|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="IDFilter" name="IDFilter" version="2.0.0">
|
|
|
3 <description>Filters results from protein or peptide identification engines based on different criteria.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">IDFilter</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>IDFilter
|
|
|
11
|
|
|
12 #if $param_in:
|
|
|
13 -in $param_in
|
|
|
14 #end if
|
|
|
15 #if $param_out:
|
|
|
16 -out $param_out
|
|
|
17 #end if
|
|
|
18 #if $param_min_length:
|
|
|
19 -min_length $param_min_length
|
|
|
20 #end if
|
|
|
21 #if $param_max_length:
|
|
|
22 -max_length $param_max_length
|
|
|
23 #end if
|
|
|
24 #if $param_min_charge:
|
|
|
25 -min_charge $param_min_charge
|
|
|
26 #end if
|
|
|
27 #if $param_var_mods:
|
|
|
28 -var_mods
|
|
|
29 #end if
|
|
|
30 #if $param_unique:
|
|
|
31 -unique
|
|
|
32 #end if
|
|
|
33 #if $param_unique_per_protein:
|
|
|
34 -unique_per_protein
|
|
|
35 #end if
|
|
|
36 #if $param_keep_unreferenced_protein_hits:
|
|
|
37 -keep_unreferenced_protein_hits
|
|
|
38 #end if
|
|
|
39 #if $param_remove_decoys:
|
|
|
40 -remove_decoys
|
|
|
41 #end if
|
|
|
42 #if $param_delete_unreferenced_peptide_hits:
|
|
|
43 -delete_unreferenced_peptide_hits
|
|
|
44 #end if
|
|
|
45 -threads \${GALAXY_SLOTS:-24}
|
|
|
46 #if $param_precursor_rt:
|
|
|
47 -precursor:rt "$param_precursor_rt"
|
|
|
48 #end if
|
|
|
49 #if $param_precursor_mz:
|
|
|
50 -precursor:mz "$param_precursor_mz"
|
|
|
51 #end if
|
|
|
52 #if $param_precursor_allow_missing:
|
|
|
53 -precursor:allow_missing
|
|
|
54 #end if
|
|
|
55 #if $param_score_pep:
|
|
|
56 -score:pep $param_score_pep
|
|
|
57 #end if
|
|
|
58 #if $param_score_prot:
|
|
|
59 -score:prot $param_score_prot
|
|
|
60 #end if
|
|
|
61 #if $param_thresh_pep:
|
|
|
62 -thresh:pep $param_thresh_pep
|
|
|
63 #end if
|
|
|
64 #if $param_thresh_prot:
|
|
|
65 -thresh:prot $param_thresh_prot
|
|
|
66 #end if
|
|
|
67 #if $param_whitelist_proteins:
|
|
|
68 -whitelist:proteins $param_whitelist_proteins
|
|
|
69 #end if
|
|
|
70 #if $param_whitelist_by_seq_only:
|
|
|
71 -whitelist:by_seq_only
|
|
|
72 #end if
|
|
|
73 #if $param_blacklist_peptides:
|
|
|
74 -blacklist:peptides $param_blacklist_peptides
|
|
|
75 #end if
|
|
|
76 #if $param_blacklist_ignore_modifications:
|
|
|
77 -blacklist:ignore_modifications
|
|
|
78 #end if
|
|
|
79 #if $param_rt_p_value:
|
|
|
80 -rt:p_value $param_rt_p_value
|
|
|
81 #end if
|
|
|
82 #if $param_rt_p_value_1st_dim:
|
|
|
83 -rt:p_value_1st_dim $param_rt_p_value_1st_dim
|
|
|
84 #end if
|
|
|
85 #if $param_mz_error:
|
|
|
86 -mz:error $param_mz_error
|
|
|
87 #end if
|
|
|
88 #if $param_mz_unit:
|
|
|
89 -mz:unit
|
|
|
90 #if " " in str($param_mz_unit):
|
|
|
91 "$param_mz_unit"
|
|
|
92 #else
|
|
|
93 $param_mz_unit
|
|
|
94 #end if
|
|
|
95 #end if
|
|
|
96 #if $param_best_n_peptide_hits:
|
|
|
97 -best:n_peptide_hits $param_best_n_peptide_hits
|
|
|
98 #end if
|
|
|
99 #if $param_best_n_protein_hits:
|
|
|
100 -best:n_protein_hits $param_best_n_protein_hits
|
|
|
101 #end if
|
|
|
102 #if $param_best_strict:
|
|
|
103 -best:strict
|
|
|
104 #end if
|
|
|
105 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
106 #if $adv_opts.param_force:
|
|
|
107 -force
|
|
|
108 #end if
|
|
|
109 #if $adv_opts.param_best_n_to_m_peptide_hits:
|
|
|
110 -best:n_to_m_peptide_hits "$adv_opts.param_best_n_to_m_peptide_hits"
|
|
|
111 #end if
|
|
|
112 #end if
|
|
|
113 </command>
|
|
|
114 <inputs>
|
|
|
115 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
|
|
|
116 <param name="param_min_length" type="integer" min="0" optional="True" value="0" label="Keep only peptide hits with a length greater or equal this value" help="(-min_length) Value 0 will have no filter effect"/>
