or Obj'..b'ensor shall be under the terms and conditions of\n+ this License, without any additional terms or conditions.\n+ Notwithstanding the above, nothing herein shall supersede or modify\n+ the terms of any separate license agreement you may have executed\n+ with Licensor regarding such Contributions.\n+\n+ 6. Trademarks. This License does not grant permission to use the trade\n+ names, trademarks, service marks, or product names of the Licensor,\n+ except as required for reasonable and customary use in describing the\n+ origin of the Work and reproducing the content of the NOTICE file.\n+\n+ 7. Disclaimer of Warranty. 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However, in accepting such obligations, You may act only\n+ on Your own behalf and on Your sole responsibility, not on behalf\n+ of any other Contributor, and only if You agree to indemnify,\n+ defend, and hold each Contributor harmless for any liability\n+ incurred by, or claims asserted against, such Contributor by reason\n+ of your accepting any such warranty or additional liability.\n+\n+ END OF TERMS AND CONDITIONS\n+\n+ APPENDIX: How to apply the Apache License to your work.\n+\n+ To apply the Apache License to your work, attach the following\n+ boilerplate notice, with the fields enclosed by brackets "[]"\n+ replaced with your own identifying information. (Don\'t include\n+ the brackets!) The text should be enclosed in the appropriate\n+ comment syntax for the file format. We also recommend that a\n+ file or class name and description of purpose be included on the\n+ same "printed page" as the copyright notice for easier\n+ identification within third-party archives.\n+\n+ Copyright 2012 University of Minnesota\n+\n+ Licensed under the Apache License, Version 2.0 (the "License");\n+ you may not use this file except in compliance with the License.\n+ You may obtain a copy of the License at\n+\n+ http://www.apache.org/licenses/LICENSE-2.0\n+\n+ Unless required by applicable law or agreed to in writing, software\n+ distributed under the License is distributed on an "AS IS" BASIS,\n+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n+ See the License for the specific language governing permissions and\n+ limitations under the License.\n' |
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| diff -r 000000000000 -r 10f4a0356342 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Dec 19 00:10:08 2012 -0500 |
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| @@ -0,0 +1,47 @@ +# msconvert + +This repository contains Galaxy tool wrappers for msconvert, part of +the ProteoWizard (http://proteowizard.sourceforge.net/) package. + +# Installing + +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+). +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. |
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| diff -r 000000000000 -r 10f4a0356342 README_GALAXYP.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_GALAXYP.md Wed Dec 19 00:10:08 2012 -0500 |
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| @@ -0,0 +1,22 @@ +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. |
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| diff -r 000000000000 -r 10f4a0356342 README_REPO.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_REPO.md Wed Dec 19 00:10:08 2012 -0500 |
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| @@ -0,0 +1,25 @@ +# msconvert + +This repository contains Galaxy tool wrappers for msconvert, part of +the ProteoWizard (http://proteowizard.sourceforge.net/) package. + +# Installing + +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+). |
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| diff -r 000000000000 -r 10f4a0356342 msconvert.xml.template --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert.xml.template Wed Dec 19 00:10:08 2012 -0500 |
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| b'@@ -0,0 +1,386 @@\n+<tool id="msconvert$VERSION$DESCRIPTION" name="msconvert$VERSION$DESCRIPTION" version="0.1.0">\n+ <!-- BEGIN_VERSION_RAW -->\n+ <description>Convert and filter a Thermo Finnigan RAW file</description>\n+ <!-- END_VERSION_RAW -->\n+ <!-- BEGIN_VERSION_DEFAULT -->\n+ <description>Convert and filter a mass spec peak list</description>\n+ <!-- END_VERSION_DEFAULT -->\n+\n+ <command interpreter="python">\n+ msconvert_wrapper.py \n+ --input=${input}\n+ #if hasattr($input, \'display_name\')\n+ --input_name=\'${input.display_name}\'\n+ #end if\n+ --output=${output} \n+ ## BEGIN_VERSION_DEFAULT \n+ --fromextension=${input.ext} \n+ ## END_VERSION_DEFAULT\n+\n+ ## BEGIN_VERSION_RAW\n+ --fromextension=RAW\n+ ## END_VERSION_RAW\n+\n+ --toextension=${output_type} \n+\n+ #if $settings.settingsType == "full"\n+ --binaryencoding=${settings.binary_encoding} \n+ --mzencoding=${settings.mz_encoding} \n+ --intensityencoding=${settings.intensity_encoding}\n+ --zlib=${settings.zlib}\n+ #end if\n+\n+ #if $filtering.filtering_use\n+\n+ #if $filtering.precursor_recalculation.value\n+ --filter "precursorRecalculation"\n+ #end if\n+\n+ #if $filtering.peak_picking.pick_peaks\n+ --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"\n+ #end if\n+\n+ #if str($filtering.activation) != "false"\n+ --filter "activation $filtering.activation"\n+ #end if\n+\n+ #if len($filtering.indices) > 0\n+ --filter "index\n+ #for $index in $filtering.indices\n+ [${index.from},${index.to}]\n+ #end for\n+ "\n+ #end if\n+\n+ #if len($filtering.scan_numbers) > 0\n+ --filter "scanNumber\n+ #for $scan_number in $filtering.scan_numbers\n+ [${scan_number.from},${scan_number.to}]\n+ #end for\n+ "\n+ #end if\n+\n+ #for threshold_entry in $filtering.threshold_repeat\n+ --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"\n+ #end for\n+\n+\n+ #if $filtering.strip_it.value\n+ --filter "stripIT"\n+ #end if\n+\n+ #if $filtering.filter_mz_windows.do_filter\n+ --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"\n+ #end if\n+\n+ \n+ #if $filtering.filter_ms_levels.do_filter\n+ --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"\n+ #end if\n+\n+ #if str($filtering.etd_filtering.do_etd_filtering) == "default"\n+ --filter "ETDFilter"\n+ #end if\n+\n+ #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"\n+ --filter "ETDFilter removePrecursor:$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"\n+ #end if\n+\n+ ## BEGIN_VERSION_3\n+\n+ #if $filtering.precursor_refine.value\n+ --filter "precursorRefine"\n+ #end if\n+\n+ #if $filtering.ms2denoise.denoise\n+ --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"\n+ #end if \n+\n+ #if str($filtering.ms2deisotope) == "true"\n+ --filter "MS2Deisotope"\n+ #end if\n+\n+ #if str($filtering.polarity) != "false"\n+ --filter "polarity $filtering.polarity"\n+ #end if\n+\n+ #if str($filtering.analyzer) != "false"\n+ --filter "analyzer $filtering.analyzer"\n+ #end if\n+\n+ ## END_VERSION_3\n+\n+ #end if\n+\n+ </command>\n+\n+ <inputs>\n+ <!-- BEGIN_VERSION_RAW -->\n+ <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>\n+ <!-- END_VERSION_RAW -->\n+\n+ <!-- BEGIN_VERSION_DEFAULT -->\n+ <conditional name="type">\n+ <param name="input_type" type="select" label="Input Type">\n+ <option value="mzml">mzML</option>\n+ <optio'..b'val">\n+ <option value="true" selected="true">yes</option> \n+ <option value="false">no</option>\n+ </param>\n+ </when>\n+ </conditional>\n+\n+\n+ <!-- BEGIN_VERSION_3 -->\n+ <conditional name="ms2denoise">\n+ <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />\n+ <when value="true">\n+ <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />\n+ <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />\n+ <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />\n+ </when>\n+ <when value="false" />\n+ </conditional>\n+ <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />\n+\n+ <param name="polarity" type="select" label="Filter by Polarity">\n+ <option value="false" selected="true">no</option>\n+ <option value="positive">positive</option>\n+ <option value="negative">negative</option>\n+ </param>\n+\n+ <param name="analyzer" type="select" label="Filter by Analyzer">\n+ <option value="false" selected="true">no</option>\n+ <option value="quad">quad</option>\n+ <option value="orbi">orbi</option>\n+ <option value="FT">FT</option>\n+ <option value="IT">IT</option>\n+ <option value="TOF">TOF</option>\n+ </param>\n+ <!-- END_VERSION_3 -->\n+ </when>\n+ </conditional>\n+\n+ <conditional name="settings">\n+ <param name="settingsType" type="select" label="Advanced Settings" help="">\n+ <option value="default">Use Defaults</option>\n+ <option value="full">Full Parameter List</option>\n+ </param>\n+ <when value="default" />\n+ <when value="full">\n+ <param type="select" name="binary_encoding" label="Binary Encoding Precision">\n+ <option value="64" selected="true">64</option>\n+ <option value="32">32</option>\n+ </param>\n+ <param type="select" name="mz_encoding" label="m/z Encoding Precision">\n+ <option value="64" selected="true">64</option>\n+ <option value="32">32</option>\n+ </param>\n+ <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">\n+ <option value="64">64</option>\n+ <option value="32" selected="true">32</option>\n+ </param>\n+ <param type="boolean" name="zlib" label="Use zlib"> \n+ </param>\n+ </when>\n+ </conditional>\n+\n+\n+ </inputs>\n+ <outputs>\n+ <data format="mzml" name="output">\n+ <change_format>\n+ <when input="output_type" value="mzXML" format="mzxml" />\n+ <when input="output_type" value="unindexed_mzXML" format="mzxml" />\n+ <when input="output_type" value="ms2" format="ms2" />\n+ <when input="output_type" value="mgf" format="mgf" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+\n+ <requirements>\n+ <requirement type="package">proteowizard</requirement> \n+ </requirements>\n+\n+ <help>\n+**What it does**\n+\n+Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.\n+\n+You can view the original documentation here_.\n+ \n+.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n+\n+------\n+\n+**Citation**\n+\n+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.`\n+\n+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert\n+\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r 10f4a0356342 msconvert2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert2.xml Wed Dec 19 00:10:08 2012 -0500 |
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| b'@@ -0,0 +1,314 @@\n+<tool id="msconvert2" name="msconvert2" version="0.1.0">\n+ <!-- BEGIN_VERSION_DEFAULT -->\n+ <description>Convert and filter a mass spec peak list</description>\n+ <!