| Next changeset 1:b2ae577a321c (2016-05-23) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty |
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README.rst datatypes_conf.xml hardklor.conf hardklor.py hardklor.xml kronik.xml test-data/hardklor_result.hk test-data/kronik_result.kr test-data/ms1_spectra.mzml tool_dependencies.xml |
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| diff -r 000000000000 -r d796e6613d19 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon May 23 11:12:40 2016 -0400 |
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| @@ -0,0 +1,37 @@ +GalaxyP - Hardklör +======================= + +- Home: <https://github.com/galaxyproteomics/tools-galaxyp/> +- Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/hardklor +- Tool ID: `hardklor`, `kronik` + + +Description +----------- + +Hardklör identifies peptide or protein-like features in mass spectra. It deconvolves overlapping ion signals and can be used on a variety of input formats. +This package contains both Hardklör and its auxiliary tool Krönik, which filters, validates, and summarizes peptide features identified with Hardklör from data obtained during liquid chromatography mass spectrometry (LC-MS). + + +GalaxyP Community +----------------- + +Current governing community policies for GalaxyP_ and other information can be found at: + +<https://github.com/galaxyproteomics> + +.. _GalaxyP: https://github.com/galaxyproteomics/ + + +Contributing +------------ + +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> + + +Authors +------- + +Authors and contributors: + +* Jorrit Boekel |
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| diff -r 000000000000 -r d796e6613d19 datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Mon May 23 11:12:40 2016 -0400 |
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| @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<datatypes> + <registration> + <datatype extension="hk" type="galaxy.datatypes.text:Tabular" subclass="true" /> + <datatype extension="kr" type="galaxy.datatypes.text:Tabular" subclass="true" /> + </registration> +</datatypes> |
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| diff -r 000000000000 -r d796e6613d19 hardklor.conf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hardklor.conf Mon May 23 11:12:40 2016 -0400 |
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| @@ -0,0 +1,65 @@ +# Hardklor parameter file +# Version 2.3.0 +# Please see online documentation for detailed explanations: +# https://code.google.com/p/hardklor/wiki/Documentation + +# All parameters are separated from their values by an equals sign ('=') +# Anything after a '#' will be ignored for the remainder of the line. +# All data files (including paths if necessary) to be analyzed are discussed below. + +# Parameters used to described the data being input to Hardklor +instrument = {instrument} #Values are: FTICR, Orbitrap, TOF, QIT +resolution = {resolution} #Resolution at 400 m/z (def. 60000) +centroided = {centroided} #0=no, 1=yes + +# Parameters used in preprocessing spectra prior to analysis +ms_level = {mslvl} #1=MS1, 2=MS2, 3=MS3, 0=all +scan_range_min = 0 #ignore any spectra lower than this number, 0=off +scan_range_max = 0 #ignore any spectra higher than this number, 0=off +signal_to_noise = 0 #set signal-to-noise ratio, 0=off +sn_window = 250.0 #size in m/z for computing localized noise level in a spectrum. +static_sn = 0 #0=off, 1=on. Apply lowest localized noise level to entire spectrum. +boxcar_averaging = 0 #0=off, or specify number of scans to average together, use odd numbers only +boxcar_filter = 0 #0=off, when using boxcar_averaging, only keep peaks seen in this number of scans + # currently being averaged together. When on, signal_to_noise is not used. +boxcar_filter_ppm = 5 #Tolerance in ppm for matching peaks across spectra in boxcar_filter +mz_min = 0 #Sets lower bound of spectrum m/z range to analyze, 0=off +mz_max = 0 #Sets upper bound of spectrum m/z range to analyze, 0=off +smooth = 0 #Peforms Savitzky-Golay smoothing of peaks data. 0=off + # Not recommended for high resolution data. + +# Parameters used to customize the Hardklor analysis. Some of these parameters will drastically +# affect the analysis speed and results. Please consult the documentation and choose carefully! +algorithm = {algorithm} #Algorithms include: Basic, Version1, Version2 +charge_algorithm = {charge_algo} #Preferred method for feature charge identification. + # Values are: Quick, FFT, Patterson, Senko, None + # If None is set, all charge states are assumed, slowing Hardklor +charge_min = {mincharge} #Lowest charge state allowed in the analysis. +charge_max = {maxcharge} #Highest charge state allowed in the analysis. +correlation = {correlation} #Correlation threshold to accept a peptide feature. +averagine_mod = 0 #Formula containing modifications to the averagine model. + # Read documentation carefully before using! 