Mercurial > repos > galaxyp > openms_peptideindexer

comparison PeptideIndexer.xml @ 1:6b0add7e424d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:44:22 -0400
parents 539a3a4dcc9e
children fc6ccd403439
comparison
equal deleted inserted replaced
0:539a3a4dcc9e 1:6b0add7e424d
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="PeptideIndexer" name="PeptideIndexer" version="2.1.0"> 4 <tool id="PeptideIndexer" name="PeptideIndexer" version="2.2.0">
5 <description>Refreshes the protein references for all peptide hits.</description> 5 <description>Refreshes the protein references for all peptide hits.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PeptideIndexer</token> 7 <token name="@EXECUTABLE@">PeptideIndexer</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
23 #end if 23 #end if
24 #if $param_decoy_string: 24 #if $param_decoy_string:
25 -decoy_string "$param_decoy_string" 25 -decoy_string "$param_decoy_string"
26 #end if 26 #end if
27 #if $param_decoy_string_position: 27 #if $param_decoy_string_position:
28 -decoy_string_position $param_decoy_string_position 28 -decoy_string_position
29 #if " " in str($param_decoy_string_position):
30 "$param_decoy_string_position"
31 #else
32 $param_decoy_string_position
33 #end if
29 #end if 34 #end if
30 #if $param_missing_decoy_action: 35 #if $param_missing_decoy_action:
31 -missing_decoy_action $param_missing_decoy_action 36 -missing_decoy_action
37 #if " " in str($param_missing_decoy_action):
38 "$param_missing_decoy_action"
39 #else
40 $param_missing_decoy_action
41 #end if
32 #end if 42 #end if
33 #if $param_write_protein_sequence: 43 #if $param_write_protein_sequence:
34 -write_protein_sequence 44 -write_protein_sequence
35 #end if 45 #end if
36 #if $param_write_protein_description: 46 #if $param_write_protein_description:
56 #end if 66 #end if
57 #if $param_filter_aaa_proteins: 67 #if $param_filter_aaa_proteins:
58 -filter_aaa_proteins 68 -filter_aaa_proteins
59 #end if 69 #end if
60 #if $param_enzyme_name: 70 #if $param_enzyme_name:
61 -enzyme:name $param_enzyme_name 71 -enzyme:name
72 #if " " in str($param_enzyme_name):
73 "$param_enzyme_name"
74 #else
75 $param_enzyme_name
76 #end if
62 #end if 77 #end if
63 #if $param_enzyme_specificity: 78 #if $param_enzyme_specificity:
64 -enzyme:specificity $param_enzyme_specificity 79 -enzyme:specificity
80 #if " " in str($param_enzyme_specificity):
81 "$param_enzyme_specificity"
82 #else
83 $param_enzyme_specificity
84 #end if
65 #end if 85 #end if
66 #if $adv_opts.adv_opts_selector=='advanced': 86 #if $adv_opts.adv_opts_selector=='advanced':
67 #if $adv_opts.param_force: 87 #if $adv_opts.param_force:
68 -force 88 -force
69 #end if 89 #end if
96 <param name="param_aaa_max" type="integer" min="0" optional="True" value="4" label="[tolerant search only] Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="(-aaa_max) AAAs are 'B', 'Z' and 'X'"/> 116 <param name="param_aaa_max" type="integer" min="0" optional="True" value="4" label="[tolerant search only] Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="(-aaa_max) AAAs are 'B', 'Z' and 'X'"/>
97 <param name="param_mismatches_max" type="integer" min="0" optional="True" value="0" label="[tolerant search only] Maximal number of real mismatches (will be used after checking for ambiguous AA's (see 'aaa_max' option)" help="(-mismatches_max) In general this param should only be changed if you want to look for other potential origins of a peptide which might have unknown SNPs or the like"/> 117 <param name="param_mismatches_max" type="integer" min="0" optional="True" value="0" label="[tolerant search only] Maximal number of real mismatches (will be used after checking for ambiguous AA's (see 'aaa_max' option)" help="(-mismatches_max) In general this param should only be changed if you want to look for other potential origins of a peptide which might have unknown SNPs or the like"/>
