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annotate msgfplus.xml @ 1:797c755b9e74 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit bdb474693831a3375db79755e88641ad32b3b4e6-dirty
author galaxyp
date Sun, 21 Feb 2016 11:27:00 -0500
parents ee56530a559f
children 058a2ab1d462
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1 <tool id="msgfplus" name="MS-GF+" version="0.1">
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2 <description>
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3 Identifies peptides in tandem mass spectra using the MS-GF+ search engine.
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="v10089">msgfplus</requirement>
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7 <environment_variable name="LC_ALL" action="set_to">C</environment_variable>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" description="Job Failed" />
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11 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
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12 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
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13 </stdio>
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14 <command>
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15 <![CDATA[
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16 #set $db_name = $d.display_name.replace(".fasta", "") + ".fasta"
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17 #set $input_name = $s.display_name
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18 #set $output_name = $input_name.replace(".mzML", "") + ".mzid"
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19 ln -s '$s' '${input_name}' &&
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20 ln -s '$d' '${db_name}' &&
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22 echo \\#Mods > Mods.txt &&
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23 #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications)
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24 #for $mod in $common_mods.split(",")
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25 echo '$mod.replace("_", ",")' >> Mods.txt &&
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26 #end for
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27
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28 #for $mod in $custom_mods
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29 echo '${mod.formula_or_mass},${mod.aa_specificity},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt &&
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30 #end for
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32 msgfjar=\$(which MSGFPlus.jar) &&
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33 ( [ -f "\$msgfjar" ] || (echo MSGFPlus.jar not found && exit 1)) &&
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35 java -jar \$msgfjar
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36 -s '$input_name'
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37 -d '$db_name'
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38 -thread \${GALAXY_SLOTS:-1}
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39 -mod Mods.txt
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40 -tda $tda
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41 -t $t$precursor_ion_tol_units
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42 -ti $advanced.isotope_low,$advanced.isotope_high
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43 -m $advanced.m
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44 -inst $inst
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45 -e $e
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46 -protocol $advanced.protocol
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47 -ntt $ntt
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48 -minLength $advanced.minLength
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49 -maxLength $advanced.maxLength
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50 -minCharge $advanced.minCharge
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51 -maxCharge $advanced.maxCharge
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52 -n $advanced.n
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53 -addFeatures $advanced.addFeatures
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54 &&
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55 mv '$output_name' output
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56 ]]>
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57 </command>
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58 <inputs>
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59 <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/>
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60 <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/>
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61 <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" />
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62 <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/>
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63 <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments">
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64 <option value="ppm" selected="true">Parts per million (ppm)</option>
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65 <option value="Da">Daltons</option>
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66 </param>
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67 <param argument="-inst" label="Instrument type" type="select" help="The instrument type that generated the MS/MS spectra is used to determine the scoring model">
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68 <option value="0" selected="true">Low-res (LCQ/LTQ)</option>
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69 <option value="1" >High-res (LTQ-Orbitrap)</option>
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70 <option value="2" >Q-TOF</option>
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71 <option value="3" >Q-Exactive</option>
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72 </param>
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73 <param argument="-e" type="select" label="Enzyme" help="Enzyme used to digest proteins in sample preparation; trypsin is the most commonly used enzyme">
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74 <option value="0">Unspecific cleavage</option>
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75 <option value="1" selected="true">Trypsin, no P rule</option>
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76 <option value="2">Chymotrypsin, no P rule (FYWL)</option>
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77 <option value="3">Lys-C, no P rule</option>
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78 <option value="4">Lys-N</option>
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79 <option value="5">Glu-C (glutamyl endopeptidase)</option>
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80 <option value="6">Arg-C</option>
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81 <option value="7">Asp-N</option>
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82 <option value="8">Alpha-lytic protease</option>
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83 <option value="9">No enzyme</option>
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84 </param>
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85 <param argument="-ntt" type="select" format="text" label="Number of tolerable termini" help="Semi-specific requires more time than fully specific; non-specific requires much more.">
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86 <option value="2" selected="true">Fully specific (both termini match cleavage rules)</option>
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87 <option value="1">Semi-specific (at least one terminus must match cleavage rules)</option>
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88 <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option>
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89 </param>
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90
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91 <param name="common_fixed_modifications" type="select" label="Common Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
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92 <option value="C2H3N1O1_C_fix_any_Carbamidomethyl" selected="true">Carbamidomethyl C</option>
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galaxyp
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93 <option value="144.102063_*_fix_N-term_iTRAQ4plex">iTRAQ 4-plex N-term</option>
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galaxyp
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94 <option value="144.102063_K_fix_any_iTRAQ4plex">iTRAQ 4-plex K</option>
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galaxyp
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95 <option value="225.155833_*_fix_N-term_TMT6plex">TMT 2-plex N-term</option>