0=off +mz_window = 5.25 #Breaks spectrum into windows not larger than this value for Version1 algorithm. +sensitivity = {sensitivity} #Values are 0 (lowest) to 3 (highest). Increasing sensitivity + # identifies more features near the noise where the isotope distribution + # may not be fully visible. However, these features are also more + # likely to be false. +depth = {depth} #Depth of combinatorial analysis. This is the maximum number of overlapping + # features allowed in any mz_window. Each increase requires exponential + # computation. In other words, keep this as low as necessary!!! +max_features = {maxfeat} #Maximum number of potential features in an mz_window to combinatorially solve. + # Setting this too high results in wasted computation time trying to mix-and-match + # highly improbable features. + +# Parameters used to customize the Hardklor output +distribution_area = 1 #Report sum of distribution peaks instead of highest peak only. 0=off, 1=on +xml = 0 #Output results as XML. 0=off, 1=on + + +# Below this point is where files to be analyzed should go. They should be listed contain +# both the input file name, and the output file name. Each file to be analyzed should begin +# on a new line. By convention Hardklor output should have this extension: .hk +# Example: +#YourData.mzXML YourData.hk +#Data.mzXML Data.hk +{inputfile} {outputfile} |
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| diff -r 000000000000 -r d796e6613d19 hardklor.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hardklor.py Mon May 23 11:12:40 2016 -0400 |
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| @@ -0,0 +1,62 @@ +""" +Usage: +python hardklor.py ms1extenstion ms2extension ms1file +ms2file outputfile +""" +import sys +import os +import subprocess + + +CONFIG_FILE = 'hk.conf' +extension_lookup = { + 'mzml' : 'mzML', + 'mzxml' : 'mzXML', + 'ms1' : 'MS1', + } + +# input: +ms1_ext = sys.argv[1] +ms1_file = sys.argv[2] +output_file = sys.argv[3] +config_load = os.path.join(os.path.split(sys.argv[0])[0], 'hardklor.conf') + +# parse options +options = {} +for arg in [x.split('=') for x in sys.argv[4:]]: + if arg[1] != '': + options[arg[0].replace('-', '')] = arg[1] + + +# create softlinks since hardklor needs "proper" extensions for input files +if ms1_ext in extension_lookup: + ms1_ext = extension_lookup[ms1_ext] + linkname = 'ms1_dsetlink.{0}'.format(ms1_ext) + os.symlink(ms1_file, linkname) + ms1_file = linkname + +# load template and dump to config file +with open(config_load) as fp: + config_str = fp.read() +config_to_dump = config_str.format( + instrument=options['instrument'], + resolution=options['resolution'], + centroided=options['centroided'], + mslvl=options['mslvl'], + depth=options['depth'], + algorithm=options['algorithm'], + charge_algo=options['charge_algo'], + mincharge=options['mincharge'], + maxcharge=options['maxcharge'], + correlation=options['correlation'], + sensitivity=options['sensitivity'], + maxfeat=options['maxfeat'], + inputfile=ms1_file, + outputfile=output_file, + ) +with open(CONFIG_FILE, 'w') as fp: + fp.write(config_to_dump) + +# Run hardklor +err = subprocess.call(['hardklor', CONFIG_FILE]) +sys.exit(err) |
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| diff -r 000000000000 -r d796e6613d19 hardklor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hardklor.xml Mon May 23 11:12:40 2016 -0400 |
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| @@ -0,0 +1,75 @@ +<tool id="hardklor" name="Hardklor" version="2.30"> + <description>identification of features from mass spectra</description> + <requirements> + <requirement type="package" version="2.30">hardklor</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + <command>python $__tool_directory__/hardklor.py "$ms1_in.extension" "$ms1_in" + "$output" -charge_algo=$cdm -resolution=$res -centroided=$centroided -instrument=$instrument -algorithm=$algorithm -mincharge=$chMin + -maxcharge=$chMax -mslvl=$mslvl -correlation=$corr -depth=$depth -sensitivity=$sens -maxfeat=$maxfeat</command> + <inputs> + <param name="ms1_in" type="data" format="mzml" label="MS1 files with precursor spectra " /> + <param name="res" type="integer" value="60000" label="Spectral resolution at 400m/z" /> + <param name="centroided" type="select" display="radio" label="Centroided data?"> + <option value="0" selected="true">No</option> + <option value="1">Yes</option> + </param> + <param name="instrument" type="select" label="Instrument" > + <option value="Orbitrap" selected="true">Orbitrap</option> + <option value="FTICR" >FTICR</option> + <option value="TOF" >TOF</option> + <option value="QIT" >Quadrupole ion trap</option> + </param> + <param name="mslvl" type="select" display="radio" label="MS level"> + <option value="0" >All</option> + <option value="1" selected="true">MS1</option> + <option value="2">MS2</option> + <option value="3">MS3</option> + </param> + <param name="algorithm" type="select" label="Algorithm"> + <option value="Basic">Basic</option> + <option value="Version1">Version 1</option> + <option value="Version2" selected="true">Version 2</option> + </param> + <param name="cdm" type="select" label="Charge determination method"> + <option value="None">None</option> + <option value="FFT">Fast Fourier Transform</option> + <option value="Patterson">Patterson Algorithm</option> + <option value="Quick" selected="true">Quick</option> + <option value="Senko">Senko</option> + </param> + + <param name="chMin" type="integer" value="1" label="Min charge state" /> + <param name="chMax" type="integer" value="5" label="Max charge state" /> + + <param name="corr" type="float" value="0.95" label="Correlation threshold" /> + <param name="sens" type="integer" value="2" label="Sensitivity level" help="Ranges from 0 (min, fast) to 3 (max, slow)" /> + <param name="depth" type="integer" value="2" label="Depth of combinatorial analysis" +help="Max number of overlapping features in any mz window. Keep as low as necessary for speed" /> + <param name="maxfeat" type="integer" value="12" label="Max nr. of features for mz-window to solve" /> + +<!