Mercurial > repos > galaxyp > openms_lowmempeakpickerhires_randomaccess
changeset 5:9050f8fbee85 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
| author | galaxyp |
|---|---|
| date | Mon, 12 Feb 2018 13:12:32 -0500 |
| parents | 25e388f2b21e |
| children | 5ef9c166272d |
| files | LowMemPeakPickerHiResRandomAccess.xml LowMemPeakPickerHiRes_RandomAccess.xml SKIP_TOOLS_FILE.txt macros.xml readme.md tools_blacklist.txt |
| diffstat | 6 files changed, 156 insertions(+), 156 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LowMemPeakPickerHiResRandomAccess.xml Mon Feb 12 13:12:32 2018 -0500 @@ -0,0 +1,137 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> +<!--Proposed Tool Section: [Utilities]--> +<tool id="LowMemPeakPickerHiRes_RandomAccess" name="LowMemPeakPickerHiResRandomAccess" version="2.3.0"> + <description>Finds mass spectrometric peaks in profile mass spectra.</description> + <macros> + <token name="@EXECUTABLE@">LowMemPeakPickerHiResRandomAccess</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>LowMemPeakPickerHiResRandomAccess + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_algorithm_signal_to_noise: + -algorithm:signal_to_noise $param_algorithm_signal_to_noise +#end if + +#if $rep_param_algorithm_ms_levels: +-algorithm:ms_levels + #for token in $rep_param_algorithm_ms_levels: + #if " " in str(token): + "$token.param_algorithm_ms_levels" + #else + $token.param_algorithm_ms_levels + #end if + #end for +#end if +#if $param_algorithm_report_FWHM: + -algorithm:report_FWHM +#end if +#if $param_algorithm_report_FWHM_unit: + -algorithm:report_FWHM_unit + #if " " in str($param_algorithm_report_FWHM_unit): + "$param_algorithm_report_FWHM_unit" + #else + $param_algorithm_report_FWHM_unit + #end if +#end if +#if $param_algorithm_SignalToNoise_win_len: + -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len +#end if +#if $param_algorithm_SignalToNoise_bin_count: + -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count +#end if +#if $param_algorithm_SignalToNoise_min_required_elements: + -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements +#end if +#if $param_algorithm_SignalToNoise_write_log_messages: + -algorithm:SignalToNoise:write_log_messages + #if " " in str($param_algorithm_SignalToNoise_write_log_messages): + "$param_algorithm_SignalToNoise_write_log_messages" + #else + $param_algorithm_SignalToNoise_write_log_messages + #end if +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_spacing_difference_gap: + -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap +#end if + #if $adv_opts.param_algorithm_spacing_difference: + -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference +#end if + #if $adv_opts.param_algorithm_missing: + -algorithm:missing $adv_opts.param_algorithm_missing +#end if + #if $adv_opts.param_algorithm_SignalToNoise_max_intensity: + -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor: + -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile: + -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_mode: + -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode +#end if + #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window: + -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window +#end if +#end if +</command> + <inputs> + <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> + <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help="(-signal_to_noise) "/> + <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels"> + <param name="param_algorithm_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="List of MS levels for which the peak picking is applied" help="(-ms_levels) Other scans are copied to the output without changes"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param name="param_algorithm_report_FWHM" display="radio" type="boolean" truevalue="-algorithm:report_FWHM" falsevalue="" checked="false" optional="True" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help="(-report_FWHM) "/> + <param name="param_algorithm_report_FWHM_unit" display="radio" type="select" optional="False" value="relative" label="Unit of FWHM. Either absolute in the unit of input," help="(-report_FWHM_unit) e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)"> + <option value="relative" selected="true">relative</option> + <option value="absolute">absolute</option> + </param> + <param name="param_algorithm_SignalToNoise_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/> + <param name="param_algorithm_SignalToNoise_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/> + <param name="param_algorithm_SignalToNoise_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements) "/> + <param name="param_algorithm_SignalToNoise_write_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help="(-write_log_messages) "> + <option value="true" selected="true">true</option> + <option value="false">false</option> + </param> + <expand macro="advanced_options"> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <param name="param_algorithm_spacing_difference_gap" type="float" min="0.0" optional="True" value="4.0" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" help="(-spacing_difference_gap) 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms"/> + <param name="param_algorithm_spacing_difference" type="float" min="0.0" optional="True" value="1.5" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" help="(-spacing_difference) If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms"/> + <param name="param_algorithm_missing" type="integer" min="0" optional="True" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="(-missing) A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms"/> + <param name="param_algorithm_SignalToNoise_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/> + <param name="param_algorithm_SignalToNoise_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor) "/> + <param name="param_algorithm_SignalToNoise_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile) "/> + <param name="param_algorithm_SignalToNoise_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" help="(-auto_mode) "/> + <param name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" format="mzml"/> + </outputs> + <help>Finds mass spectrometric peaks in profile mass spectra. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LowMemPeakPickerHiResRandomAccess.html</help> +</tool>
--- a/LowMemPeakPickerHiRes_RandomAccess.xml Thu Jan 11 18:01:21 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,137 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> -<!--Proposed Tool Section: [Utilities]--> -<tool id="LowMemPeakPickerHiRes_RandomAccess" name="LowMemPeakPickerHiRes_RandomAccess" version="2.2.0"> - <description>Finds mass spectrometric peaks in profile mass spectra.</description> - <macros> - <token name="@EXECUTABLE@">LowMemPeakPickerHiRes_RandomAccess</token> - <import>macros.xml</import> - </macros> - <expand macro="references"/> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>LowMemPeakPickerHiRes_RandomAccess - -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_algorithm_signal_to_noise: - -algorithm:signal_to_noise $param_algorithm_signal_to_noise -#end if - -#if $rep_param_algorithm_ms_levels: --algorithm:ms_levels - #for token in $rep_param_algorithm_ms_levels: - #if " " in str(token): - "$token.param_algorithm_ms_levels" - #else - $token.param_algorithm_ms_levels - #end if - #end for -#end if -#if $param_algorithm_report_FWHM: - -algorithm:report_FWHM -#end if -#if $param_algorithm_report_FWHM_unit: - -algorithm:report_FWHM_unit - #if " " in str($param_algorithm_report_FWHM_unit): - "$param_algorithm_report_FWHM_unit" - #else - $param_algorithm_report_FWHM_unit - #end if -#end if -#if $param_algorithm_SignalToNoise_win_len: - -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len -#end if -#if $param_algorithm_SignalToNoise_bin_count: - -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count -#end if -#if $param_algorithm_SignalToNoise_min_required_elements: - -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements -#end if -#if $param_algorithm_SignalToNoise_write_log_messages: - -algorithm:SignalToNoise:write_log_messages - #if " " in str($param_algorithm_SignalToNoise_write_log_messages): - "$param_algorithm_SignalToNoise_write_log_messages" - #else - $param_algorithm_SignalToNoise_write_log_messages - #end if -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if - #if $adv_opts.param_algorithm_spacing_difference_gap: - -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap -#end if - #if $adv_opts.param_algorithm_spacing_difference: - -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference -#end if - #if $adv_opts.param_algorithm_missing: - -algorithm:missing $adv_opts.param_algorithm_missing -#end if - #if $adv_opts.param_algorithm_SignalToNoise_max_intensity: - -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity -#end if - #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor: - -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor -#end if - #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile: - -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile -#end if - #if $adv_opts.param_algorithm_SignalToNoise_auto_mode: - -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode -#end if - #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window: - -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window -#end if -#end if -</command> - <inputs> - <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> - <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help="(-signal_to_noise) "/> - <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels"> - <param name="param_algorithm_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="List of MS levels for which the peak picking is applied" help="(-ms_levels) Other scans are copied to the output without changes"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - </repeat> - <param name="param_algorithm_report_FWHM" display="radio" type="boolean" truevalue="-algorithm:report_FWHM" falsevalue="" checked="false" optional="True" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help="(-report_FWHM) "/> - <param name="param_algorithm_report_FWHM_unit" display="radio" type="select" optional="False" value="relative" label="Unit of FWHM. Either absolute in the unit of input," help="(-report_FWHM_unit) e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)"> - <option value="relative" selected="true">relative</option> - <option value="absolute">absolute</option> - </param> - <param name="param_algorithm_SignalToNoise_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/> - <param name="param_algorithm_SignalToNoise_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/> - <param name="param_algorithm_SignalToNoise_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements) "/> - <param name="param_algorithm_SignalToNoise_write_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help="(-write_log_messages) "> - <option value="true" selected="true">true</option> - <option value="false">false</option> - </param> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> - <param name="param_algorithm_spacing_difference_gap" type="float" min="0.0" optional="True" value="4.0" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" help="(-spacing_difference_gap) 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms"/> - <param name="param_algorithm_spacing_difference" type="float" min="0.0" optional="True" value="1.5" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" help="(-spacing_difference) If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms"/> - <param name="param_algorithm_missing" type="integer" min="0" optional="True" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="(-missing) A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms"/> - <param name="param_algorithm_SignalToNoise_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/> - <param name="param_algorithm_SignalToNoise_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor) "/> - <param name="param_algorithm_SignalToNoise_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile) "/> - <param name="param_algorithm_SignalToNoise_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" help="(-auto_mode) "/> - <param name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/> - </expand> - </inputs> - <outputs> - <data name="param_out" format="mzml"/> - </outputs> - <help>Finds mass spectrometric peaks in profile mass spectra. - - -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LowMemPeakPickerHiRes_RandomAccess.html</help> -</tool>
--- a/SKIP_TOOLS_FILE.txt Thu Jan 11 18:01:21 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -OMSSAAdapter -MyriMatchAdapter -PepNovoAdapter -SeedListGenerator -SpecLibSearcher -MapAlignerIdentification -MapAlignerPoseClustering -MapAlignerSpectrum -MapAlignerRTTransformer
--- a/macros.xml Thu Jan 11 18:01:21 2018 -0500 +++ b/macros.xml Mon Feb 12 13:12:32 2018 -0500 @@ -2,10 +2,10 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.2">openms</requirement> + <requirement type="package" version="2.3">openms</requirement> <requirement type="package" version="15.12.15.2">xtandem</requirement> <requirement type="package" version="1.0">fido</requirement> - <requirement type="package" version="2016.10.26">msgf_plus</requirement> + <requirement type="package" version="2017.07.21">msgf_plus</requirement> <yield/> </requirements> </xml>
--- a/readme.md Thu Jan 11 18:01:21 2018 -0500 +++ b/readme.md Mon Feb 12 13:12:32 2018 -0500 @@ -53,29 +53,29 @@ * clone or install CTD2Galaxy ```bash - git clone https://github.com/WorkflowConversion/CTD2Galaxy.git + git clone https://github.com/WorkflowConversion/CTDConverter.git ``` - * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. + * If you have CTDopts and CTDConverter installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. Further information can be found on the CTDConverter page. ```bash - python generator.py \ + python convert.py galaxy \ -i /PATH/TO/YOUR/CTD/*.ctd \ -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ -d datatypes_conf.xml -g openms \ -b version log debug test no_progress threads \ in_type executable myrimatch_executable \ fido_executable fidocp_executable \ - omssa_executable pepnovo_executable \ + omssa_executable pepnovo_e xecutable \ xtandem_executable param_model_directory \ java_executable java_memory java_permgen \ r_executable rt_concat_trafo_out param_id_pool \ -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ - -s PATH/TO/SKIP_TOOLS_FILES.txt + -s PATH/TO/tools_blacklist.txt ``` - * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: + * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. Some of these tools might already be deprecated and the files might not exist: ``` sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml @@ -171,8 +171,8 @@ ``` - * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in - by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`: + * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in + by the automatic conversion step and are therefore in `tools_blacklist.txt`: * SeedListGenerator * SpecLibSearcher * MapAlignerIdentification