|
|
|
117 <param name="param_max_length" type="integer" min="0" optional="True" value="0" label="Keep only peptide hits with a length less or equal this value" help="(-max_length) Value 0 will have no filter effect. Value is overridden by min_length, i.e. if max_length < min_length, max_length will be ignored"/>
|
|
|
118 <param name="param_min_charge" type="integer" min="1" optional="True" value="1" label="Keep only peptide hits for tandem spectra with charge greater or equal this value" help="(-min_charge) "/>
|
|
|
119 <param name="param_var_mods" type="boolean" truevalue="-var_mods" falsevalue="" checked="false" optional="True" label="Keep only peptide hits with variable modifications (fixed modifications from SearchParameters will be ignored)" help="(-var_mods) "/>
|
|
|
120 <param name="param_unique" type="boolean" truevalue="-unique" falsevalue="" checked="false" optional="True" label="If a peptide hit occurs more than once per PSM, only one instance is kept" help="(-unique) "/>
|
|
|
121 <param name="param_unique_per_protein" type="boolean" truevalue="-unique_per_protein" falsevalue="" checked="false" optional="True" label="Only peptides matching exactly one protein are kept" help="(-unique_per_protein) Remember that isoforms count as different proteins!"/>
|
|
|
122 <param name="param_keep_unreferenced_protein_hits" type="boolean" truevalue="-keep_unreferenced_protein_hits" falsevalue="" checked="false" optional="True" label="Proteins not referenced by a peptide are retained in the ids" help="(-keep_unreferenced_protein_hits) "/>
|
|
|
123 <param name="param_remove_decoys" type="boolean" truevalue="-remove_decoys" falsevalue="" checked="false" optional="True" label="Remove proteins according to the information in the user parameters" help="(-remove_decoys) Usually used in combination with 'delete_unreferenced_peptide_hits'"/>
|
|
|
124 <param name="param_delete_unreferenced_peptide_hits" type="boolean" truevalue="-delete_unreferenced_peptide_hits" falsevalue="" checked="false" optional="True" label="Peptides not referenced by any protein are deleted in the ids" help="(-delete_unreferenced_peptide_hits) Usually used in combination with 'score:prot' or 'thresh:prot'"/>
|
|
|
125 <param name="param_precursor_rt" type="text" size="30" value=":" label="Retention time range to extract" help="(-rt) ">
|
|
|
126 <sanitizer>
|
|
|
127 <valid initial="string.printable">
|
|
|
128 <remove value="'"/>
|
|
|
129 <remove value="""/>
|
|
|
130 </valid>
|
|
|
131 </sanitizer>
|
|
|
132 </param>
|
|
|
133 <param name="param_precursor_mz" type="text" size="30" value=":" label="Mass-to-charge range to extract" help="(-mz) ">
|
|
|
134 <sanitizer>
|
|
|
135 <valid initial="string.printable">
|
|
|
136 <remove value="'"/>
|
|
|
137 <remove value="""/>
|
|
|
138 </valid>
|
|
|
139 </sanitizer>
|
|
|
140 </param>
|
|
|
141 <param name="param_precursor_allow_missing" type="boolean" truevalue="-precursor:allow_missing" falsevalue="" checked="false" optional="True" label="When filtering by precursor RT or m/z, keep peptide IDs with missing precursor information ('RT'/'MZ' meta values)?" help="(-allow_missing) "/>
|
|
|
142 <param name="param_score_pep" type="float" value="0.0" label="The score which should be reached by a peptide hit to be kept" 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"/>
|
|
|
143 <param name="param_score_prot" type="float" value="0.0" label="The score which should be reached by a protein hit to be kept" help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/>
|
|
|
144 <param name="param_thresh_pep" type="float" value="0.0" label="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold" help="(-pep) "/>
