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annotate IDFilter.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="IDFilter" name="IDFilter" version="2.0.0">
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5 <description>Filters results from protein or peptide identification engines based on different criteria.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDFilter</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>IDFilter
0
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14
4
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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:
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19 -out $param_out
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20 #end if
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21 #if $param_min_length:
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22 -min_length $param_min_length
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23 #end if
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24 #if $param_max_length:
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25 -max_length $param_max_length
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26 #end if
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27 #if $param_min_charge:
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28 -min_charge $param_min_charge
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29 #end if
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30 #if $param_var_mods:
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31 -var_mods
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32 #end if
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33 #if $param_unique:
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34 -unique
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35 #end if
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36 #if $param_unique_per_protein:
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37 -unique_per_protein
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38 #end if
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39 #if $param_keep_unreferenced_protein_hits:
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40 -keep_unreferenced_protein_hits
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41 #end if
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42 #if $param_remove_decoys:
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43 -remove_decoys
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44 #end if
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45 #if $param_delete_unreferenced_peptide_hits:
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46 -delete_unreferenced_peptide_hits
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47 #end if
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48 -threads \${GALAXY_SLOTS:-24}
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49 #if $param_precursor_rt:
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50 -precursor:rt &quot;$param_precursor_rt&quot;
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51 #end if
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52 #if $param_precursor_mz:
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53 -precursor:mz &quot;$param_precursor_mz&quot;
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54 #end if
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55 #if $param_precursor_allow_missing:
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56 -precursor:allow_missing
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57 #end if
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58 #if $param_score_pep:
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59 -score:pep $param_score_pep
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60 #end if
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61 #if $param_score_prot:
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62 -score:prot $param_score_prot
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63 #end if
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64 #if $param_thresh_pep:
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65 -thresh:pep $param_thresh_pep
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66 #end if
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67 #if $param_thresh_prot:
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68 -thresh:prot $param_thresh_prot
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69 #end if
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70 #if $param_whitelist_proteins:
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71 -whitelist:proteins $param_whitelist_proteins
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72 #end if
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73 #if $param_whitelist_by_seq_only:
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74 -whitelist:by_seq_only
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75 #end if
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76
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77 #if $rep_param_whitelist_protein_accessions:
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78 -whitelist:protein_accessions
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79 #for token in $rep_param_whitelist_protein_accessions:
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80 #if &quot; &quot; in str(token):
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81 &quot;$token.param_whitelist_protein_accessions&quot;
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82 #else
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83 $token.param_whitelist_protein_accessions
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84 #end if
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85 #end for
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86 #end if
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87 #if $param_blacklist_peptides:
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88 -blacklist:peptides $param_blacklist_peptides
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89 #end if
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90 #if $param_blacklist_ignore_modifications:
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91 -blacklist:ignore_modifications
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92 #end if
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93 #if $param_rt_p_value:
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94 -rt:p_value $param_rt_p_value
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95 #end if
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96 #if $param_rt_p_value_1st_dim:
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97 -rt:p_value_1st_dim $param_rt_p_value_1st_dim
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98 #end if
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99 #if $param_mz_error:
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100 -mz:error $param_mz_error
