Mercurial > repos > galaxyp > openms_idmassaccuracy

annotate IDMassAccuracy.xml @ 16:0819fd9da302 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:31:46 +0000
parents 585f8235da7e
children
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2c96363c5a17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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1 <!--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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2 <!--Proposed Tool Section: [Identification Processing]-->
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3 <tool id="IDMassAccuracy" name="IDMassAccuracy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Calculates a distribution of the mass error from given mass spectra and IDs</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">IDMassAccuracy</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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14
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15 ## Preprocessing
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16 mkdir in_cond.in &&
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17 #if $in_cond.in_select == "no"
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18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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20 #else
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21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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22 #end if
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23 mkdir id_in_cond.id_in &&
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24 #if $id_in_cond.id_in_select == "no"
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25 mkdir ${' '.join(["'id_in_cond.id_in/%s'" % (i) for i, f in enumerate($id_in_cond.id_in) if f])} &&
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26 ${' '.join(["cp '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
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27 #else
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28 cp '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' &&
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29 #end if
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30 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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31 mkdir out_precursor &&
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32 #end if
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33 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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34 mkdir out_fragment &&
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35 #end if
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36 #if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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37 mkdir out_precursor_fit &&
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38 #end if
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39 #if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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40 mkdir out_fragment_fit &&
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41 #end if
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42
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43 ## Main program call
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44
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45 set -o pipefail &&
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46 @EXECUTABLE@ -write_ctd ./ &&
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47 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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48 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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49 -in
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50 #if $in_cond.in_select == "no"
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51 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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52 #else
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53 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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54 #end if
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55 -id_in
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56 #if $id_in_cond.id_in_select == "no"
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57 ${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
585f8235da7e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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58 #else
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59 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)'
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60 #end if
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61 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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62 -out_precursor
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63 'out_precursor/output.${gxy2omsext("tabular")}'
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64 #end if
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65 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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66 -out_fragment
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67 'out_fragment/output.${gxy2omsext("tabular")}'
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68 #end if
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69 #if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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70 -out_precursor_fit
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71 'out_precursor_fit/output.${gxy2omsext("tabular")}'
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72 #end if
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73 #if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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74 -out_fragment_fit
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75 'out_fragment_fit/output.${gxy2omsext("tabular")}'
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76 #end if
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77 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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78 | tee '$stdout'
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79 #end if
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80
11
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81 ## Postprocessing
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82 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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83 && mv 'out_precursor/output.${gxy2omsext("tabular")}' '$out_precursor'
0
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84 #end if
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85 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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86 && mv 'out_fragment/output.${gxy2omsext("tabular")}' '$out_fragment'
0
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87 #end if
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88 #if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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89 && mv 'out_precursor_fit/output.${gxy2omsext("tabular")}' '$out_precursor_fit'
0
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90 #end if
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91 #if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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92 && mv 'out_fragment_fit/output.${gxy2omsext("tabular")}' '$out_fragment_fit'
0
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93 #end if
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94 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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95 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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96 #end if]]></command>
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97 <configfiles>
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98 <inputs name="args_json" data_style="paths"/>
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99 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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100 </configfiles>
0
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101 <inputs>
15
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102 <conditional name="in_cond">
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103 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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104 <option value="no">No: process all datasets jointly</option>
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105 <option value="yes">Yes: process each dataset in an independent job</option>
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106 </param>
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107 <when value="no">
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108 <param argument="-in" type="data" format="mzml" multiple="true" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
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109 </when>
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110 <when value="yes">
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111 <param argument="-in" type="data" format="mzml" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
15
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112 </when>
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113 </conditional>
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114 <conditional name="id_in_cond">
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115 <param name="id_in_select" type="select" label="Run tool in batch mode for -id_in">
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116 <option value="no">No: process all datasets jointly</option>
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117 <option value="yes">Yes: process each dataset in an independent job</option>
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118 </param>
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119 <when value="no">
16
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120 <param argument="-id_in" type="data" format="idxml" multiple="true" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
15
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121 </when>
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122 <when value="yes">
16
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123 <param argument="-id_in" type="data" format="idxml" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
15
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124 </when>
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125 </conditional>
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126 <param 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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127 <param 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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128 <param argument="-fragment_mass_tolerance" type="float" 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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129 <expand macro="adv_opts_macro">
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130 <param argument="-number_of_bins" type="integer" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
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131 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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132 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
15
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133 <expand macro="list_string_san" name="test"/>
0
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134 </param>
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135 </expand>
13
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136 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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137 <option value="out_precursor_FLAG">out_precursor (Output file which contains the deviations from the precursors)</option>
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138 <option value="out_fragment_FLAG">out_fragment (Output file which contains the fragment ion m/z deviations)</option>
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139 <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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140 <option value="out_fragment_fit_FLAG">out_fragment_fit (Gaussian fit to the histogram of mass deviations from the fragments)</option>
11
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141 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
0
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142 </param>
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143 </inputs>
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144 <outputs>
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145 <data name="out_precursor" label="${tool.name} on ${on_string}: out_precursor" format="tabular">
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146 <filter>OPTIONAL_OUTPUTS is not None and "out_precursor_FLAG" in OPTIONAL_OUTPUTS</filter>
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147 </data>
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148 <data name="out_fragment" label="${tool.name} on ${on_string}: out_fragment" format="tabular">
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149 <filter>OPTIONAL_OUTPUTS is not None and "out_fragment_FLAG" in OPTIONAL_OUTPUTS</filter>
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150 </data>
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151 <data name="out_precursor_fit" label="${tool.name} on ${on_string}: out_precursor_fit" format="tabular">
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152 <filter>OPTIONAL_OUTPUTS is not None and "out_precursor_fit_FLAG" in OPTIONAL_OUTPUTS</filter>
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153 </data>
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154 <data name="out_fragment_fit" label="${tool.name} on ${on_string}: out_fragment_fit" format="tabular">
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155 <filter>OPTIONAL_OUTPUTS is not None and "out_fragment_fit_FLAG" in OPTIONAL_OUTPUTS</filter>
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156 </data>
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157 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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158 <filter>OPTIONAL_OUTPUTS is None</filter>
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159 </data>
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160 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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161 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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162 </data>
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163 </outputs>
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164 <tests>
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165 <!-- TOPP_IDMassAccuracy_1 -->
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166 <test expect_num_outputs="5">
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167 <section name="adv_opts">
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168 <param name="number_of_bins" value="10"/>
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169 <param name="force" value="false"/>
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170 <param name="test" value="true"/>
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171 </section>
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172 <conditional name="in_cond">
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173 <param name="in" value="spectra.mzML"/>
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174 </conditional>
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175 <conditional name="id_in_cond">
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176 <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/>
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177 </conditional>
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178 <output name="out_precursor" value="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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179 <param name="precursor_error_ppm" value="false"/>
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180 <output name="out_fragment" value="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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181 <param name="fragment_error_ppm" value="false"/>
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182 <param name="fragment_mass_tolerance" value="0.5"/>
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183 <output name="out_precursor_fit" value="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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184 <output name="out_fragment_fit" value="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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185 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/>
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186 <output name="ctd_out" ftype="xml">
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187 <assert_contents>
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188 <is_valid_xml/>
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189 </assert_contents>
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190 </output>
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191 <assert_stdout>
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192 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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193 </assert_stdout>
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194 </test>
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195 </tests>
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196 <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs.
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197
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198
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199 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDMassAccuracy.html]]></help>
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200 <expand macro="references"/>
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201 </tool>