Mercurial > repos > galaxyp > peptideshaker

annotate macros.xml @ 20:2375ad43661f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
author galaxyp
date Fri, 13 Jan 2017 14:15:29 -0500
parents ef4ac2d49ff0
children ba5377754cce
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1 <macros>
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2 <xml name="stdio">
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3 <stdio>
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4 <exit_code range="1:" level="fatal" description="Job Failed" />
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5 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
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6 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
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7 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
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8 </stdio>
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9 </xml>
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10 <token name="@GENERAL_PARAMETERS@">
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11 -frag_tol "${fragment_tol}"
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12 ### -frag_ppm
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13 -prec_tol "${precursor_ion_tol}"
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14 -prec_ppm "${precursor_ion_tol_units}"
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15 ### -digestion
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16 ### multiple enzymes?
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17 -enzyme "${enzyme}"
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18 ### -specificity
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19 #set $fixed_mods_str = $fixed_modifications or ''
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20 #set $variable_mods_str = $variable_modifications or ''
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21 #if $fixed_mods_str
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22 -fixed_mods "$fixed_mods_str"
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23 #end if
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24 #if $variable_mods_str
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25 -variable_mods "$variable_mods_str"
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26 #end if
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27 -min_charge $min_charge
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28 -max_charge $max_charge
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29 ### value per enzyme
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30 -mc $missed_cleavages
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31 -fi $forward_ion
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32 -ri $reverse_ion
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33 </token>
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34 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
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35 <token name="@SEARCHGUI_VERSION@">3.1.4</token>
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36 <xml name="general_options">
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37 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
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38 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
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39 <option value="1">Parts per million (ppm)</option>
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40 <option value="2">Daltons</option>
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41 </param>
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42 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"
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43 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
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44 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
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45 help="Provide error value for fragment ions, based on instrument used"/>
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46 <param name="enzyme" type="select" label="Enzyme"
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47 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
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48 <option value="Trypsin">Trypsin</option>
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49 <option value="Arg-C">Arg-C</option>
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50 <option value="CNBr">CNBr</option>
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51 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
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52 <option value="Formic Acid">Formic Acid</option>
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53 <option value="Lys-C">Lys-C</option>
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54 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
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55 <option value="Pepsin A">Pepsin A</option>
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56 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
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57 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
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58 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
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59 <option value="Whole Protein">Whole Protein</option>
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60 <option value="Asp-N">Asp-N</option>
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61 <option value="Glu-C">Glu-C</option>
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62 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
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63 <option value="Top-Down">Top-Down</option>
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64 <option value="Semi-Tryptic">Semi-Tryptic</option>
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65 <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
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66 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
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67 <option value="Asp-N (DE)">Asp-N (DE)</option>
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68 <option value="Glu-C (DE)">Glu-C (DE)</option>
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69 <option value="Lys-N (K)">Lys-N (K)</option>
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70 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
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71 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
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72 <option value="Semi-Glu-C">Semi-Glu-C</option>
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73 <option value="LysargiNase">LysargiNase</option>
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74 <option value="Semi-LysargiNase">Semi-LysargiNase</option>
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75 <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
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76 <option value="Semi-Arg-C">Semi-Arg-C</option>
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77 <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
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78 <option value="Arg-N">Arg-N</option>
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79 <option value="Semi-Arg-N">Semi-Arg-N</option>
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80 </param>
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81 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
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82 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
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83 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
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84 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
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85 <options from_file="searchgui_mods.loc">
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86 <column name="name" index="0" />
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87 <column name="value" index="0" />
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88 </options>
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89 </param>
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90 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
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91 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
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92 <options from_file="searchgui_mods.loc">
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93 <column name="name" index="0" />
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94 <column name="value" index="0" />
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95 </options>
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96 </param>
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97 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
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98 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
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99 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
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100 <option value="a">a</option>
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101 <option value="b" selected="true">b</option>
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102 <option value="c">c</option>
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103 </param>
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104 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
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105 <option value="x">x</option>
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106 <option value="y" selected="true">y</option>
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107 <option value="z">z</option>
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108 </param>
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109 </xml>
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110
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111 <xml name="citations">
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112 <citations>
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113 <citation type="doi">10.1186/1471-2105-12-70</citation>
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114 <citation type="doi">10.1002/pmic.201000595</citation>
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115 <citation type="doi">doi:10.1038/nbt.3109</citation>
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116 </citations>
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117 </xml>
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118
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119 </macros>