Mercurial > repos > galaxyp > openms_internalcalibration

annotate InternalCalibration.xml @ 17:25f49e5a4a8e draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author galaxyp
date Fri, 06 Nov 2020 18:22:56 +0000
parents 03bec4747f9c
children
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3206df836c4c 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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9ea8cffda926 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
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4 <tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Applies an internal mass recalibration.</description>
3206df836c4c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros>
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7 <token name="@EXECUTABLE@">InternalCalibration</token>
3206df836c4c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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3206df836c4c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 </macros>
3206df836c4c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
1774a8ba674d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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21 mkdir out &&
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22 #if $cal.id_in:
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23 mkdir cal.id_in &&
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24 ln -s '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' &&
1774a8ba674d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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25 #end if
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26 #if $cal.lock_in:
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27 mkdir cal.lock_in &&
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28 ln -s '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' &&
1774a8ba674d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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29 #end if
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30 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
1774a8ba674d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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31 mkdir cal_lock_out &&
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32 #end if
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33 #if "lock_fail_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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34 mkdir cal_lock_fail_out &&
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35 #end if
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36 #if "models_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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37 mkdir quality_control_models &&
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38 #end if
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39 #if "models_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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40 mkdir quality_control_models_plot &&
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41 #end if
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42 #if "residuals_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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43 mkdir quality_control_residuals &&
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44 #end if
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45 #if "residuals_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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46 mkdir quality_control_residuals_plot &&
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47 #end if
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48
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49 ## Main program call
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50
1774a8ba674d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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51 set -o pipefail &&
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52 @EXECUTABLE@ -write_ctd ./ &&
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53 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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54 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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55 -in
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56 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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57 -out
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58 'out/output.${gxy2omsext("mzml")}'
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59 #if $cal.id_in:
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60 -cal:id_in
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61 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)'
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62 #end if
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63 #if $cal.lock_in:
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64 -cal:lock_in
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65 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)'
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66 #end if
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67 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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68 -cal:lock_out
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69 'cal_lock_out/output.${gxy2omsext("mzml")}'
0
3206df836c4c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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70 #end if
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71 #if "lock_fail_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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72 -cal:lock_fail_out
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73 'cal_lock_fail_out/output.${gxy2omsext("mzml")}'
1774a8ba674d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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74 #end if
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75 #if "models_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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76 -quality_control:models
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77 'quality_control_models/output.${gxy2omsext("csv")}'
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78 #end if
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79 #if "models_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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80 -quality_control:models_plot
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81 'quality_control_models_plot/output.${gxy2omsext("png")}'
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82 #end if
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83 #if "residuals_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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84 -quality_control:residuals
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85 'quality_control_residuals/output.${gxy2omsext("csv")}'
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86 #end if
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87 #if "residuals_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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88 -quality_control:residuals_plot
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89 'quality_control_residuals_plot/output.${gxy2omsext("png")}'
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90 #end if
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91 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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92 | tee '$stdout'
0
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93 #end if
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94
14
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95 ## Postprocessing
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96 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
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97 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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98 && mv 'cal_lock_out/output.${gxy2omsext("mzml")}' '$cal_lock_out'
0
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99 #end if
14
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100 #if "lock_fail_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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101 && mv 'cal_lock_fail_out/output.${gxy2omsext("mzml")}' '$cal_lock_fail_out'
0
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102 #end if
14
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103 #if "models_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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104 && mv 'quality_control_models/output.${gxy2omsext("csv")}' '$quality_control_models'
0
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105 #end if
14
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106 #if "models_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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107 && mv 'quality_control_models_plot/output.${gxy2omsext("png")}' '$quality_control_models_plot'
0
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108 #end if
14
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109 #if "residuals_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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110 && mv 'quality_control_residuals/output.${gxy2omsext("csv")}' '$quality_control_residuals'
0
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111 #end if
14
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112 #if "residuals_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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113 && mv 'quality_control_residuals_plot/output.${gxy2omsext("png")}' '$quality_control_residuals_plot'
0
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114 #end if
14
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115 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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116 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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117 #end if]]></command>
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118 <configfiles>
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119 <inputs name="args_json" data_style="paths"/>