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galaxyp
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96 <option value="225.155833_K_fix_any_TMT6plex">TMT 2-plex K</option>
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97 <option value="229.162932_*_fix_N-term_TMT6plex">TMT 6-or-10-plex N-term</option>
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galaxyp
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98 <option value="229.162932_K_fix_any_TMT6plex">TMT 6-or-10-plex K</option>
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99 <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer>
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100 </param>
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101 <param name="common_variable_modifications" type="select" label="Common Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
ee56530a559f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit bdb474693831a3375db79755e88641ad32b3b4e6
galaxyp
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102 <option value="C2H2O1_K_opt_any_Acetyl">Acetylation K</option>
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galaxyp
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103 <option value="C2H2O_*_opt_Prot-N-term_Acetyl">Acetylation Protein N-term</option>
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104 <option value="C2H3NO_C_opt_any_Carbamidomethyl">Carbamidomethyl C</option>
ee56530a559f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit bdb474693831a3375db79755e88641ad32b3b4e6
galaxyp
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105 <option value="C2H3NO_*_opt_N-term_Carbamidomethyl">Carbamidomethyl N-term</option>
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galaxyp
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106 <option value="H-1N-1O1_N_opt_any_Deamidated">Deamidation N</option>
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galaxyp
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107 <option value="H-1N-1O1_Q_opt_any_Deamidated">Deamidation Q</option>
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108 <option value="CH2_K_opt_any_Methyl">Methylation K</option>
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109 <option value="O1_M_opt_any_Oxidation" selected="true">Oxidation M</option>
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110 <option value="HO3P_S_opt_any_Phospho">Phosphorylation S</option>
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111 <option value="HO3P_T_opt_any_Phospho">Phosphorylation T</option>
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112 <option value="HO3P_Y_opt_any_Phospho">Phosphorylation Y</option>
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113 <option value="H-2O-1_E_opt_N-term_Glu-&gt;pyro-Glu">Pyro-glu from E</option>
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114 <option value="H-3N-1_Q_opt_N-term_Gln-&gt;pyro-Glu">Pyro-glu from Q</option>
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115 <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer>
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116 </param>
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117
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118 <repeat name="custom_mods" title="Custom Modifications" help="Specify modifications with custom parameters">
ee56530a559f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit bdb474693831a3375db79755e88641ad32b3b4e6
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119 <param name="formula_or_mass" type="text" label="Formula or Mass">
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120 <sanitizer>
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121 <valid initial="string.digits">
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122 <add value="C"/>
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123 <add value="H"/>
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124 <add value="O"/>
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125 <add value="N"/>
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126 <add value="S"/>
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127 <add value="P"/>
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128 <add value="B"/><add value="r"/>
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129 <add value="C"/><add value="l"/>
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130 <add value="F"/><add value="e"/>
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131 <add value="S"/>
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132 <add value="."/>
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133 <add value="-"/>
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134 </valid>
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135 </sanitizer>
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136 </param>
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137 <param name="aa_specificity" type="select" multiple="true" label="Amino Acid Specificity">
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138 <option value="*" selected="true">Any</option>
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139 <option value="A">A</option>
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140 <option value="C">C</option>
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141 <option value="D">D</option>
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142 <option value="E">E</option>
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143 <option value="F">F</option>
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144 <option value="G">G</option>
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145 <option value="H">H</option>
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146 <option value="I">I</option>
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147 <option value="K">K</option>
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148 <option value="L">L</option>
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149 <option value="M">M</option>
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150 <option value="N">N</option>
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151 <option value="P">P</option>
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152 <option value="Q">Q</option>
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153 <option value="R">R</option>
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154 <option value="S">S</option>
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155 <option value="T">T</option>
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156 <option value="V">V</option>
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157 <option value="W">W</option>
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158 <option value="Y">Y</option>
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159 </param>
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160 <param name="fix_or_opt" type="select" label="Variable or Fixed?">
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161 <option value="opt" selected="true">Variable</option>
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162 <option value="fix">Fixed</option>
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163 </param>
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164 <param name="position_specificity" type="select" label="Positional Specificity">
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165 <option value="any" selected="true">Any</option>
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166 <option value="n-term">Peptide N-terminal</option>
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167 <option value="c-term">Peptide C-terminal</option>
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galaxyp
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168 <option value="prot-n-term">Protein N-terminal</option>
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169 <option value="prot-c-term">Protein C-terminal</option>
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170 </param>
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171 <param name="mod_name" type="text" label="Name" help="If this mod has an entry there in Unimod, this name should match its name there" />
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172 </repeat>
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173
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174 <!-- MS-GF+ ADVANCED PARAMETERS -->
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175 <section name="advanced" title="Advanced Options">
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176 <param argument="-minCharge" label="Minimum precursor charge" value="2" type="integer" help="Minimum precursor charge to consider if charges are not specified in the spectrum file"/>
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177 <param argument="-maxCharge" label="Maximum precursor charge" value="3" type="integer" help="Maximum precursor charge to consider if charges are not specified in the spectrum file"/>
