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comparison InternalCalibration.xml @ 1:eab8c1365b7d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:25:50 -0400
parents 975efdac387b
children ed8100768631
comparison
equal deleted inserted replaced
0:975efdac387b 1:eab8c1365b7d
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="InternalCalibration" name="InternalCalibration" version="2.1.0"> 4 <tool id="InternalCalibration" name="InternalCalibration" version="2.2.0.1">
5 <description>Applies an internal mass recalibration.</description> 5 <description>Applies an internal mass recalibration.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">InternalCalibration</token> 7 <token name="@EXECUTABLE@">InternalCalibration</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
55 #end if 55 #end if
56 #if $param_cal_lock_require_iso: 56 #if $param_cal_lock_require_iso:
57 -cal:lock_require_iso 57 -cal:lock_require_iso
58 #end if 58 #end if
59 #if $param_cal_model_type: 59 #if $param_cal_model_type:
60 -cal:model_type $param_cal_model_type 60 -cal:model_type
61 #if " " in str($param_cal_model_type):
62 "$param_cal_model_type"
63 #else
64 $param_cal_model_type
65 #end if
61 #end if 66 #end if
62 #if $param_RANSAC_enabled: 67 #if $param_RANSAC_enabled:
63 -RANSAC:enabled 68 -RANSAC:enabled
64 #end if 69 #end if
65 #if $param_RANSAC_threshold: 70 #if $param_RANSAC_threshold:
95 #end if 100 #end if
96 #end if 101 #end if
97 </command> 102 </command>
98 <inputs> 103 <inputs>
99 <param name="param_in" type="data" format="mzml" optional="False" label="Input peak file" help="(-in) "/> 104 <param name="param_in" type="data" format="mzml" optional="False" label="Input peak file" help="(-in) "/>
100 <param name="param_rscript_executable" type="data" format="text" value="Rscript" label="Path to the Rscript executable (default: 'Rscript')" help="(-rscript_executable) "/> 105 <param name="param_rscript_executable" type="data" format="txt" value="Rscript" label="Path to the Rscript executable (default: 'Rscript')" help="(-rscript_executable) "/>
101 <param name="param_ppm_match_tolerance" type="float" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help="(-ppm_match_tolerance) "/> 106 <param name="param_ppm_match_tolerance" type="float" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help="(-ppm_match_tolerance) "/>
102 <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level"> 107 <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level">
103 <param name="param_ms_level" type="text" size="30" value="1 2 3" label="Target MS levels to apply the transformation onto" help="(-ms_level) Does not affect calibrant collection"> 108 <param name="param_ms_level" type="text" size="30" value="1 2 3" label="Target MS levels to apply the transformation onto" help="(-ms_level) Does not affect calibrant collection">
104 <sanitizer> 109 <sanitizer>
105 <valid initial="string.printable"> 110 <valid initial="string.printable">
108 </valid> 113 </valid>
109 </sanitizer> 114 </sanitizer>
110 </param> 115 </param>
111 </repeat> 116 </repeat>
112 <param name="param_RT_chunking" type="float" value="300.0" label="RT window (one-sided, i.e" help="(-RT_chunking) left-&gt;center, or center-&gt;right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/> 117 <param name="param_RT_chunking" type="float" value="300.0" label="RT window (one-sided, i.e" help="(-RT_chunking) left-&gt;center, or center-&gt;right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/>
113 <param name="param_cal_id_in" type="data" format="featurexml,idxml" optional="True" label="Identifications or features whose peptide ID's serve as calibration masses" help="(-id_in) "/> 118 <param name="param_cal_id_in" type="data" format="idxml,featurexml" optional="True" label="Identifications or features whose peptide ID's serve as calibration masses" help="(-id_in) "/>
114 <param name="param_cal_lock_in" type="data" format="tabular" optional="True" label="Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans" help="(-lock_in) "/> 119 <param name="param_cal_lock_in" type="data" format="tabular" optional="True" label="Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans" help="(-lock_in) "/>
115 <param name="param_cal_lock_require_mono" display="radio" type="boolean" truevalue="-cal:lock_require_mono" falsevalue="" checked="false" optional="True" label="Require all lock masses to be monoisotopic, i.e" help="(-lock_require_mono) not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used"/> 120 <param name="param_cal_lock_require_mono" display="radio" type="boolean" truevalue="-cal:lock_require_mono" falsevalue="" checked="false" optional="True" label="Require all lock masses to be monoisotopic, i.e" help="(-lock_require_mono) not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used"/>
116 <param name="param_cal_lock_require_iso" display="radio" type="boolean" truevalue="-cal:lock_require_iso" falsevalue="" checked="false" optional="True" label="Require all lock masses to have at least the +1 isotope" help="(-lock_require_iso) Peaks without isotope pattern are not used"/> 121 <param name="param_cal_lock_require_iso" display="radio" type="boolean" truevalue="-cal:lock_require_iso" falsevalue="" checked="false" optional="True" label="Require all lock masses to have at least the +1 isotope" help="(-lock_require_iso) Peaks without isotope pattern are not used"/>
117 <param name="param_cal_model_type" display="radio" type="select" optional="False" value="linear_weighted" label="Type of function to be fitted to the calibration points" help="(-model_type) "> 122 <param name="param_cal_model_type" display="radio" type="select" optional="False" value="linear_weighted" label="Type of function to be fitted to the calibration points" help="(-model_type) ">
118 <option value="linear">linear</option> 123 <option value="linear">linear</option>