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120 <configfile name="hardcoded_json"><![CDATA[{"rscript_executable": "Rscript", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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121 </configfiles>
0
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122 <inputs>
14
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123 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/>
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124 <param name="ppm_match_tolerance" argument="-ppm_match_tolerance" type="float" optional="true" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help=""/>
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125 <param name="ms_level" argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Does not affect calibrant collection (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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126 <expand macro="list_integer_valsan"/>
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127 </param>
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128 <param name="RT_chunking" argument="-RT_chunking" type="float" optional="true" value="300.0" label="RT window (one-sided" help="i.e. 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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129 <section name="cal" title="Chose one of two optional input files ('id_in' or 'lock_in') to define the calibration masses/function" help="" expanded="false">
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130 <param name="id_in" argument="-cal:id_in" type="data" format="featurexml,idxml" optional="true" label="Identifications or features whose peptide ID's serve as calibration masses" help=" select featurexml,idxml data sets(s)"/>
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131 <param name="lock_in" argument="-cal:lock_in" type="data" format="csv" 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=" select csv data sets(s)"/>
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132 <param name="lock_require_mono" argument="-cal:lock_require_mono" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to be monoisotopic" help="i.e. 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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133 <param name="lock_require_iso" argument="-cal:lock_require_iso" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to have at least the +1 isotope" help="Peaks without isotope pattern are not used"/>
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134 <param name="model_type" argument="-cal:model_type" display="radio" type="select" optional="false" label="Type of function to be fitted to the calibration points" help="">
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135 <option value="linear">linear</option>
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136 <option value="linear_weighted" selected="true">linear_weighted</option>
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137 <option value="quadratic">quadratic</option>
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138 <option value="quadratic_weighted">quadratic_weighted</option>
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139 <expand macro="list_string_san"/>
0
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140 </param>
14
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141 </section>
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142 <section name="RANSAC" title="Robust outlier removal using RANSAC" help="" expanded="false">
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143 <param name="enabled" argument="-RANSAC:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply RANSAC to calibration points to remove outliers before fitting a model" help=""/>
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144 <param name="threshold" argument="-RANSAC:threshold" type="float" optional="true" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help=""/>
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145 <param name="pc_inliers" argument="-RANSAC:pc_inliers" type="integer" optional="true" min="1" max="99" value="30" label="Minimum percentage (of available data) of inliers (&lt;threshold away from model) to accept the model" help=""/>
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146 <param name="iter" argument="-RANSAC:iter" type="integer" optional="true" value="70" label="Maximal # iterations" help=""/>
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147 </section>
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148 <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false">
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149 <param name="median" argument="-goodness:median" type="float" optional="true" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help=""/>
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150 <param name="MAD" argument="-goodness:MAD" type="float" optional="true" value="2.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help=""/>
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151 </section>
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152 <expand macro="adv_opts_macro">
16
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153 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
14
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154 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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155 <expand macro="list_string_san"/>
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156 </param>
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157 </expand>
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158 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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159 <option value="lock_out_FLAG">lock_out (Optional output file containing peaks from 'in' which were matched to reference m/z values)</option>
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160 <option value="lock_fail_out_FLAG">lock_fail_out (Optional output file containing lock masses which were NOT found or accepted(!) in data from 'in')</option>
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161 <option value="models_FLAG">models (Table of model parameters for each spectrum)</option>
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162 <option value="models_plot_FLAG">models_plot (Plot image of model parameters for each spectrum)</option>
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163 <option value="residuals_FLAG">residuals (Table of pre- and post calibration errors)</option>
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164 <option value="residuals_plot_FLAG">residuals_plot (Plot image of pre- and post calibration errors)</option>
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165 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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166 </param>
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167 </inputs>
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168 <outputs>
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169 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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170 <data name="cal_lock_out" label="${tool.name} on ${on_string}: cal:lock_out" format="mzml">
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171 <filter>OPTIONAL_OUTPUTS is not None and "lock_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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172 </data>
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173 <data name="cal_lock_fail_out" label="${tool.name} on ${on_string}: cal:lock_fail_out" format="mzml">
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174 <filter>OPTIONAL_OUTPUTS is not None and "lock_fail_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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175 </data>
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176 <data name="quality_control_models" label="${tool.name} on ${on_string}: quality_control:models" format="csv">
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177 <filter>OPTIONAL_OUTPUTS is not None and "models_FLAG" in OPTIONAL_OUTPUTS</filter>
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178 </data>
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179 <data name="quality_control_models_plot" label="${tool.name} on ${on_string}: quality_control:models_plot" format="png">
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180 <filter>OPTIONAL_OUTPUTS is not None and "models_plot_FLAG" in OPTIONAL_OUTPUTS</filter>
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181 </data>
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182 <data name="quality_control_residuals" label="${tool.name} on ${on_string}: quality_control:residuals" format="csv">
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183 <filter>OPTIONAL_OUTPUTS is not None and "residuals_FLAG" in OPTIONAL_OUTPUTS</filter>
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184 </data>
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185 <data name="quality_control_residuals_plot" label="${tool.name} on ${on_string}: quality_control:residuals_plot" format="png">
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186 <filter>OPTIONAL_OUTPUTS is not None and "residuals_plot_FLAG" in OPTIONAL_OUTPUTS</filter>
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187 </data>
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188 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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189 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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190 </data>
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191 </outputs>
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192 <tests>
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193 <expand macro="autotest_InternalCalibration"/>
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194 <expand macro="manutest_InternalCalibration"/>
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195 </tests>
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196 <help><![CDATA[Applies an internal mass recalibration.
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197
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198
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199 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_InternalCalibration.html]]></help>
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200 <expand macro="references"/>
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201 </tool>