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178 <param argument="-minLength" label="Minimum peptide length" value="6" type="integer" help="Minimum peptide length to consider"/>
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179 <param argument="-maxLength" label="Maximum peptide length" value="40" type="integer" help="Maximum peptide length to consider"/>
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180 <param name="num_ptms" label="Maximum modifications allowed per peptide" type="integer" value="2" />
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181 <param argument="-m" label="Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
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182 <option value="0" selected="True">As written in the spectrum or CID if no info</option>
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183 <option value="1" >CID</option>
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184 <option value="2" >ETD</option>
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185 <option value="3" >HCD</option>
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186 </param>
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187 <param argument="-protocol" label="Protocol type" type="select" help="Protocols are used to enable scoring parameters for enriched and/or labeled samples">
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188 <option value="0" selected="True">Automatic</option>
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189 <option value="1" >Phosphorylation</option>
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190 <option value="2" >iTRAQ</option>
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191 <option value="3" >iTRAQPhospho</option>
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192 <option value="4" >TMT</option>
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193 <option value="5" >Standard</option>
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194 </param>
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195 <param argument="-n" label="Maximum matches per spectrum" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
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196 <param argument="-addFeatures" label="Calculate additional scoring features?" type="boolean" truevalue="1" falsevalue="0" help="If true, several extra derivative scores are calculated for each match" />
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197 <param name="isotope_low" label="Lower isotope error range" type="integer" value="0" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation (-ti)" />
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198 <param name="isotope_high" label="Upper isotope error range" type="integer" value="1" />
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199 </section>
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200 </inputs>
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201 <outputs>
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202 <data name="output" format="mzid" from_work_dir="output" />
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203 </outputs>
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204 <tests>
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205 <test>
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206 <param name="s" value="input/201208-378803.mzML" />
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207 <param name="d" value="input/cow.protein.PRG2012-subset.fasta" />
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208 <param name="tda" value="1" />
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209 <param name="ntt" value="1" />
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210 <param name="t" value="50" />
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211 <param name="precursor_ion_tol_units" value="ppm" />
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212 <param name="common_fixed_modifications" value="" />
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213 <param name="common_variable_modifications" value="" />
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214 <output name="output" file="201208-378803-msgf-50ppm-semitryptic-no_mods.mzid" lines_diff="6" />
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215 </test>
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216 <test>
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217 <param name="s" value="input/201208-378803.mzML" />
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218 <param name="d" value="input/cow.protein.PRG2012-subset.fasta" />
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219 <param name="tda" value="1" />
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220 <param name="t" value="0.02" />
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221 <param name="precursor_ion_tol_units" value="Da" />
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222 <param name="isotope_low" value="-1" />
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223 <param name="isotope_high" value="0" />
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224 <param name="m" value="3" />
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225 <param name="inst" value="2" />
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226 <param name="e" value="3" />
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227 <param name="protocol" value="2" />
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228 <param name="minLength" value="10" />
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229 <param name="maxLength" value="20" />
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230 <param name="minCharge" value="2" />
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231 <param name="maxCharge" value="6" />
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232 <param name="n" value="2" />
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233 <param name="addFeatures" value="1" />
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234
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235 <param name="common_fixed_modifications" value="C2H3N1O1_C_fix_any_Carbamidomethyl,144.102063_*_fix_N-term_iTRAQ4plex,144.102063_K_fix_any_iTRAQ4plex" />
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236 <param name="common_variable_modifications" value="O1_M_opt_any_Oxidation,H-3N-1_Q_opt_N-term_Gln->pyro-Glu" />
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237
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238 <param name="custom_mods_0|formula_or_mass" value="C-2H-2O-2" />
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239 <param name="custom_mods_0|aa_specificity" value="G" />
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240 <param name="custom_mods_0|fix_or_opt" value="opt" />
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241 <param name="custom_mods_0|position_specificity" value="c-term" />
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242 <param name="custom_mods_0|mod_name" value="Gly-loss+Amide" />
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243
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244 <param name="custom_mods_1|formula_or_mass" value="C10H10N5O7P" />
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245 <param name="custom_mods_1|aa_specificity" value="CS" />
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246 <param name="custom_mods_1|fix_or_opt" value="opt" />
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247 <param name="custom_mods_1|position_specificity" value="any" />
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248 <param name="custom_mods_1|mod_name" value="cGMP" />
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249
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250 <output name="output" file="201208-378803-msgf-2mmu-tryptic-many_mods.mzid" lines_diff="6" />
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251 </test>
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252 </tests>
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253 <help>
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254 **What it does**
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255
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256 Performs protein identification via database search using MS-GF+.
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257
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258 </help>
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259 <citations>
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260 <citation type="doi">10.1038/ncomms6277</citation>
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261 <citation type="doi">10.1021/pr8001244</citation>
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262 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Gruening, B, Chambers, MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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263 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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264 </citations>
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265 </tool>