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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="PeptideIndexer" name="PeptideIndexer" version="2.0.0">
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3 <description>Refreshes the protein references for all peptide hits.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">PeptideIndexer</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>PeptideIndexer
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11
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12 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_fasta:
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16 -fasta $param_fasta
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_decoy_string:
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22 -decoy_string "$param_decoy_string"
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23 #end if
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24 #if $param_missing_decoy_action:
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25 -missing_decoy_action
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26 #if " " in str($param_missing_decoy_action):
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27 "$param_missing_decoy_action"
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28 #else
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29 $param_missing_decoy_action
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30 #end if
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31 #end if
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32 #if $param_prefix:
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33 -prefix
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34 #end if
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35 #if $param_annotate_proteins:
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36 -annotate_proteins
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37 #end if
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38 #if $param_write_protein_sequence:
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39 -write_protein_sequence
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40 #end if
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41 #if $param_keep_unreferenced_proteins:
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42 -keep_unreferenced_proteins
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43 #end if
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44 #if $param_allow_unmatched:
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45 -allow_unmatched
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46 #end if
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47 #if $param_full_tolerant_search:
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48 -full_tolerant_search
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49 #end if
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50 #if $param_aaa_max:
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51 -aaa_max $param_aaa_max
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52 #end if
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53 #if $param_IL_equivalent:
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54 -IL_equivalent
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55 #end if
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56 -threads \${GALAXY_SLOTS:-24}
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57 #if $param_enzyme_name:
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58 -enzyme:name
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59 #if " " in str($param_enzyme_name):
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60 "$param_enzyme_name"
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61 #else
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62 $param_enzyme_name
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63 #end if
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64 #end if
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65 #if $param_enzyme_specificity:
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66 -enzyme:specificity
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67 #if " " in str($param_enzyme_specificity):
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68 "$param_enzyme_specificity"
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69 #else
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70 $param_enzyme_specificity
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71 #end if
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72 #end if
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73 #if $adv_opts.adv_opts_selector=='advanced':
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74 #if $adv_opts.param_force:
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75 -force
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76 #end if
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77 #end if
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78 </command>
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79 <inputs>
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80 <param name="param_in" type="data" format="idxml" optional="False" label="Input idXML file containing the identifications" help="(-in) "/>
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81 <param name="param_fasta" type="data" format="fasta" optional="False" label="Input sequence database in FASTA format" help="(-fasta) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
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82 <param name="param_decoy_string" type="text" size="30" value="_rev" label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" help="(-decoy_string) ">
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83 <sanitizer>
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84 <valid initial="string.printable">
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85 <remove value="'"/>
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86 <remove value="""/>
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87 </valid>
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88 </sanitizer>
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89 </param>
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90 <param name="param_missing_decoy_action" type="select" optional="True" value="error" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message)" help="(-missing_decoy_action) ">
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91 <option value="error">error</option>
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92 <option value="warn">warn</option>
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93 </param>
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94 <param name="param_prefix" type="boolean" truevalue="-prefix" falsevalue="" checked="false" optional="True" label="If set, protein accessions in the database contain 'decoy_string' as prefix" help="(-prefix) "/>
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95 <param name="param_annotate_proteins" type="boolean" truevalue="-annotate_proteins" falsevalue="" checked="false" optional="True" label="If set, add target/decoy information to proteins (as well as peptides)" help="(-annotate_proteins) "/>
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96 <param name="param_write_protein_sequence" type="boolean" truevalue="-write_protein_sequence" falsevalue="" checked="false" optional="True" label="If set, the protein sequences are stored as well" help="(-write_protein_sequence) "/>
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97 <param name="param_keep_unreferenced_proteins" type="boolean" truevalue="-keep_unreferenced_proteins" falsevalue="" checked="false" optional="True" label="If set, protein hits which are not referenced by any peptide are kept" help="(-keep_unreferenced_proteins) "/>
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98 <param name="param_allow_unmatched" type="boolean" truevalue="-allow_unmatched" falsevalue="" checked="false" optional="True" label="If set, unmatched peptide sequences are allowed" help="(-allow_unmatched) By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides"/>
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99 <param name="param_full_tolerant_search" type="boolean" truevalue="-full_tolerant_search" falsevalue="" checked="false" optional="True" label="If set, all peptide sequences are matched using tolerant search" help="(-full_tolerant_search) Thus potentially more proteins (containing ambiguous amino acids) are associated. This is much slower!"/>
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100 <param name="param_aaa_max" type="integer" min="0" optional="True" value="4" label="Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein database with AAA's" help="(-aaa_max) AAA's are 'B', 'Z' and 'X'"/>
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101 <param name="param_IL_equivalent" type="boolean" truevalue="-IL_equivalent" falsevalue="" checked="false" optional="True" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="(-IL_equivalent) "/>
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102 <param name="param_enzyme_name" type="select" optional="True" value="Trypsin" label="Enzyme which determines valid cleavage sites -" help="(-name) e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)">
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103 <option value="Trypsin">Trypsin</option>
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104 <option value="none">none</option>
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105 </param>
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106 <param name="param_enzyme_specificity" type="select" optional="True" value="full" label="Specificity of the enzyme" help="(-specificity) <br> 'full': both internal cleavage sites must match. <br> 'semi': one of two internal cleavage sites must match. <br> 'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here">
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107 <option value="full">full</option>
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108 <option value="semi">semi</option>
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109 <option value="none">none</option>
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110 </param>
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111 <expand macro="advanced_options">
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112 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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113 </expand>
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114 </inputs>
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115 <outputs>
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116 <data name="param_out" format="idxml"/>
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117 </outputs>
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118 <help>**What it does**
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119
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120 Refreshes the protein references for all peptide hits.
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121
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122
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123 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeptideIndexer.html</help>
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124 <expand macro="references"/>
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125 </tool>
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