-- END_VERSION_DEFAULT -->\n+\n+ <command interpreter="python">\n+ msconvert_wrapper.py \n+ --input=${input}\n+ #if hasattr($input, \'display_name\')\n+ --input_name=\'${input.display_name}\'\n+ #end if\n+ --output=${output} \n+ ## BEGIN_VERSION_DEFAULT \n+ --fromextension=${input.ext} \n+ ## END_VERSION_DEFAULT\n+\n+\n+ --toextension=${output_type} \n+\n+ #if $settings.settingsType == "full"\n+ --binaryencoding=${settings.binary_encoding} \n+ --mzencoding=${settings.mz_encoding} \n+ --intensityencoding=${settings.intensity_encoding}\n+ --zlib=${settings.zlib}\n+ #end if\n+\n+ #if $filtering.filtering_use\n+\n+ #if $filtering.precursor_recalculation.value\n+ --filter "precursorRecalculation"\n+ #end if\n+\n+ #if $filtering.peak_picking.pick_peaks\n+ --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"\n+ #end if\n+\n+ #if str($filtering.activation) != "false"\n+ --filter "activation $filtering.activation"\n+ #end if\n+\n+ #if len($filtering.indices) > 0\n+ --filter "index\n+ #for $index in $filtering.indices\n+ [${index.from},${index.to}]\n+ #end for\n+ "\n+ #end if\n+\n+ #if len($filtering.scan_numbers) > 0\n+ --filter "scanNumber\n+ #for $scan_number in $filtering.scan_numbers\n+ [${scan_number.from},${scan_number.to}]\n+ #end for\n+ "\n+ #end if\n+\n+ #for threshold_entry in $filtering.threshold_repeat\n+ --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"\n+ #end for\n+\n+\n+ #if $filtering.strip_it.value\n+ --filter "stripIT"\n+ #end if\n+\n+ #if $filtering.filter_mz_windows.do_filter\n+ --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"\n+ #end if\n+\n+ \n+ #if $filtering.filter_ms_levels.do_filter\n+ --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"\n+ #end if\n+\n+ #if str($filtering.etd_filtering.do_etd_filtering) == "default"\n+ --filter "ETDFilter"\n+ #end if\n+\n+ #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"\n+ --filter "ETDFilter removePrecursor:$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"\n+ #end if\n+\n+\n+ #end if\n+\n+ </command>\n+\n+ <inputs>\n+\n+ <!-- BEGIN_VERSION_DEFAULT -->\n+ <conditional name="type">\n+ <param name="input_type" type="select" label="Input Type">\n+ <option value="mzml">mzML</option>\n+ <option value="mzxml">mzXML</option>\n+ <option value="mgf">mgf</option>\n+ <option value="ms2">ms2</option>\n+ </param>\n+ <when value="mzml">\n+ <param format="mzml" name="input" type="data" label="Input mzML"/>\n+ </when>\n+ <when value="mzxml">\n+ <param format="mzxml" name="input" type="data" label="Input mzXML"/>\n+ </when>\n+ <when value="mgf">\n+ <param format="mgf" name="input" type="data" label="Input mgf"/>\n+ </when>\n+ <when value="ms2">\n+ <param format="ms2" name="input" type="data" label="Input ms2"/>\n+ </when>\n+ </conditional>\n+ <!-- END_VERSION_DEFAULT --> \n+ <param name="output_type" type="select" label="Output Type">\n+ <option value="mzML">mzML (indexed)</option>\n+ <option value="unindexed_mzML">mzML (unindexed)</option>\n+ <option value="mzXML">mzXML (indexed)</option> \n+ <option value="unindexed_mzXML">mzXML (unindexed)</option>\n+ <option value="mgf">mgf</option>\n+ '..b'<option value="default">yes (with default options)</option>\n+ <option value="advanced">yes (show advanced options) </option>\n+ </param>\n+ <when value="none" />\n+ <when value="default" />\n+ <when value="advanced">\n+ <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">\n+ </param>\n+ <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">\n+ <option value="MZ" selected="true">mz</option> \n+ <option value="PPM">ppm</option>\n+ </param>\n+ <param name="remove_precursor" type="select" label="ETD Remove Precursor">\n+ <option value="true" selected="true">yes</option> \n+ <option value="false">no</option>\n+ </param>\n+ <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">\n+ <option value="true" selected="true">yes</option> \n+ <option value="false">no</option>\n+ </param> \n+ <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">\n+ <option value="true" selected="true">yes</option> \n+ <option value="false">no</option>\n+ </param>\n+ <param name="blanket_removal" type="select" label="ETD Blanket Removal">\n+ <option value="true" selected="true">yes</option> \n+ <option value="false">no</option>\n+ </param>\n+ </when>\n+ </conditional>\n+\n+\n+ </when>\n+ </conditional>\n+\n+ <conditional name="settings">\n+ <param name="settingsType" type="select" label="Advanced Settings" help="">\n+ <option value="default">Use Defaults</option>\n+ <option value="full">Full Parameter List</option>\n+ </param>\n+ <when value="default" />\n+ <when value="full">\n+ <param type="select" name="binary_encoding" label="Binary Encoding Precision">\n+ <option value="64" selected="true">64</option>\n+ <option value="32">32</option>\n+ </param>\n+ <param type="select" name="mz_encoding" label="m/z Encoding Precision">\n+ <option value="64" selected="true">64</option>\n+ <option value="32">32</option>\n+ </param>\n+ <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">\n+ <option value="64">64</option>\n+ <option value="32" selected="true">32</option>\n+ </param>\n+ <param type="boolean" name="zlib" label="Use zlib"> \n+ </param>\n+ </when>\n+ </conditional>\n+\n+\n+ </inputs>\n+ <outputs>\n+ <data format="mzml" name="output">\n+ <change_format>\n+ <when input="output_type" value="mzXML" format="mzxml" />\n+ <when input="output_type" value="unindexed_mzXML" format="mzxml" />\n+ <when input="output_type" value="ms2" format="ms2" />\n+ <when input="output_type" value="mgf" format="mgf" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+\n+ <requirements>\n+ <requirement type="package">proteowizard</requirement> \n+ </requirements>\n+\n+ <help>\n+**What it does**\n+\n+Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.\n+\n+You can view the original documentation here_.\n+ \n+.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n+\n+------\n+\n+**Citation**\n+\n+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.`\n+\n+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert\n+\n+ </help>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 10f4a0356342 msconvert2_raw.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert2_raw.xml Wed Dec 19 00:10:08 2012 -0500 |
| [ |