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101 #end if
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102 #if $param_mz_unit:
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103 -mz:unit
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104 #if &quot; &quot; in str($param_mz_unit):
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105 &quot;$param_mz_unit&quot;
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106 #else
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107 $param_mz_unit
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108 #end if
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109 #end if
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110 #if $param_best_n_peptide_hits:
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111 -best:n_peptide_hits $param_best_n_peptide_hits
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112 #end if
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113 #if $param_best_n_protein_hits:
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114 -best:n_protein_hits $param_best_n_protein_hits
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115 #end if
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116 #if $param_best_strict:
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117 -best:strict
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118 #end if
0
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119 #if $adv_opts.adv_opts_selector=='advanced':
4
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120 #if $adv_opts.param_force:
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121 -force
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122 #end if
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123 #if $adv_opts.param_best_n_to_m_peptide_hits:
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124 -best:n_to_m_peptide_hits &quot;$adv_opts.param_best_n_to_m_peptide_hits&quot;
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125 #end if
0
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126 #end if
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127 </command>
4
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128 <inputs>
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129 <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
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130 <param help="(-min_length) Value 0 will have no filter effect" label="Keep only peptide hits with a length greater or equal this value" min="0" name="param_min_length" optional="True" type="integer" value="0"/>
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131 <param help="(-max_length) Value 0 will have no filter effect. Value is overridden by min_length, i.e. if max_length &lt; min_length, max_length will be ignored" label="Keep only peptide hits with a length less or equal this value" min="0" name="param_max_length" optional="True" type="integer" value="0"/>
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132 <param help="(-min_charge) " label="Keep only peptide hits for tandem spectra with charge greater or equal this value" min="1" name="param_min_charge" optional="True" type="integer" value="1"/>
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133 <param checked="false" falsevalue="" help="(-var_mods) " label="Keep only peptide hits with variable modifications (fixed modifications from SearchParameters will be ignored)" name="param_var_mods" optional="True" truevalue="-var_mods" type="boolean"/>
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134 <param checked="false" falsevalue="" help="(-unique) " label="If a peptide hit occurs more than once per PSM, only one instance is kept" name="param_unique" optional="True" truevalue="-unique" type="boolean"/>
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135 <param checked="false" falsevalue="" help="(-unique_per_protein) Remember that isoforms count as different proteins!" label="Only peptides matching exactly one protein are kept" name="param_unique_per_protein" optional="True" truevalue="-unique_per_protein" type="boolean"/>
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136 <param checked="false" falsevalue="" help="(-keep_unreferenced_protein_hits) " label="Proteins not referenced by a peptide are retained in the ids" name="param_keep_unreferenced_protein_hits" optional="True" truevalue="-keep_unreferenced_protein_hits" type="boolean"/>
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137 <param checked="false" falsevalue="" help="(-remove_decoys) Usually used in combination with 'delete_unreferenced_peptide_hits'" label="Remove proteins according to the information in the user parameters" name="param_remove_decoys" optional="True" truevalue="-remove_decoys" type="boolean"/>
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138 <param checked="false" falsevalue="" help="(-delete_unreferenced_peptide_hits) Usually used in combination with 'score:prot' or 'thresh:prot'" label="Peptides not referenced by any protein are deleted in the ids" name="param_delete_unreferenced_peptide_hits" optional="True" truevalue="-delete_unreferenced_peptide_hits" type="boolean"/>
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139 <param help="(-rt) " label="Retention time range to extract" name="param_precursor_rt" size="30" type="text" value=":">
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140 <sanitizer>
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141 <valid initial="string.printable">
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142 <remove value="'"/>
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143 <remove value="&quot;"/>
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144 </valid>
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145 </sanitizer>
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146 </param>
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147 <param help="(-mz) " label="Mass-to-charge range to extract" name="param_precursor_mz" size="30" type="text" value=":">
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148 <sanitizer>
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149 <valid initial="string.printable">
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150 <remove value="'"/>
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151 <remove value="&quot;"/>
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152 </valid>
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153 </sanitizer>
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154 </param>
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155 <param checked="false" falsevalue="" help="(-allow_missing) " label="When filtering by precursor RT or m/z, keep peptide IDs with missing precursor information ('RT'/'MZ' meta values)?" name="param_precursor_allow_missing" optional="True" truevalue="-precursor:allow_missing" type="boolean"/>
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156 <param help="(-pep) The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc" label="The score which should be reached by a peptide hit to be kept" name="param_score_pep" type="float" value="0.0"/>
