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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd |
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modified:
README.md msconvert.xml msconvert_macros.xml |
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| diff -r 6153e8ada1ee -r 545054b15d7c README.md --- a/README.md Mon Nov 30 16:01:10 2020 +0000 +++ b/README.md Sun Mar 24 11:13:43 2024 +0000 |
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| @@ -11,7 +11,10 @@ msconvert from ProteoWizard. -Note: This requires manual installation of ProteoWizard, and may require a Windows environment. +Convert and/or filter mass spectrometry files using the offical Docker container. +Using the Docker container requires agreeing to each vendor's license (for using their proprietary data access libraries): http://www.proteowizard.org/licenses.html + +Main web site: http://www.proteowizard.org See: @@ -19,8 +22,9 @@ * <http://proteowizard.sourceforge.net/tools/msconvert.html> -Installing ----------- +#### Note about installing older versions: + +Version 0.3.0 (2016) and earlier require manual installation of ProteoWizard, and may require a Windows environment. 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: |
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| diff -r 6153e8ada1ee -r 545054b15d7c msconvert.xml --- a/msconvert.xml Mon Nov 30 16:01:10 2020 +0000 +++ b/msconvert.xml Sun Mar 24 11:13:43 2024 +0000 |
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| @@ -1,25 +1,34 @@ -<tool id="msconvert" name="msconvert" version="@VERSION@.2"> - <description>Convert and/or filter mass spectrometry files</description> - <macros> - <import>msconvert_macros.xml</import> - </macros> - <requirements> - <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container> - </requirements> - <stdio> - <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." /> - </stdio> - <expand macro="msconvertCommand" /> - <inputs> - <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" /> - <expand macro="msconvertInputParameters" /> - </inputs> - <expand macro="msconvertOutput" /> - <tests> - <expand macro="msconvert_tests" /> - </tests> - <help> - <expand macro="msconvert_help" /> - </help> - <expand macro="citations" /> +<tool id="msconvert" name="msconvert" version="@VERSION@.3"> + <description>Convert and/or filter mass spectrometry files</description> + <macros> + <import>msconvert_macros.xml</import> + </macros> + <xrefs> + <xref type="bio.tools">msconvert</xref> + </xrefs> + <requirements> + <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container> + </requirements> + <stdio> + <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." /> + </stdio> + <expand macro="msconvertCommand" /> + <inputs> + <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" /> + <expand macro="msconvertInputParameters" /> + </inputs> + <expand macro="msconvertOutput" /> + <tests> + <expand macro="msconvert_tests" /> + </tests> + <help><![CDATA[ +**What it does** + +Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. 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 +]]></help> + <expand macro="citations" /> </tool> |
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| diff -r 6153e8ada1ee -r 545054b15d7c msconvert_macros.xml --- a/msconvert_macros.xml Mon Nov 30 16:01:10 2020 +0000 +++ b/msconvert_macros.xml Sun Mar 24 11:13:43 2024 +0000 |
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| b'@@ -221,7 +221,7 @@\n && mv \'outputs/${os.path.splitext($basename)[0]}.${output_type}\' \'${output}\'\n #else\n ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file\n- ## TODO this won\'t be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803\n+ ## this won\'t be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803\n #if $output_type == \'mzML\' or $output_type == \'mzXML\'\n && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c \'mv FILE outputs/\\$(basename FILE .$output_type).#echo str($output_type).lower()\n ## a newline is needed after `#echo ...` therefore the `;\'` on the next line\n@@ -251,7 +251,10 @@\n \n <section name="data_processing" title="Data Processing Filters">\n <conditional name="peak_picking">\n- <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />\n+ <param type="select" name="pick_peaks" label="Apply peak picking?">\n+ <option value="true">Yes</option>\n+ <option value="false">No</option>\n+ </param>\n <when value="false" />\n <when value="true">\n <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">\n@@ -268,7 +271,10 @@\n </conditional>\n \n <conditional name="precursor_refinement">\n- <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />\n+ <param type="select" name="use_mzrefinement" label="Apply m/z refinement with identification data?">\n+ <option value="true">Yes</option>\n+ <option value="false" selected="true">No</option>\n+ </param>\n <when value="false"></when>\n <when value="true">\n <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />\n@@ -337,7 +343,10 @@\n </repeat>\n \n <conditional name="filter_mz_windows">\n- <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />\n+ <param name="do_mzwindow_filter" type="select" label="Filter m/z Window" help="">\n+ <option value="true">Yes</option>\n+ <option value="false">No</option>\n+ </param>\n <when value="false" />\n <when value="true">\n <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />\n@@ -346,7 +355,10 @@\n </conditional>\n \n <conditional name="etd_filtering">\n- <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />\n+ <param type="select" name="do_etd_filtering" label="Filter out ETD precursor peaks?">\n+ <option value="true">Yes</option>\n+ <option value="false">No</option>\n+ </param>\n <when value="false" />\n <when value="true">\n <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">\n@@ -374,7 +386,10 @@\n </conditional>\n \n <conditional name="ms2denoise">\n- <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />\n+ <param name="denoise" type="select" label="De-noise MS2 with moving window filter">\n+ <option value="true">Yes</option>\n+ <option value="false">No</option>\n+ </param>\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@@ -386,7 +401,10 @@\n <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" true'..b'le="small-denoise.mzML" lines_diff="114" ftype="mzml" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n@@ -827,7 +854,7 @@\n <param name="binary_compression" value="numpressLinearPic" />\n <output name="output" file="small-deisotope.mzML" lines_diff="114" ftype="mzml" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n@@ -835,7 +862,7 @@\n <param name="binary_compression" value="numpressLinearPic" />\n <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n@@ -848,7 +875,7 @@\n <param name="binary_compression" value="numpressLinearPic" />\n <output name="output" file="small-index-filter.mzML" lines_diff="32" ftype="mzml" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n@@ -856,7 +883,7 @@\n <param name="binary_compression" value="numpressLinearPic" />\n <output name="output" file="small-strip-it.mzML" lines_diff="100" ftype="mzml" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n@@ -866,7 +893,7 @@\n <param name="binary_compression" value="numpressLinearPic" />\n <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" ftype="mzml" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n@@ -874,7 +901,7 @@\n <param name="binary_compression" value="numpressLinearPic" />\n <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n@@ -882,7 +909,7 @@\n <param name="binary_compression" value="numpressLinearPic" />\n <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" ftype="mzml" />\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n@@ -902,16 +929,6 @@\n <output name="output" file="small-deisotope-poisson.mzML" />\n </test>-->\n </xml>\n- <xml name="msconvert_help">\n-**What it does**\n-\n-Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. 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- </xml>\n-\n <xml name="citations">\n <citations>\n <citation type="doi">10.1093/bioinformatics/btn323</citation>\n' |