| b'@@ -0,0 +1,295 @@\n+<tool id="msconvert2_raw" name="msconvert2_raw" version="0.1.0">\n+ <!-- BEGIN_VERSION_RAW -->\n+ <description>Convert and filter a Thermo Finnigan RAW file</description>\n+ <!-- END_VERSION_RAW -->\n+\n+ <command interpreter="python">\n+ msconvert_wrapper.py \n+ --input=${input}\n+ #if hasattr($input, \'display_name\')\n+ --input_name=\'${input.display_name}\'\n+ #end if\n+ --output=${output} \n+\n+ ## BEGIN_VERSION_RAW\n+ --fromextension=RAW\n+ ## END_VERSION_RAW\n+\n+ --toextension=${output_type} \n+\n+ #if $settings.settingsType == "full"\n+ --binaryencoding=${settings.binary_encoding} \n+ --mzencoding=${settings.mz_encoding} \n+ --intensityencoding=${settings.intensity_encoding}\n+ --zlib=${settings.zlib}\n+ #end if\n+\n+ #if $filtering.filtering_use\n+\n+ #if $filtering.precursor_recalculation.value\n+ --filter "precursorRecalculation"\n+ #end if\n+\n+ #if $filtering.peak_picking.pick_peaks\n+ --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"\n+ #end if\n+\n+ #if str($filtering.activation) != "false"\n+ --filter "activation $filtering.activation"\n+ #end if\n+\n+ #if len($filtering.indices) > 0\n+ --filter "index\n+ #for $index in $filtering.indices\n+ [${index.from},${index.to}]\n+ #end for\n+ "\n+ #end if\n+\n+ #if len($filtering.scan_numbers) > 0\n+ --filter "scanNumber\n+ #for $scan_number in $filtering.scan_numbers\n+ [${scan_number.from},${scan_number.to}]\n+ #end for\n+ "\n+ #end if\n+\n+ #for threshold_entry in $filtering.threshold_repeat\n+ --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"\n+ #end for\n+\n+\n+ #if $filtering.strip_it.value\n+ --filter "stripIT"\n+ #end if\n+\n+ #if $filtering.filter_mz_windows.do_filter\n+ --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"\n+ #end if\n+\n+ \n+ #if $filtering.filter_ms_levels.do_filter\n+ --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"\n+ #end if\n+\n+ #if str($filtering.etd_filtering.do_etd_filtering) == "default"\n+ --filter "ETDFilter"\n+ #end if\n+\n+ #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"\n+ --filter "ETDFilter removePrecursor:$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"\n+ #end if\n+\n+\n+ #end if\n+\n+ </command>\n+\n+ <inputs>\n+ <!-- BEGIN_VERSION_RAW -->\n+ <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>\n+ <!-- END_VERSION_RAW -->\n+\n+ <param name="output_type" type="select" label="Output Type">\n+ <option value="mzML">mzML (indexed)</option>\n+ <option value="unindexed_mzML">mzML (unindexed)</option>\n+ <option value="mzXML">mzXML (indexed)</option> \n+ <option value="unindexed_mzXML">mzXML (unindexed)</option>\n+ <option value="mgf">mgf</option>\n+ <option value="ms2">ms2</option> \n+ </param> \n+ <conditional name="filtering">\n+ <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />\n+ <when value="false" />\n+ <when value="true">\n+ <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />\n+\n+\n+ <conditional name="peak_picking">\n+ <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />\n+ <when value="false" />\n+ <when value="true">\n+ <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">\n+ <option value="1">M'..b'<option value="default">yes (with default options)</option>\n+ <option value="advanced">yes (show advanced options) </option>\n+ </param>\n+ <when value="none" />\n+ <when value="default" />\n+ <when value="advanced">\n+ <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">\n+ </param>\n+ <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">\n+ <option value="MZ" selected="true">mz</option> \n+ <option value="PPM">ppm</option>\n+ </param>\n+ <param name="remove_precursor" type="select" label="ETD Remove Precursor">\n+ <option value="true" selected="true">yes</option> \n+ <option value="false">no</option>\n+ </param>\n+ <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">\n+ <option value="true" selected="true">yes</option> \n+ <option value="false">no</option>\n+ </param> \n+ <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">\n+ <option value="true" selected="true">yes</option> \n+ <option value="false">no</option>\n+ </param>\n+ <param name="blanket_removal" type="select" label="ETD Blanket Removal">\n+ <option value="true" selected="true">yes</option> \n+ <option value="false">no</option>\n+ </param>\n+ </when>\n+ </conditional>\n+\n+\n+ </when>\n+ </conditional>\n+\n+ <conditional name="settings">\n+ <param name="settingsType" type="select" label="Advanced Settings" help="">\n+ <option value="default">Use Defaults</option>\n+ <option value="full">Full Parameter List</option>\n+ </param>\n+ <when value="default" />\n+ <when value="full">\n+ <param type="select" name="binary_encoding" label="Binary Encoding Precision">\n+ <option value="64" selected="true">64</option>\n+ <option value="32">32</option>\n+ </param>\n+ <param type="select" name="mz_encoding" label="m/z Encoding Precision">\n+ <option value="64" selected="true">64</option>\n+ <option value="32">32</option>\n+ </param>\n+ <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">\n+ <option value="64">64</option>\n+ <option value="32" selected="true">32</option>\n+ </param>\n+ <param type="boolean" name="zlib" label="Use zlib"> \n+ </param>\n+ </when>\n+ </conditional>\n+\n+\n+ </inputs>\n+ <outputs>\n+ <data format="mzml" name="output">\n+ <change_format>\n+ <when input="output_type" value="mzXML" format="mzxml" />\n+ <when input="output_type" value="unindexed_mzXML" format="mzxml" />\n+ <when input="output_type" value="ms2" format="ms2" />\n+ <when input="output_type" value="mgf" format="mgf" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+\n+ <requirements>\n+ <requirement type="package">proteowizard</requirement> \n+ </requirements>\n+\n+ <help>\n+**What it does**\n+\n+Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.\n+\n+You can view the original documentation here_.\n+ \n+.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n+\n+------\n+\n+**Citation**\n+\n+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.`\n+\n+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert\n+\n+ </help>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 10f4a0356342 msconvert3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert3.xml Wed Dec 19 00:10:08 2012 -0500 |
