Mercurial > repos > galaxyp > openms_mrmtransitiongrouppicker
diff MRMTransitionGroupPicker.xml @ 1:289009115eb2 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
| author | galaxyp |
|---|---|
| date | Wed, 09 Aug 2017 09:27:49 -0400 |
| parents | 2c8729a286ea |
| children | 7dca11634139 |
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--- a/MRMTransitionGroupPicker.xml Wed Mar 01 12:38:23 2017 -0500 +++ b/MRMTransitionGroupPicker.xml Wed Aug 09 09:27:49 2017 -0400 @@ -1,7 +1,8 @@ <?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="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.1.0"> +<tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.2.0"> + <description>Picks peaks in SRM/MRM chromatograms.</description> <macros> <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token> <import>macros.xml</import> @@ -36,7 +37,12 @@ -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width #end if #if $param_algorithm_PeakPickerMRM_use_gauss: - -algorithm:PeakPickerMRM:use_gauss $param_algorithm_PeakPickerMRM_use_gauss + -algorithm:PeakPickerMRM:use_gauss + #if " " in str($param_algorithm_PeakPickerMRM_use_gauss): + "$param_algorithm_PeakPickerMRM_use_gauss" + #else + $param_algorithm_PeakPickerMRM_use_gauss + #end if #end if #if $param_algorithm_PeakPickerMRM_peak_width: -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width @@ -51,13 +57,23 @@ -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count #end if #if $param_algorithm_PeakPickerMRM_write_sn_log_messages: - -algorithm:PeakPickerMRM:write_sn_log_messages $param_algorithm_PeakPickerMRM_write_sn_log_messages + -algorithm:PeakPickerMRM:write_sn_log_messages + #if " " in str($param_algorithm_PeakPickerMRM_write_sn_log_messages): + "$param_algorithm_PeakPickerMRM_write_sn_log_messages" + #else + $param_algorithm_PeakPickerMRM_write_sn_log_messages + #end if #end if #if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks: -algorithm:PeakPickerMRM:remove_overlapping_peaks #end if #if $param_algorithm_PeakPickerMRM_method: - -algorithm:PeakPickerMRM:method $param_algorithm_PeakPickerMRM_method + -algorithm:PeakPickerMRM:method + #if " " in str($param_algorithm_PeakPickerMRM_method): + "$param_algorithm_PeakPickerMRM_method" + #else + $param_algorithm_PeakPickerMRM_method + #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: @@ -67,10 +83,18 @@ -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width #end if #if $adv_opts.param_algorithm_background_subtraction: - -algorithm:background_subtraction $adv_opts.param_algorithm_background_subtraction + -algorithm:background_subtraction + #if " " in str($adv_opts.param_algorithm_background_subtraction): + "$adv_opts.param_algorithm_background_subtraction" + #else + $adv_opts.param_algorithm_background_subtraction + #end if #end if #if $adv_opts.param_algorithm_recalculate_peaks: - -algorithm:recalculate_peaks "$adv_opts.param_algorithm_recalculate_peaks" + -algorithm:recalculate_peaks +#end if + #if $adv_opts.param_algorithm_use_precursors: + -algorithm:use_precursors #end if #if $adv_opts.param_algorithm_recalculate_peaks_max_z: -algorithm:recalculate_peaks_max_z $adv_opts.param_algorithm_recalculate_peaks_max_z @@ -79,7 +103,7 @@ -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality #end if #if $adv_opts.param_algorithm_compute_peak_quality: - -algorithm:compute_peak_quality "$adv_opts.param_algorithm_compute_peak_quality" + -algorithm:compute_peak_quality #end if #end if </command> @@ -117,31 +141,18 @@ <option value="smoothed">smoothed</option> <option value="original">original</option> </param> - <param name="param_algorithm_recalculate_peaks" type="text" size="30" value="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> + <param name="param_algorithm_recalculate_peaks" display="radio" type="boolean" truevalue="-algorithm:recalculate_peaks" falsevalue="" checked="false" optional="True" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"/> + <param name="param_algorithm_use_precursors" display="radio" type="boolean" truevalue="-algorithm:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/> <param name="param_algorithm_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/> <param name="param_algorithm_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/> - <param name="param_algorithm_compute_peak_quality" type="text" size="30" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> + <param name="param_algorithm_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/> </expand> </inputs> <outputs> <data name="param_out" format="featurexml"/> </outputs> - <help>None + <help>Picks peaks in SRM/MRM chromatograms. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MRMTransitionGroupPicker.html</help> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMTransitionGroupPicker.html</help> </tool>