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157 <param help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides" label="The score which should be reached by a protein hit to be kept" name="param_score_prot" type="float" value="0.0"/>
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158 <param help="(-pep) " label="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold" name="param_thresh_pep" type="float" value="0.0"/>
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159 <param help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides" label="Keep a protein hit only if its score is above this fraction of the protein significance threshold" name="param_thresh_prot" type="float" value="0.0"/>
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160 <param format="fasta" help="(-proteins) &lt;br&gt;All peptides that are not a substring of a sequence in this file are removed &lt;br&gt;All proteins whose accession is not present in this file are removed" label="filename of a FASTA file containing protein sequences" name="param_whitelist_proteins" optional="True" type="data"/>
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161 <param checked="false" falsevalue="" help="(-by_seq_only) " label="Match peptides with FASTA file by sequence instead of accession and disable protein filtering" name="param_whitelist_by_seq_only" optional="True" truevalue="-whitelist:by_seq_only" type="boolean"/>
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162 <repeat min="0" name="rep_param_whitelist_protein_accessions" title="param_whitelist_protein_accessions">
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163 <param help="(-protein_accessions) &lt;br&gt;Only proteins of the provided list are retained" label="All peptides that are not referencing at least one of the provided protein accession are removed" name="param_whitelist_protein_accessions" size="30" type="text">
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164 <sanitizer>
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165 <valid initial="string.printable">
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166 <remove value="'"/>
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167 <remove value="&quot;"/>
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168 </valid>
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169 </sanitizer>
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170 </param>
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171 </repeat>
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172 <param format="xml" help="(-peptides) Use with blacklist:ignore_modification flag to only compare by sequence. &lt;br&gt;" label="Peptides having the same sequence and modification assignment as any peptide in this file will be filtered out" name="param_blacklist_peptides" optional="True" type="data"/>
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173 <param checked="false" falsevalue="" help="(-ignore_modifications) &lt;br&gt;" label="Compare blacklisted peptides by sequence only" name="param_blacklist_ignore_modifications" optional="True" truevalue="-blacklist:ignore_modifications" type="boolean"/>
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174 <param help="(-p_value) " label="Retention time filtering by the p-value predicted by RTPredict" max="1.0" min="0.0" name="param_rt_p_value" optional="True" type="float" value="0.0"/>
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175 <param help="(-p_value_1st_dim) " label="Retention time filtering by the p-value predicted by RTPredict for first dimension" max="1.0" min="0.0" name="param_rt_p_value_1st_dim" optional="True" type="float" value="0.0"/>
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176 <param help="(-error) " label="Filtering by deviation to theoretical mass (disabled for negative values)" name="param_mz_error" type="float" value="-1.0"/>
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177 <param help="(-unit) " label="Absolute or relative erro" name="param_mz_unit" optional="True" type="select" value="ppm">
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178 <option value="Da">Da</option>
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179 <option value="ppm">ppm</option>
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180 </param>
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181 <param help="(-n_peptide_hits) " label="Keep only the 'n' highest scoring peptide hits per spectrum (for n&gt;0)" min="0" name="param_best_n_peptide_hits" optional="True" type="integer" value="0"/>
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182 <param help="(-n_protein_hits) " label="Keep only the 'n' highest scoring protein hits (for n&gt;0)" min="0" name="param_best_n_protein_hits" optional="True" type="integer" value="0"/>
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183 <param checked="false" falsevalue="" help="(-strict) &lt;br&gt;Similar to n_peptide_hits=1, but if there are two or more highest scoring hits, none are kept" label="Keep only the highest scoring peptide hit" name="param_best_strict" optional="True" truevalue="-best:strict" type="boolean"/>
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184 <expand macro="advanced_options">
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185 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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186 <param help="(-n_to_m_peptide_hits) " label="peptide hit rank range to extracts" name="param_best_n_to_m_peptide_hits" size="30" type="text" value=":">
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187 <sanitizer>
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188 <valid initial="string.printable">
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189 <remove value="'"/>
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190 <remove value="&quot;"/>
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191 </valid>
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192 </sanitizer>
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193 </param>
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194 </expand>
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195 </inputs>
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196 <outputs>
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197 <data format="xml" name="param_out"/>
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198 </outputs>
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199 <help>Filters results from protein or peptide identification engines based on different criteria.
0
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200
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201
4
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202 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFilter.html</help>
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203 </tool>