| [ |
| b'@@ -0,0 +1,377 @@\n+<tool id="msconvert3" name="msconvert3" version="0.1.0">\n+ <!-- BEGIN_VERSION_DEFAULT -->\n+ <description>Convert and filter a mass spec peak list</description>\n+ <!-- END_VERSION_DEFAULT -->\n+\n+ <command interpreter="python">\n+ msconvert_wrapper.py \n+ --input=${input}\n+ #if hasattr($input, \'display_name\')\n+ --input_name=\'${input.display_name}\'\n+ #end if\n+ --output=${output} \n+ ## BEGIN_VERSION_DEFAULT \n+ --fromextension=${input.ext} \n+ ## END_VERSION_DEFAULT\n+\n+\n+ --toextension=${output_type} \n+\n+ #if $settings.settingsType == "full"\n+ --binaryencoding=${settings.binary_encoding} \n+ --mzencoding=${settings.mz_encoding} \n+ --intensityencoding=${settings.intensity_encoding}\n+ --zlib=${settings.zlib}\n+ #end if\n+\n+ #if $filtering.filtering_use\n+\n+ #if $filtering.precursor_recalculation.value\n+ --filter "precursorRecalculation"\n+ #end if\n+\n+ #if $filtering.peak_picking.pick_peaks\n+ --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"\n+ #end if\n+\n+ #if str($filtering.activation) != "false"\n+ --filter "activation $filtering.activation"\n+ #end if\n+\n+ #if len($filtering.indices) > 0\n+ --filter "index\n+ #for $index in $filtering.indices\n+ [${index.from},${index.to}]\n+ #end for\n+ "\n+ #end if\n+\n+ #if len($filtering.scan_numbers) > 0\n+ --filter "scanNumber\n+ #for $scan_number in $filtering.scan_numbers\n+ [${scan_number.from},${scan_number.to}]\n+ #end for\n+ "\n+ #end if\n+\n+ #for threshold_entry in $filtering.threshold_repeat\n+ --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"\n+ #end for\n+\n+\n+ #if $filtering.strip_it.value\n+ --filter "stripIT"\n+ #end if\n+\n+ #if $filtering.filter_mz_windows.do_filter\n+ --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"\n+ #end if\n+\n+ \n+ #if $filtering.filter_ms_levels.do_filter\n+ --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"\n+ #end if\n+\n+ #if str($filtering.etd_filtering.do_etd_filtering) == "default"\n+ --filter "ETDFilter"\n+ #end if\n+\n+ #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"\n+ --filter "ETDFilter removePrecursor:$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"\n+ #end if\n+\n+ ## BEGIN_VERSION_3\n+\n+ #if $filtering.precursor_refine.value\n+ --filter "precursorRefine"\n+ #end if\n+\n+ #if $filtering.ms2denoise.denoise\n+ --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"\n+ #end if \n+\n+ #if str($filtering.ms2deisotope) == "true"\n+ --filter "MS2Deisotope"\n+ #end if\n+\n+ #if str($filtering.polarity) != "false"\n+ --filter "polarity $filtering.polarity"\n+ #end if\n+\n+ #if str($filtering.analyzer) != "false"\n+ --filter "analyzer $filtering.analyzer"\n+ #end if\n+\n+ ## END_VERSION_3\n+\n+ #end if\n+\n+ </command>\n+\n+ <inputs>\n+\n+ <!-- BEGIN_VERSION_DEFAULT -->\n+ <conditional name="type">\n+ <param name="input_type" type="select" label="Input Type">\n+ <option value="mzml">mzML</option>\n+ <option value="mzxml">mzXML</option>\n+ <option value="mgf">mgf</option>\n+ <option value="ms2">ms2</option>\n+ </param>\n+ <when value="mzml">\n+ <param format="mzml" name="input" type="data" label="Input mzML"/>\n+ </when>\n+ <when value="mzxml">\n+ <param format="mzxml" name="input" type="data" label="Input mzXML"/>\n+ </when>\n+ <when value="mgf">'..b'val">\n+ <option value="true" selected="true">yes</option> \n+ <option value="false">no</option>\n+ </param>\n+ </when>\n+ </conditional>\n+\n+\n+ <!-- BEGIN_VERSION_3 -->\n+ <conditional name="ms2denoise">\n+ <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />\n+ <when value="true">\n+ <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />\n+ <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />\n+ <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />\n+ </when>\n+ <when value="false" />\n+ </conditional>\n+ <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />\n+\n+ <param name="polarity" type="select" label="Filter by Polarity">\n+ <option value="false" selected="true">no</option>\n+ <option value="positive">positive</option>\n+ <option value="negative">negative</option>\n+ </param>\n+\n+ <param name="analyzer" type="select" label="Filter by Analyzer">\n+ <option value="false" selected="true">no</option>\n+ <option value="quad">quad</option>\n+ <option value="orbi">orbi</option>\n+ <option value="FT">FT</option>\n+ <option value="IT">IT</option>\n+ <option value="TOF">TOF</option>\n+ </param>\n+ <!-- END_VERSION_3 -->\n+ </when>\n+ </conditional>\n+\n+ <conditional name="settings">\n+ <param name="settingsType" type="select" label="Advanced Settings" help="">\n+ <option value="default">Use Defaults</option>\n+ <option value="full">Full Parameter List</option>\n+ </param>\n+ <when value="default" />\n+ <when value="full">\n+ <param type="select" name="binary_encoding" label="Binary Encoding Precision">\n+ <option value="64" selected="true">64</option>\n+ <option value="32">32</option>\n+ </param>\n+ <param type="select" name="mz_encoding" label="m/z Encoding Precision">\n+ <option value="64" selected="true">64</option>\n+ <option value="32">32</option>\n+ </param>\n+ <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">\n+ <option value="64">64</option>\n+ <option value="32" selected="true">32</option>\n+ </param>\n+ <param type="boolean" name="zlib" label="Use zlib"> \n+ </param>\n+ </when>\n+ </conditional>\n+\n+\n+ </inputs>\n+ <outputs>\n+ <data format="mzml" name="output">\n+ <change_format>\n+ <when input="output_type" value="mzXML" format="mzxml" />\n+ <when input="output_type" value="unindexed_mzXML" format="mzxml" />\n+ <when input="output_type" value="ms2" format="ms2" />\n+ <when input="output_type" value="mgf" format="mgf" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+\n+ <requirements>\n+ <requirement type="package">proteowizard</requirement> \n+ </requirements>\n+\n+ <help>\n+**What it does**\n+\n+Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.