98 <param name="param_IL_equivalent" display="radio" 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) "/> 118 <param name="param_IL_equivalent" display="radio" 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) "/>
99 <param name="param_filter_aaa_proteins" display="radio" type="boolean" truevalue="-filter_aaa_proteins" falsevalue="" checked="false" optional="True" label="In the tolerant search for matches to proteins with ambiguous amino acids (AAAs), rebuild the search database to only consider proteins with AAAs" help="(-filter_aaa_proteins) This may save time if most proteins don't contain AAAs and if there is a significant number of peptides that enter the tolerant search"/> 119 <param name="param_filter_aaa_proteins" display="radio" type="boolean" truevalue="-filter_aaa_proteins" falsevalue="" checked="false" optional="True" label="In the tolerant search for matches to proteins with ambiguous amino acids (AAAs), rebuild the search database to only consider proteins with AAAs" help="(-filter_aaa_proteins) This may save time if most proteins don't contain AAAs and if there is a significant number of peptides that enter the tolerant search"/>
100 <param name="param_enzyme_name" type="select" optional="False" 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)"> 120 <param name="param_enzyme_name" type="select" optional="False" 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)">
121 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
122 <option value="CNBr">CNBr</option>
123 <option value="Asp-N_ambic">Asp-N_ambic</option>
124 <option value="Trypsin" selected="true">Trypsin</option>
125 <option value="Formic_acid">Formic_acid</option>
126 <option value="TrypChymo">TrypChymo</option>
127 <option value="proline endopeptidase">proline endopeptidase</option>
101 <option value="Lys-C/P">Lys-C/P</option> 128 <option value="Lys-C/P">Lys-C/P</option>
129 <option value="Chymotrypsin">Chymotrypsin</option>
130 <option value="Arg-C">Arg-C</option>
131 <option value="PepsinA">PepsinA</option>
132 <option value="Asp-N">Asp-N</option>
133 <option value="Trypsin/P">Trypsin/P</option>
134 <option value="Lys-C">Lys-C</option>
135 <option value="no cleavage">no cleavage</option>
102 <option value="unspecific cleavage">unspecific cleavage</option> 136 <option value="unspecific cleavage">unspecific cleavage</option>
103 <option value="Lys-C">Lys-C</option>
104 <option value="Formic_acid">Formic_acid</option>
105 <option value="Trypsin" selected="true">Trypsin</option>
106 <option value="V8-DE">V8-DE</option>
107 <option value="2-iodobenzoate">2-iodobenzoate</option> 137 <option value="2-iodobenzoate">2-iodobenzoate</option>
108 <option value="Asp-N_ambic">Asp-N_ambic</option>
109 <option value="no cleavage">no cleavage</option>
110 <option value="V8-E">V8-E</option> 138 <option value="V8-E">V8-E</option>
111 <option value="leukocyte elastase">leukocyte elastase</option> 139 <option value="leukocyte elastase">leukocyte elastase</option>
112 <option value="CNBr">CNBr</option> 140 <option value="V8-DE">V8-DE</option>
113 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
114 <option value="TrypChymo">TrypChymo</option>
115 <option value="PepsinA">PepsinA</option>
116 <option value="Asp-N">Asp-N</option>
117 <option value="Arg-C">Arg-C</option>
118 <option value="proline endopeptidase">proline endopeptidase</option>
119 <option value="Chymotrypsin">Chymotrypsin</option>
120 <option value="Trypsin/P">Trypsin/P</option>
121 </param> 141 </param>
122 <param name="param_enzyme_specificity" display="radio" type="select" optional="False" 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"> 142 <param name="param_enzyme_specificity" display="radio" type="select" optional="False" 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">
123 <option value="full" selected="true">full</option> 143 <option value="full" selected="true">full</option>
124 <option value="semi">semi</option> 144 <option value="semi">semi</option>
125 <option value="none">none</option> 145 <option value="none">none</option>