|
|
|
145 <param name="param_thresh_prot" type="float" value="0.0" label="Keep a protein hit only if its score is above this fraction of the protein significance threshold" help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/>
|
|
|
146 <param name="param_whitelist_proteins" type="data" format="fasta" optional="True" label="filename of a FASTA file containing protein sequences" help="(-proteins) <br>All peptides that are not a substring of a sequence in this file are removed <br>All proteins whose accession is not present in this file are removed"/>
|
|
|
147 <param name="param_whitelist_by_seq_only" type="boolean" truevalue="-whitelist:by_seq_only" falsevalue="" checked="false" optional="True" label="Match peptides with FASTA file by sequence instead of accession and disable protein filtering" help="(-by_seq_only) "/>
|
|
|
148 <param name="param_blacklist_peptides" type="data" format="idxml" optional="True" label="Peptides having the same sequence and modification assignment as any peptide in this file will be filtered out" help="(-peptides) Use with blacklist:ignore_modification flag to only compare by sequence. <br>"/>
|
|
|
149 <param name="param_blacklist_ignore_modifications" type="boolean" truevalue="-blacklist:ignore_modifications" falsevalue="" checked="false" optional="True" label="Compare blacklisted peptides by sequence only" help="(-ignore_modifications) <br>"/>
|
|
|
150 <param name="param_rt_p_value" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict" help="(-p_value) "/>
|
|
|
151 <param name="param_rt_p_value_1st_dim" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict for first dimension" help="(-p_value_1st_dim) "/>
|
|
|
152 <param name="param_mz_error" type="float" value="-1.0" label="Filtering by deviation to theoretical mass (disabled for negative values)" help="(-error) "/>
|
|
|
153 <param name="param_mz_unit" type="select" optional="True" value="ppm" label="Absolute or relative erro" help="(-unit) ">
|
|
|
154 <option value="Da">Da</option>
|
|
|
155 <option value="ppm">ppm</option>
|
|
|
156 </param>
|
|
|
157 <param name="param_best_n_peptide_hits" type="integer" min="0" optional="True" value="0" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n>0)" help="(-n_peptide_hits) "/>
|
|
|
158 <param name="param_best_n_protein_hits" type="integer" min="0" optional="True" value="0" label="Keep only the 'n' highest scoring protein hits (for n>0)" help="(-n_protein_hits) "/>
|
|
|
159 <param name="param_best_strict" type="boolean" truevalue="-best:strict" falsevalue="" checked="false" optional="True" label="Keep only the highest scoring peptide hit" help="(-strict) <br>Similar to n_peptide_hits=1, but if there are two or more highest scoring hits, none are kept"/>
|
|
|
160 <expand macro="advanced_options">
|
|
|
161 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
162 <param name="param_best_n_to_m_peptide_hits" type="text" size="30" value=":" label="peptide hit rank range to extracts" help="(-n_to_m_peptide_hits) ">
|
|
|
163 <sanitizer>
|
|
|
164 <valid initial="string.printable">
|
|
|
165 <remove value="'"/>
|
|
|
166 <remove value="""/>
|
|
|
167 </valid>
|
|
|
168 </sanitizer>
|
|
|
169 </param>
|
|
|
170 </expand>
|
|
|
171 </inputs>
|
|
|
172 <outputs>
|
|
|
173 <data name="param_out" format="idxml"/>
|
|
|
174 </outputs>
|
|
|
175 <help>**What it does**
|
|
|
176
|
|
|
177 Filters results from protein or peptide identification engines based on different criteria.
|
|
|
178
|
|
|
179
|
|
|
180 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFilter.html</help>
|
|
|
181 <expand macro="references"/>
|
|
|
182 </tool>
|