\n+\n+You can view the original documentation here_.\n+ \n+.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n+\n+------\n+\n+**Citation**\n+\n+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.`\n+\n+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert\n+\n+ </help>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 10f4a0356342 msconvert3_raw.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert3_raw.xml Wed Dec 19 00:10:08 2012 -0500 |
| [ |
| b'@@ -0,0 +1,358 @@\n+<tool id="msconvert3_raw" name="msconvert3_raw" version="0.1.0">\n+ <!-- BEGIN_VERSION_RAW -->\n+ <description>Convert and filter a Thermo Finnigan RAW file</description>\n+ <!-- END_VERSION_RAW -->\n+\n+ <command interpreter="python">\n+ msconvert_wrapper.py \n+ --input=${input}\n+ #if hasattr($input, \'display_name\')\n+ --input_name=\'${input.display_name}\'\n+ #end if\n+ --output=${output} \n+\n+ ## BEGIN_VERSION_RAW\n+ --fromextension=RAW\n+ ## END_VERSION_RAW\n+\n+ --toextension=${output_type} \n+\n+ #if $settings.settingsType == "full"\n+ --binaryencoding=${settings.binary_encoding} \n+ --mzencoding=${settings.mz_encoding} \n+ --intensityencoding=${settings.intensity_encoding}\n+ --zlib=${settings.zlib}\n+ #end if\n+\n+ #if $filtering.filtering_use\n+\n+ #if $filtering.precursor_recalculation.value\n+ --filter "precursorRecalculation"\n+ #end if\n+\n+ #if $filtering.peak_picking.pick_peaks\n+ --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"\n+ #end if\n+\n+ #if str($filtering.activation) != "false"\n+ --filter "activation $filtering.activation"\n+ #end if\n+\n+ #if len($filtering.indices) > 0\n+ --filter "index\n+ #for $index in $filtering.indices\n+ [${index.from},${index.to}]\n+ #end for\n+ "\n+ #end if\n+\n+ #if len($filtering.scan_numbers) > 0\n+ --filter "scanNumber\n+ #for $scan_number in $filtering.scan_numbers\n+ [${scan_number.from},${scan_number.to}]\n+ #end for\n+ "\n+ #end if\n+\n+ #for threshold_entry in $filtering.threshold_repeat\n+ --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"\n+ #end for\n+\n+\n+ #if $filtering.strip_it.value\n+ --filter "stripIT"\n+ #end if\n+\n+ #if $filtering.filter_mz_windows.do_filter\n+ --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"\n+ #end if\n+\n+ \n+ #if $filtering.filter_ms_levels.do_filter\n+ --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"\n+ #end if\n+\n+ #if str($filtering.etd_filtering.do_etd_filtering) == "default"\n+ --filter "ETDFilter"\n+ #end if\n+\n+ #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"\n+ --filter "ETDFilter removePrecursor:$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"\n+ #end if\n+\n+ ## BEGIN_VERSION_3\n+\n+ #if $filtering.precursor_refine.value\n+ --filter "precursorRefine"\n+ #end if\n+\n+ #if $filtering.ms2denoise.denoise\n+ --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"\n+ #end if \n+\n+ #if str($filtering.ms2deisotope) == "true"\n+ --filter "MS2Deisotope"\n+ #end if\n+\n+ #if str($filtering.polarity) != "false"\n+ --filter "polarity $filtering.polarity"\n+ #end if\n+\n+ #if str($filtering.analyzer) != "false"\n+ --filter "analyzer $filtering.analyzer"\n+ #end if\n+\n+ ## END_VERSION_3\n+\n+ #end if\n+\n+ </command>\n+\n+ <inputs>\n+ <!-- BEGIN_VERSION_RAW -->\n+ <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>\n+ <!-- END_VERSION_RAW -->\n+\n+ <param name="output_type" type="select" label="Output Type">\n+ <option value="mzML">mzML (indexed)</option>\n+ <option value="unindexed_mzML">mzML (unindexed)</option>\n+ <option value="mzXML">mzXML (indexed)</option> \n+ <option value="unindexed_mzXML">mzXML (unindexed)</option>\n+ <option value="mgf">mgf</option>\n+ <option value="ms2">ms2</option> \n+ </param> \n+ <conditional name="filtering">\n+ <para'..b'val">\n+ <option value="true" selected="true">yes</option> \n+ <option value="false">no</option>\n+ </param>\n+ </when>\n+ </conditional>\n+\n+\n+ <!-- BEGIN_VERSION_3 -->\n+ <conditional name="ms2denoise">\n+ <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />\n+ <when value="true">\n+ <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />\n+ <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />\n+ <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />\n+ </when>\n+ <when value="false" />\n+ </conditional>\n+ <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />\n+\n+ <param name="polarity" type="select" label="Filter by Polarity">\n+ <option value="false" selected="true">no</option>\n+ <option value="positive">positive</option>\n+ <option value="negative">negative</option>\n+ </param>\n+\n+ <param name="analyzer" type="select" label="Filter by Analyzer">\n+ <option value="false" selected="true">no</option>\n+ <option value="quad">quad</option>\n+ <option value="orbi">orbi</option>\n+ <option value="FT">FT</option>\n+ <option value="IT">IT</option>\n+ <option value="TOF">TOF</option>\n+ </param>\n+ <!