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comparison PeptideIndexer.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="PeptideIndexer" name="PeptideIndexer" version="2.0.0">
3 <description>Refreshes the protein references for all peptide hits.</description>
4 <macros>
5 <token name="@EXECUTABLE@">PeptideIndexer</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>PeptideIndexer
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_fasta:
16 -fasta $param_fasta
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_decoy_string:
22 -decoy_string "$param_decoy_string"
23 #end if
24 #if $param_missing_decoy_action:
25 -missing_decoy_action
26 #if " " in str($param_missing_decoy_action):
27 "$param_missing_decoy_action"
28 #else
29 $param_missing_decoy_action
30 #end if
31 #end if
32 #if $param_prefix:
33 -prefix
34 #end if
35 #if $param_annotate_proteins:
36 -annotate_proteins
37 #end if
38 #if $param_write_protein_sequence:
39 -write_protein_sequence
40 #end if
41 #if $param_keep_unreferenced_proteins:
42 -keep_unreferenced_proteins
43 #end if
44 #if $param_allow_unmatched:
45 -allow_unmatched
46 #end if
47 #if $param_full_tolerant_search:
48 -full_tolerant_search
49 #end if
50 #if $param_aaa_max:
51 -aaa_max $param_aaa_max
52 #end if
53 #if $param_IL_equivalent:
54 -IL_equivalent
55 #end if
56 -threads \${GALAXY_SLOTS:-24}
57 #if $param_enzyme_name:
58 -enzyme:name
59 #if " " in str($param_enzyme_name):
60 "$param_enzyme_name"
61 #else
62 $param_enzyme_name
63 #end if
64 #end if
65 #if $param_enzyme_specificity:
66 -enzyme:specificity
67 #if " " in str($param_enzyme_specificity):
68 "$param_enzyme_specificity"
69 #else
70 $param_enzyme_specificity
71 #end if
72 #end if
73 #if $adv_opts.adv_opts_selector=='advanced':
74 #if $adv_opts.param_force:
75 -force
76 #end if
77 #end if
78 </command>
79 <inputs>
80 <param name="param_in" type="data" format="idxml" optional="False" label="Input idXML file containing the identifications" help="(-in) "/>
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'"/>
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) ">
83 <sanitizer>
84 <valid initial="string.printable">
85 <remove value="'"/>
86 <remove value="&quot;"/>
87 </valid>
88 </sanitizer>
89 </param>
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) ">
91 <option value="error">error</option>
92 <option value="warn">warn</option>
93 </param>
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) "/>
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) "/>
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) "/>
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) "/>
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"/>
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!"/>
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'"/>
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) "/>
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)">
103 <option value="Trypsin">Trypsin</option>
104 <option value="none">none</option>
105 </param>
106 <param name="param_enzyme_specificity" type="select" optional="True" value="full" label="Specificity of the enzyme" help="(-specificity) &lt;br&gt; 'full': both internal cleavage sites must match. &lt;br&gt; 'semi': one of two internal cleavage sites must match. &lt;br&gt; 'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here">
107 <option value="full">full</option>
108 <option value="semi">semi</option>
109 <option value="none">none</option>
110 </param>
111 <expand macro="advanced_options">
112 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
113 </expand>
114 </inputs>
115 <outputs>
116 <data name="param_out" format="idxml"/>
117 </outputs>
118 <help>**What it does**
119
120 Refreshes the protein references for all peptide hits.
121
122
123 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeptideIndexer.html</help>
124 <expand macro="references"/>
125 </tool>