Mercurial > repos > galaxyp > openms_siriusadapter

annotate SiriusAdapter.xml @ 2:8a3a17bbcb63 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 08:07:01 -0400
parents 7c78a40e68d7
children 01731de4b735
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7c78a40e68d7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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="SiriusAdapter" name="SiriusAdapter" version="2.3.0">
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5 <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SiriusAdapter</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 detect_errors="aggressive"><![CDATA[SiriusAdapter
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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_sirius:
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19 -out_sirius $param_out_sirius
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20 #end if
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21 #if $param_out_fingerid:
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22 -out_fingerid $param_out_fingerid
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23 #end if
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24 #if $param_profile:
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25 -profile
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26 #if " " in str($param_profile):
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27 "$param_profile"
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28 #else
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29 $param_profile
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30 #end if
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31 #end if
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32 #if $param_candidates:
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33 -candidates $param_candidates
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34 #end if
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35 #if $param_database:
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36 -database
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37 #if " " in str($param_database):
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38 "$param_database"
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39 #else
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40 $param_database
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41 #end if
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42 #end if
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43 #if $param_noise:
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44 -noise $param_noise
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45 #end if
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46 #if $param_ppm_max:
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47 -ppm_max $param_ppm_max
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48 #end if
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49 #if $param_isotope:
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50 -isotope
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51 #if " " in str($param_isotope):
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52 "$param_isotope"
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53 #else
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54 $param_isotope
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55 #end if
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56 #end if
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57 #if $param_elements:
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58 -elements "$param_elements"
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59 #end if
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60 #if $param_number:
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61 -number $param_number
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62 #end if
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63 #if $param_auto_charge:
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64 -auto_charge
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65 #end if
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66 #if $param_iontree:
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67 -iontree
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68 #end if
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69 #if $param_no_recalibration:
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70 -no_recalibration
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71 #end if
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72 #if $adv_opts.adv_opts_selector=='advanced':
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73 #if $adv_opts.param_force:
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74 -force
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75 #end if
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76 #end if
2
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77 ]]></command>
0
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78 <inputs>
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79 <param name="param_in" type="data" format="mzml" optional="False" label="MzML Input file" help="(-in) "/>
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80 <param name="param_profile" display="radio" type="select" optional="False" value="qtof" label="Specify the used analysis profile" help="(-profile) ">
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81 <option value="qtof" selected="true">qtof</option>
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82 <option value="orbitrap">orbitrap</option>
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83 <option value="fticr">fticr</option>
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84 </param>
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85 <param name="param_candidates" type="integer" value="5" label="The number of candidates in the output" help="(-candidates) Default 5 best candidates"/>
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86 <param name="param_database" type="select" optional="False" value="all" label="search formulas in given database" help="(-database) ">
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87 <option value="all" selected="true">all</option>
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88 <option value="chebi">chebi</option>
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89 <option value="custom">custom</option>
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90 <option value="kegg">kegg</option>
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91 <option value="bio">bio</option>
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92 <option value="natural products">natural products</option>
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93 <option value="pubmed">pubmed</option>
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94 <option value="hmdb">hmdb</option>
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95 <option value="biocyc">biocyc</option>
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96 <option value="hsdb">hsdb</option>
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97 <option value="knapsack">knapsack</option>
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98 <option value="biological">biological</option>
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99 <option value="zinc bio">zinc bio</option>
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100 <option value="gnps">gnps</option>
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101 <option value="pubchem">pubchem</option>
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102 <option value="mesh">mesh</option>
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103 <option value="maconda">maconda</option>
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104 </param>
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105 <param name="param_noise" type="integer" value="0" label="median intensity of noise peaks" help="(-noise) "/>
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106 <param name="param_ppm_max" type="integer" value="10" label="allowed ppm for decomposing masses" help="(-ppm_max) "/>
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107 <param name="param_isotope" display="radio" type="select" optional="False" value="both" label="how to handle isotope pattern data" help="(-isotope) Use 'score' to use them for ranking or 'filter' if you just want to remove candidates with bad isotope pattern. With 'both' you can use isotopes for filtering and scoring (default). Use 'omit' to ignore isotope pattern">
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108 <option value="score">score</option>
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109 <option value="filter">filter</option>
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110 <option value="both" selected="true">both</option>
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111 <option value="omit">omit</option>
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112 </param>
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113 <param name="param_elements" type="text" size="30" value="CHNOP[5]S" label="The allowed elements" help="(-elements) Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the maximal allowed occurence of these elements: CHNOP[5]S[8]Cl[1]. By default CHNOP[5]S is used">
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114 <sanitizer>
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115 <valid initial="string.printable">
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116 <remove value="'"/>
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117 <remove value="&quot;"/>
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118 </valid>
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119 </sanitizer>
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120 </param>
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121 <param name="param_number" type="integer" value="10" label="The number of compounds used in the output" help="(-number) "/>
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122 <param name="param_auto_charge" display="radio" type="boolean" truevalue="-auto_charge" falsevalue="" checked="false" optional="True" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="(-auto_charge) With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/>
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123 <param name="param_iontree" display="radio" type="boolean" truevalue="-iontree" falsevalue="" checked="false" optional="True" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help="(-iontree) "/>
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124 <param name="param_no_recalibration" display="radio" type="boolean" truevalue="-no_recalibration" falsevalue="" checked="false" optional="True" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help="(-no_recalibration) "/>
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125 <expand macro="advanced_options">
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126 <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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127 </expand>
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128 </inputs>
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129 <outputs>
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130 <data name="param_out_sirius" format="tabular"/>
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131 <data name="param_out_fingerid" format="tabular"/>
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132 </outputs>
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133 <help>Tool for metabolite identification using single and tandem mass spectrometry
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134
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135
2
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136 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SiriusAdapter.html</help>
0
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137 </tool>