-- END_VERSION_3 -->\n+ </when>\n+ </conditional>\n+\n+ <conditional name="settings">\n+ <param name="settingsType" type="select" label="Advanced Settings" help="">\n+ <option value="default">Use Defaults</option>\n+ <option value="full">Full Parameter List</option>\n+ </param>\n+ <when value="default" />\n+ <when value="full">\n+ <param type="select" name="binary_encoding" label="Binary Encoding Precision">\n+ <option value="64" selected="true">64</option>\n+ <option value="32">32</option>\n+ </param>\n+ <param type="select" name="mz_encoding" label="m/z Encoding Precision">\n+ <option value="64" selected="true">64</option>\n+ <option value="32">32</option>\n+ </param>\n+ <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">\n+ <option value="64">64</option>\n+ <option value="32" selected="true">32</option>\n+ </param>\n+ <param type="boolean" name="zlib" label="Use zlib"> \n+ </param>\n+ </when>\n+ </conditional>\n+\n+\n+ </inputs>\n+ <outputs>\n+ <data format="mzml" name="output">\n+ <change_format>\n+ <when input="output_type" value="mzXML" format="mzxml" />\n+ <when input="output_type" value="unindexed_mzXML" format="mzxml" />\n+ <when input="output_type" value="ms2" format="ms2" />\n+ <when input="output_type" value="mgf" format="mgf" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+\n+ <requirements>\n+ <requirement type="package">proteowizard</requirement> \n+ </requirements>\n+\n+ <help>\n+**What it does**\n+\n+Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.\n+\n+You can view the original documentation here_.\n+ \n+.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n+\n+------\n+\n+**Citation**\n+\n+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.`\n+\n+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert\n+\n+ </help>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 10f4a0356342 msconvert_raw_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_raw_wrapper.py Wed Dec 19 00:10:08 2012 -0500 |
| [ |
| @@ -0,0 +1,124 @@ +#!/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__() |
| b |
| diff -r 000000000000 -r 10f4a0356342 msconvert_subset.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_subset.xml Wed Dec 19 00:10:08 2012 -0500 |
| b |
| @@ -0,0 +1,105 @@ +<tool id="msconvert_subset" name="Subset Peak List" version="0.1.0"> + <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=${settings.zlib} + #end if + --filter_table="$filter.filterList" + #if $filter.filterType == "scan_number" + --filter_table_type="number" + #else + --filter_table_type="index" + #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> |
| b |
| diff -r 000000000000 -r 10f4a0356342 msconvert_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_wrapper.py Wed Dec 19 00:10:08 2012 -0500 |
| [ |
| b'@@ -0,0 +1,272 @@\n+#!/usr/bin/env python\n+import optparse\n+import os\n+import sys\n+import tempfile\n+import shutil\n+import subprocess\n+import re\n+import logging\n+\n+assert sys.version_info[:2] >= (2, 6)\n+\n+log = logging.getLogger(__name__)\n+working_directory = os.getcwd()\n+tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stderr\').name\n+tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stdout\').name\n+\n+\n+def stop_err(msg):\n+ sys.stderr.write("%s\\n" % msg)\n+ sys.exit()\n+\n+\n+def read_stderr():\n+ stderr = \'\'\n+ if(os.path.exists(tmp_stderr_name)):\n+ with open(tmp_stderr_name, \'rb\') as tmp_stderr:\n+ buffsize = 1048576\n+ try:\n+ while True:\n+ stderr += tmp_stderr.read(buffsize)\n+ if not stderr or len(stderr) % buffsize != 0:\n+ break\n+ except OverflowError:\n+ pass\n+ return stderr\n+\n+\n+def execute(command, stdin=None):\n+ try:\n+ with open(tmp_stderr_name, \'wb\') as tmp_stderr:\n+ with open(tmp_stdout_name, \'wb\') as tmp_stdout:\n+ proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)\n+ returncode = proc.wait()\n+ if returncode != 0:\n+ raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))\n+ finally:\n+ print open(tmp_stderr_name, "r").read()\n+ print open(tmp_stdout_name, "r").read()\n+\n+\n+def delete_file(path):\n+ if os.path.exists(path):\n+ try:\n+ os.remove(path)\n+ except:\n+ pass\n+\n+\n+def delete_directory(directory):\n+ if os.path.exists(directory):\n+ try:\n+ shutil.rmtree(directory)\n+ except:\n+ pass\n+\n+\n+def symlink(source, link_name):\n+ import platform\n+ if platform.system() == \'Windows\':\n+ try:\n+ import win32file\n+ win32file.CreateSymbolicLink(source, link_name, 1)\n+ except:\n+ shutil.copy(source, link_name)\n+ else:\n+ os.symlink(source, link_name)\n+\n+\n+def copy_to_working_directory(data_file, relative_path):\n+ if os.path.abspath(data_file) != os.path.abspath(relative_path):\n+ symlink(data_file, relative_path)\n+ return relative_path\n+\n+\n+def __main__():\n+ run_script()\n+\n+#ENDTEMPLATE\n+\n+to_extensions = [\'mzML\', \'mzXML\', \'unindexed_mzML\', \'unindexed_mzXML\', \'mgf\', \'txt\', \'ms2\', \'cms2\']\n+\n+\n+def str_to_bool(v):\n+ """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """\n+ return v.lower() in ["yes", "true", "t", "1"]\n+\n+\n+def _add_filter(filters_file, contents):\n+ filters_file.write("filter=%s\\n" % contents)\n+\n+\n+def _skip_line(options, file_num, line_parts):\n+ file_num_column = options.filter_table_file_column\n+ if not file_num_column:\n+ return False\n+ else:\n+ target_file_num_val = str(file_num).strip()\n+ query_file_num_val = line_parts[int(file_num_column) - 1].strip()\n+ #print "target %s, query %s" % (target_file_num_val, query_file_num_val)\n+ return target_file_num_val != query_file_num_val\n+\n+\n+def _read_table_numbers(path, options, file_num=None):\n+ unique_numbers = set([])\n+ column_num = options.filter_table_column\n+ input = open(path, "r")\n+ first_line = True\n+ for line in input:\n+ if not line:\n+ continue\n+ line = line.strip()\n+ if line.startswith("#"):\n+ first_line = False\n+ continue\n+ if column_num == None:\n+ column = line\n+ else:\n+ line_parts = line.split("\\t")\n+ if _skip_line(options, file_num, line_parts):\n+ continue\n+ column = line_parts[int(column_num) - 1]\n+ match = re.match("\\d+", column)\n+ if match:\n+ '..b'ns.intensityencoding)\n+ return cmd\n+\n+\n+def _run(base_cmd, output_dir=\'output\', inputs=[], debug=False):\n+ inputs_as_str = " ".join([\'%s\' % shellquote(input) for input in inputs])\n+ os.mkdir(output_dir)\n+ cmd = "%s -o %s %s" % (base_cmd, shellquote(output_dir), inputs_as_str)\n+ if debug:\n+ print cmd\n+ execute(cmd)\n+ output_files = os.listdir(output_dir)\n+ assert len(output_files) == 1\n+ output_file = output_files[0]\n+ return os.path.join(output_dir, output_file)\n+\n+\n+def run_script():\n+ parser = optparse.OptionParser()\n+ parser.add_option(\'--input\', dest=\'inputs\', action=\'append\', default=[])\n+ parser.add_option(\'--input_name\', dest=\'input_names\', action=\'append\', default=[])\n+ parser.add_option(\'--output\', dest=\'output\')\n+ parser.add_option(\'--fromextension\', dest=\'fromextension\')\n+ parser.add_option(\'--toextension\', dest=\'toextension\', default=\'mzML\', choices=to_extensions)\n+ parser.add_option(\'--binaryencoding\', dest=\'binaryencoding\', choices=[\'32\', \'64\'])\n+ parser.add_option(\'--mzencoding\', dest=\'mzencoding\', choices=[\'32\', \'64\'])\n+ parser.add_option(\'--intensityencoding\', dest=\'intensityencoding\', choices=[\'32\', \'64\'])\n+ parser.add_option(\'--zlib\', dest=\'zlib\', default="false")\n+ parser.add_option(\'--filter\', dest=\'filter\', action=\'append\', default=[])\n+ parser.add_option(\'--filters_file\', dest=\'filters_file\', default=None)\n+ parser.add_option(\'--filter_table\', default=None)\n+ parser.add_option(\'--filter_table_type\', default=\'index\', choices=[\'index\', \'number\'])\n+ parser.add_option(\'--filter_table_column\', default=None)\n+ parser.add_option(\'--filter_table_file_column\', default=None)\n+ parser.add_option(\'--debug\', dest=\'debug\', action=\'store_true\', default=False)\n+\n+ (options, args) = parser.parse_args()\n+ if len(options.inputs) < 1:\n+ stop_err("No input files to msconvert specified")\n+ if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):\n+ stop_err("Number(s) of supplied input names and input files do not match")\n+ if not options.output:\n+ stop_err("Must specify output location")\n+ input_files = []\n+ for i, input in enumerate(options.inputs):\n+ input_base = None\n+ if len(options.input_names) > i:\n+ input_base = options.input_names[i]\n+ if not input_base:\n+ input_base = \'input%s\' % i\n+ if not input_base.lower().endswith(options.fromextension.lower()):\n+ input_file = \'%s.%s\' % (input_base, options.fromextension)\n+ else:\n+ input_file = input_base\n+ input_file = input_file\n+ copy_to_working_directory(input, input_file)\n+ input_files.append(input_file)\n+\n+ cmd = _build_base_cmd(options)\n+ file_column = options.filter_table_file_column\n+ if not file_column:\n+ # Apply same filters to all files, just create a unviersal filter files\n+ # and run msconvert once.\n+ filters_file_path = _create_filters_file(options, debug=options.debug)\n+ cmd = "%s -c %s" % (cmd, filters_file_path)\n+ else:\n+ # Dispatching on a column to filter different files differently, need to filter\n+ # each input once with msconvert and then merge once.\n+ filtered_files = []\n+ for index, input_file in enumerate(input_files):\n+ filters_file_path = _create_filters_file(options, index + 1, debug=options.debug)\n+ filter_cmd = "%s -c %s" % (cmd, filters_file_path)\n+ filtered_output_file = _run(filter_cmd, output_dir=\'output%d\' % index, inputs=[input_file], debug=options.debug)\n+ filtered_files.append(filtered_output_file)\n+ input_files = filtered_files\n+ if len(input_files) > 1:\n+ cmd = "%s --merge" % cmd\n+ output_file = _run(cmd, output_dir=\'output\', inputs=input_files, debug=options.debug)\n+ shutil.copy(output_file, options.output)\n+\n+\n+if __name__ == \'__main__\':\n+ __main__()\n' |
| b |
| diff -r 000000000000 -r 10f4a0356342 update.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update.sh Wed Dec 19 00:10:08 2012 -0500 |
| [ |
| @@ -0,0 +1,35 @@ +#!/bin/bash + +LICENSE_FILE=LICENSE +# Ensure repository contains license file. +if [ ! -e "$LICENSE_FILE" ]; +then + wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE" +fi + +# Run repository specific update actions. +if [ -f update_repo.sh ]; +then + ./update_repo.sh +fi + +wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md + +# Create repository README +if [ ! -e README_REPO.md ]; +then + echo "TODO: Document this tool repository." > README_REPO.md +fi +cat README_REPO.md README_GALAXYP.md > README.md + + +# If version file exists, update all tools to this version +VERSION_FILE=version +if [ -e "$VERSION_FILE" ]; +then + VERSION=`cat $VERSION_FILE` + + # Replace tool version in each tool XML file ` + find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \; + +fi |
| b |
| diff -r 000000000000 -r 10f4a0356342 update_repo.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update_repo.sh Wed Dec 19 00:10:08 2012 -0500 |
| b |
| @@ -0,0 +1,9 @@ +#!/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 + |
| b |
| diff -r 000000000000 -r 10f4a0356342 version --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/version Wed Dec 19 00:10:08 2012 -0500 |
| b |
| @@ -0,0 +1,1 @@ +0.1.0 \ No newline at end of file |