-- <param name="sn" type="float" value="1" label="Signal to noise threshold" help="Must be >=0" /> + <param name="snWin" type="float" optional="true" label="Dynamic signal to noise window length (m/z)" + help="For spectra with varying noise levels (not for Thermo data)"/> + <param name="win" type="float" value="5.25" label="Max width of any set of peaks in a spectrum" /> --> + </inputs> + + <outputs> + <data format="hk" name="output" /> + </outputs> + <tests> + <test> + <param name="ms1_in" value="ms1_spectra.mzml"/> + <output name="output" file="hardklor_result.hk"/> + </test> + </tests> + <help> + Hardklör identifies peptide or protein-like features in mass spectra. It deconvolves overlapping ion signals and can be used on a variety of input formats. The output of Hardklör can be used by the Krönik tool which summarizes the peptide features over time in an LC-MS experiment. + </help> + <citations> + <citation type="doi">10.1021/ac0700833</citation> + <citation type="doi">10.1002/0471250953.bi1318s37</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r d796e6613d19 kronik.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kronik.xml Mon May 23 11:12:40 2016 -0400 |
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| @@ -0,0 +1,34 @@ +<tool id="kronik" name="Kronik" version="2.02"> + <description>processes Hardklör features to find peptides by chromatographic profiling</description> + <requirements> + <requirement type="package" version="2.02">kronik</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error occurred while running Kronik"/> + </stdio> + <command>kronik -c $c -d $d -g $g -m $m -n $n -p $p "$inputfile" "$output"</command> + <inputs> + <param name="inputfile" type="data" format="hk" label="Hardklör isotope distributions" /> + <param name="c" type="integer" value="5" label="Contaminant threshold in minutes" help="Peptides persisting for longer than this value are excluded" /> + <param name="d" type="integer" value="3" label="Match tolerance" help="Minimum consecutive scans peptide must be found in" /> + <param name="g" type="integer" value="1" label="Gap tolerance" help="Maximum amount of scans a peptide can skip to be considered in results" /> + <param name="m" type="integer" value="8000" label="Max mass (Da)" help="Maximum mass of peptide isotope distribution" /> + <param name="n" type="integer" value="600" label="Min mass (Da)" help="Minimum mass of peptide isotope distribution" /> + <param name="p" type="integer" value="10" label="Mass accuracy (ppm)" help="Peptides in adjacent scans must differ by less than this value to be called the same." /> + </inputs> + <outputs> + <data format="kr" name="output" /> + </outputs> + <tests> + <test> + <param name="inputfile" value="hardklor_result.hk"/> + <output name="output" file="kronik_result.kr" /> + </test> + </tests> + <help> +Krönik filters, validates, and summarizes peptide features identified with Hardklör from data obtained during liquid chromatography mass spectrometry (LC-MS). Hardklör and Krönik were designed to rapidly identify peptide and protein features in high resolution spectra of complex mixtures. These algorithms were developed to meet the demands of modern mass spectrometers that are capable of generating large amounts of robust mass spectrometry data. Spectra containing tens to hundreds of overlapping ion signals are reduced to a relevant list of observed monoisotopic mass values, charge states, and signal intensity values when using Hardklör. These features are then filtered, validated, and summarized by using Krönik for the analysis of liquid chromatography mass spectrometry (LC-MS) data. + </help> + <citations> + <citation type="doi">10.1002/0471250953.bi1318s37</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r d796e6613d19 test-data/hardklor_result.hk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hardklor_result.hk Mon May 23 11:12:40 2016 -0400 |
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| b |
| diff -r 000000000000 -r d796e6613d19 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon May 23 11:12:40 2016 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="hardklor" version="2.30"> + <repository changeset_revision="e25ed64d962b" name="package_hardklor_2_30" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="kronik" version="2.02"> + <repository changeset_revision="797b81fd9054" name="package_kronik_2_02" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |