Mercurial > repos > galaxyp > openms_internalcalibration

annotate InternalCalibration.xml @ 0:975efdac387b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:37:28 -0500
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children eab8c1365b7d
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975efdac387b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
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4 <tool id="InternalCalibration" name="InternalCalibration" version="2.1.0">
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5 <description>Applies an internal mass recalibration.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">InternalCalibration</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>InternalCalibration
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_rscript_executable:
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22 -rscript_executable $param_rscript_executable
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23 #end if
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24 #if $param_ppm_match_tolerance:
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25 -ppm_match_tolerance $param_ppm_match_tolerance
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26 #end if
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27
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28 #if $rep_param_ms_level:
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29 -ms_level
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30 #for token in $rep_param_ms_level:
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31 #if " " in str(token):
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32 "$token.param_ms_level"
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33 #else
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34 $token.param_ms_level
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35 #end if
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36 #end for
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37 #end if
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38 #if $param_RT_chunking:
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39 -RT_chunking $param_RT_chunking
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40 #end if
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41 #if $param_cal_id_in:
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42 -cal:id_in $param_cal_id_in
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43 #end if
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44 #if $param_cal_lock_in:
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45 -cal:lock_in $param_cal_lock_in
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46 #end if
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47 #if $param_cal_lock_out:
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48 -cal:lock_out $param_cal_lock_out
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49 #end if
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50 #if $param_cal_lock_fail_out:
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51 -cal:lock_fail_out $param_cal_lock_fail_out
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52 #end if
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53 #if $param_cal_lock_require_mono:
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54 -cal:lock_require_mono
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55 #end if
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56 #if $param_cal_lock_require_iso:
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57 -cal:lock_require_iso
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58 #end if
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59 #if $param_cal_model_type:
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60 -cal:model_type $param_cal_model_type
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61 #end if
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62 #if $param_RANSAC_enabled:
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63 -RANSAC:enabled
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64 #end if
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65 #if $param_RANSAC_threshold:
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66 -RANSAC:threshold $param_RANSAC_threshold
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67 #end if
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68 #if $param_RANSAC_pc_inliers:
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69 -RANSAC:pc_inliers $param_RANSAC_pc_inliers
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70 #end if
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71 #if $param_RANSAC_iter:
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72 -RANSAC:iter $param_RANSAC_iter
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73 #end if
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74 #if $param_goodness_median:
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75 -goodness:median $param_goodness_median
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76 #end if
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77 #if $param_goodness_MAD:
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78 -goodness:MAD $param_goodness_MAD
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79 #end if
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80 #if $param_quality_control_models:
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81 -quality_control:models $param_quality_control_models
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82 #end if
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83 #if $param_quality_control_models_plot:
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84 -quality_control:models_plot $param_quality_control_models_plot
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85 #end if
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86 #if $param_quality_control_residuals:
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87 -quality_control:residuals $param_quality_control_residuals
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88 #end if
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89 #if $param_quality_control_residuals_plot:
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90 -quality_control:residuals_plot $param_quality_control_residuals_plot
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91 #end if
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92 #if $adv_opts.adv_opts_selector=='advanced':
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93 #if $adv_opts.param_force:
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94 -force
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95 #end if
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96 #end if
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97 </command>
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98 <inputs>
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99 <param name="param_in" type="data" format="mzml" optional="False" label="Input peak file" help="(-in) "/>
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100 <param name="param_rscript_executable" type="data" format="text" value="Rscript" label="Path to the Rscript executable (default: 'Rscript')" help="(-rscript_executable) "/>
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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) "/>
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102 <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level">
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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">
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104 <sanitizer>
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105 <valid initial="string.printable">
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106 <remove value="'"/>
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107 <remove value="&quot;"/>
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108 </valid>
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109 </sanitizer>
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110 </param>
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111 </repeat>
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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"/>
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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) "/>
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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) "/>
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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"/>
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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"/>
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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) ">
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118 <option value="linear">linear</option>
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119 <option value="linear_weighted" selected="true">linear_weighted</option>
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120 <option value="quadratic">quadratic</option>
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121 <option value="quadratic_weighted">quadratic_weighted</option>
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122 </param>
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123 <param name="param_RANSAC_enabled" display="radio" type="boolean" truevalue="-RANSAC:enabled" falsevalue="" checked="false" optional="True" label="Apply RANSAC to calibration points to remove outliers before fitting a model" help="(-enabled) "/>
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124 <param name="param_RANSAC_threshold" type="float" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help="(-threshold) "/>
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125 <param name="param_RANSAC_pc_inliers" type="integer" min="1" max="99" optional="True" value="30" label="Minimum percentage (of available data) of inliers (&lt;threshold away from model) to accept the model" help="(-pc_inliers) "/>
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126 <param name="param_RANSAC_iter" type="integer" value="70" label="Maximal # iterations" help="(-iter) "/>
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127 <param name="param_goodness_median" type="float" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help="(-median) "/>
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128 <param name="param_goodness_MAD" type="float" value="1.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help="(-MAD) "/>
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129 <expand macro="advanced_options">
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130 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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131 </expand>
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132 </inputs>
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133 <outputs>
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134 <data name="param_out" format="mzml"/>
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135 <data name="param_cal_lock_out" format="mzml"/>
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136 <data name="param_cal_lock_fail_out" format="mzml"/>
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137 <data name="param_quality_control_models" format="tabular"/>
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138 <data name="param_quality_control_models_plot" format="png"/>
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139 <data name="param_quality_control_residuals" format="tabular"/>
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140 <data name="param_quality_control_residuals_plot" format="png"/>
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141 </outputs>
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142 <help>Applies an internal mass recalibration.
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143
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144
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145 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html</help>
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146 </tool>