annotate IDMassAccuracy.xml @ 14:b889cb83a9e1 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author galaxyp
date Fri, 06 Nov 2020 20:39:42 +0000
parents 31bc4129f589
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="IDMassAccuracy" name="IDMassAccuracy" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDMassAccuracy</token>
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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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11 </macros>
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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 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
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21 mkdir id_in &&
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22 ${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) }
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23 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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24 mkdir out_precursor &&
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25 #end if
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26 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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27 mkdir out_fragment &&
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28 #end if
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29 #if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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30 mkdir out_precursor_fit &&
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31 #end if
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32 #if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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33 mkdir out_fragment_fit &&
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34 #end if
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35
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36 ## Main program call
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38 set -o pipefail &&
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39 @EXECUTABLE@ -write_ctd ./ &&
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40 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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41 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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42 -in
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43 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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44 -id_in
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45 ${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
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46 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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47 -out_precursor
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48 'out_precursor/output.${gxy2omsext("tabular")}'
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49 #end if
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50 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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51 -out_fragment
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52 'out_fragment/output.${gxy2omsext("tabular")}'
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53 #end if
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54 #if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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55 -out_precursor_fit
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56 'out_precursor_fit/output.${gxy2omsext("tabular")}'
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57 #end if
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58 #if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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59 -out_fragment_fit
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60 'out_fragment_fit/output.${gxy2omsext("tabular")}'
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61 #end if
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62 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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63 | tee '$stdout'
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64 #end if
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65
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66 ## Postprocessing
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67 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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68 && mv 'out_precursor/output.${gxy2omsext("tabular")}' '$out_precursor'
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69 #end if
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70 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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71 && mv 'out_fragment/output.${gxy2omsext("tabular")}' '$out_fragment'
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72 #end if
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73 #if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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74 && mv 'out_precursor_fit/output.${gxy2omsext("tabular")}' '$out_precursor_fit'
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75 #end if
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76 #if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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77 && mv 'out_fragment_fit/output.${gxy2omsext("tabular")}' '$out_fragment_fit'
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78 #end if
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79 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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80 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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81 #end if]]></command>
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82 <configfiles>
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83 <inputs name="args_json" data_style="paths"/>
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84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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85 </configfiles>
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86 <inputs>
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87 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
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88 <param name="id_in" argument="-id_in" type="data" format="idxml" multiple="true" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
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89 <param name="precursor_error_ppm" argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/>
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90 <param name="fragment_error_ppm" argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/>
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91 <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
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92 <expand macro="adv_opts_macro">
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93 <param name="number_of_bins" argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
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94 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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95 <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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96 <expand macro="list_string_san"/>
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97 </param>
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98 </expand>
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99 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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100 <option value="out_precursor_FLAG">out_precursor (Output file which contains the deviations from the precursors)</option>
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101 <option value="out_fragment_FLAG">out_fragment (Output file which contains the fragment ion m/z deviations)</option>
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102 <option value="out_precursor_fit_FLAG">out_precursor_fit (Gaussian fit to the histogram of mass deviations from the precursors)</option>
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103 <option value="out_fragment_fit_FLAG">out_fragment_fit (Gaussian fit to the histogram of mass deviations from the fragments)</option>
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104 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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105 </param>
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106 </inputs>
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107 <outputs>
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108 <data name="out_precursor" label="${tool.name} on ${on_string}: out_precursor" format="tabular">
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109 <filter>OPTIONAL_OUTPUTS is not None and "out_precursor_FLAG" in OPTIONAL_OUTPUTS</filter>
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110 </data>
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111 <data name="out_fragment" label="${tool.name} on ${on_string}: out_fragment" format="tabular">
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112 <filter>OPTIONAL_OUTPUTS is not None and "out_fragment_FLAG" in OPTIONAL_OUTPUTS</filter>
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113 </data>
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114 <data name="out_precursor_fit" label="${tool.name} on ${on_string}: out_precursor_fit" format="tabular">
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115 <filter>OPTIONAL_OUTPUTS is not None and "out_precursor_fit_FLAG" in OPTIONAL_OUTPUTS</filter>
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116 </data>
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117 <data name="out_fragment_fit" label="${tool.name} on ${on_string}: out_fragment_fit" format="tabular">
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118 <filter>OPTIONAL_OUTPUTS is not None and "out_fragment_fit_FLAG" in OPTIONAL_OUTPUTS</filter>
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119 </data>
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120 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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121 <filter>OPTIONAL_OUTPUTS is None</filter>
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122 </data>
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123 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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124 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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125 </data>
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126 </outputs>
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127 <tests>
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128 <expand macro="autotest_IDMassAccuracy"/>
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129 <expand macro="manutest_IDMassAccuracy"/>
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130 </tests>
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131 <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs.
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132
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133
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134 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_IDMassAccuracy.html]]></help>
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135 <expand macro="references"/>
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136 </tool>