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comparison macros.xml @ 33:bce45e9e6d70 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
author galaxyp
date Mon, 06 Feb 2017 21:53:07 -0500
parents ff592231f118
children 0ebf3d3e4c90
comparison
equal deleted inserted replaced
32:ff592231f118 33:bce45e9e6d70
6 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> 6 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
7 <regex match="CompomicsError" level="fatal" description="Compomics Error"/> 7 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
8 </stdio> 8 </stdio>
9 </xml> 9 </xml>
10 <token name="@GENERAL_PARAMETERS@"> 10 <token name="@GENERAL_PARAMETERS@">
11 -frag_tol "${fragment_tol}" 11 -frag_tol "${precursor_options.fragment_tol}"
12 ### -frag_ppm 12 ### -frag_ppm
13 -prec_tol "${precursor_ion_tol}" 13 -prec_tol "${precursor_options.precursor_ion_tol}"
14 -prec_ppm "${precursor_ion_tol_units}" 14 -prec_ppm "${precursor_options.precursor_ion_tol_units}"
15 ### -digestion 15
16 ### multiple enzymes? 16 -min_charge $precursor_options.min_charge
17 -enzyme "${enzyme}" 17 -max_charge $precursor_options.max_charge
18 ### -specificity 18 -fi $precursor_options.forward_ion
19 ### value per enzyme 19 -ri $precursor_options.reverse_ion
20 -mc $missed_cleavages 20 -min_isotope ${precursor_options.min_isotope}
21 #set $fixed_mods_str = $fixed_modifications or '' 21 -max_isotope ${precursor_options.max_isotope}
22 #set $variable_mods_str = $variable_modifications or '' 22 #if $protein_digest_options.digestion.cleavage == 'default':
23 ## -enzyme "Trysin"
24 -mc $protein_digest_options.digestion.missed_cleavages
25 #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0:
26 #set $enzymes = []
27 #set $missed_cleavages = []
28 ## #set $specificities = []
29 #for $i, $digest in enumerate($protein_digest_options.digestion.digests):
30 #silent $enzymes.append(str($digest.enzyme))
31 #silent $missed_cleavages.append(str($digest.missed_cleavages))
32 ## #silent $specificities.append(str($digest.specificity))
33 #end for
34 -enzyme "#echo ','.join($enzymes)#"
35 -mc "#echo ','.join($missed_cleavages)#"
36 ## -specificity "#echo ','.join($specificities)#"
37 #else:
38 -digestion $protein_digest_options.digestion.cleavage
39 #end if
40
41 #set $fixed_mods_str = $protein_modification_options.fixed_modifications or ''
42 #set $variable_mods_str = $protein_modification_options.variable_modifications or ''
23 #if $fixed_mods_str 43 #if $fixed_mods_str
24 -fixed_mods "$fixed_mods_str" 44 -fixed_mods "$fixed_mods_str"
25 #end if 45 #end if
26 #if $variable_mods_str 46 #if $variable_mods_str
27 -variable_mods "$variable_mods_str" 47 -variable_mods "$variable_mods_str"
28 #end if 48 #end if
29 -min_charge $min_charge
30 -max_charge $max_charge
31 -fi $forward_ion
32 -ri $reverse_ion
33 -min_isotope ${min_isotope}
34 -max_isotope ${max_isotope}
35 49
36 </token> 50 </token>
37 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> 51 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
38 <token name="@SEARCHGUI_VERSION@">3.1.4</token> 52 <token name="@SEARCHGUI_VERSION@">3.2.5</token>
39 <xml name="general_options"> 53 <xml name="general_options">
40 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" 54
41 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> 55 <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
42 <option value="1">Parts per million (ppm)</option> 56 <conditional name="digestion">
43 <option value="2">Daltons</option> 57 <param name="cleavage" type="select" label="Digestion">
44 </param> 58 <option value="default" selected="true">Trypsin</option>
45 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" 59 <option value="0">Select Enzymes</option>
46 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> 60 <option value="1">Unspecific Cleavage</option>
47 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" 61 <option value="2">Whole Protein</option>
48 help="Provide error value for fragment ions, based on instrument used"/> 62 </param>
49 <param name="enzyme" type="select" label="Enzyme" 63 <when value="default">
50 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> 64 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
51 <option value="Trypsin">Trypsin</option> 65 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
52 <option value="Arg-C">Arg-C</option> 66 </when>
53 <option value="CNBr">CNBr</option> 67 <when value="0">
54 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> 68 <repeat name="digests" min="1" title="Enzymes">
55 <option value="Formic Acid">Formic Acid</option> 69 <param name="enzyme" type="select" label="Enzyme"
56 <option value="Lys-C">Lys-C</option> 70 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
57 <option value="Lys-C, no P rule">Lys-C, no P rule</option> 71 <option value="Trypsin">Trypsin</option>
58 <option value="Pepsin A">Pepsin A</option> 72 <option value="Arg-C">Arg-C</option>
59 <option value="Trypsin + CNBr">Trypsin + CNBr</option> 73 <option value="CNBr">CNBr</option>
60 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> 74 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
61 <option value="Trypsin, no P rule">Trypsin, no P rule</option> 75 <option value="Formic Acid">Formic Acid</option>
62 <option value="Whole Protein">Whole Protein</option> 76 <option value="Lys-C">Lys-C</option>
63 <option value="Asp-N">Asp-N</option> 77 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
64 <option value="Glu-C">Glu-C</option> 78 <option value="Pepsin A">Pepsin A</option>
65 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> 79 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
66 <option value="Top-Down">Top-Down</option> 80 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
67 <option value="Semi-Tryptic">Semi-Tryptic</option> 81 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
68 <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! --> 82 <option value="Whole Protein">Whole Protein</option>
69 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> 83 <option value="Asp-N">Asp-N</option>
70 <option value="Asp-N (DE)">Asp-N (DE)</option> 84 <option value="Glu-C">Glu-C</option>
71 <option value="Glu-C (DE)">Glu-C (DE)</option> 85 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
72 <option value="Lys-N (K)">Lys-N (K)</option> 86 <option value="Top-Down">Top-Down</option>
73 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> 87 <option value="Semi-Tryptic">Semi-Tryptic</option>
74 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> 88 <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
75 <option value="Semi-Glu-C">Semi-Glu-C</option> 89 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
76 <option value="LysargiNase">LysargiNase</option> 90 <option value="Asp-N (DE)">Asp-N (DE)</option>
77 <option value="Semi-LysargiNase">Semi-LysargiNase</option> 91 <option value="Glu-C (DE)">Glu-C (DE)</option>
78 <option value="Trypsin + Glu-C">Trypsin + Glu-C</option> 92 <option value="Lys-N (K)">Lys-N (K)</option>
79 <option value="Semi-Arg-C">Semi-Arg-C</option> 93 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
80 <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option> 94 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
81 <option value="Arg-N">Arg-N</option> 95 <option value="Semi-Glu-C">Semi-Glu-C</option>
82 <option value="Semi-Arg-N">Semi-Arg-N</option> 96 <option value="LysargiNase">LysargiNase</option>
83 </param> 97 <option value="Semi-LysargiNase">Semi-LysargiNase</option>
84 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" 98 <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
85 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> 99 <option value="Semi-Arg-C">Semi-Arg-C</option>
86 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" 100 <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
87 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> 101 <option value="Arg-N">Arg-N</option>
88 <options from_file="searchgui_mods.loc"> 102 <option value="Semi-Arg-N">Semi-Arg-N</option>
89 <column name="name" index="0" /> 103 </param>
90 <column name="value" index="0" /> 104 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
91 </options> 105 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
92 </param> 106 <!--
93 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" 107 <param name="specificity" type="select" label="Specificity">
94 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> 108 <option value="0" selected="true">Specific at both termini</option>
95 <options from_file="searchgui_mods.loc"> 109 <option value="1">Semi-Specific - one terminus</option>
96 <column name="name" index="0" /> 110 <option value="2">Specific at the N-terminus only</option>
97 <column name="value" index="0" /> 111 <option value="3">Specific at the C-terminus only</option>
98 </options> 112 </param>
99 </param> 113 -->
100 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> 114 </repeat>
101 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> 115 </when>
102 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> 116 <when value="1"/>
103 <option value="a">a</option> 117 <when value="2"/>
104 <option value="b" selected="true">b</option> 118 </conditional>
105 <option value="c">c</option> 119 </section>
106 </param> 120
107 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> 121 <section name="precursor_options" expanded="false" title="Precursor Options">
108 <option value="x">x</option> 122 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
109 <option value="y" selected="true">y</option> 123 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
110 <option value="z">z</option> 124 <option value="1">Parts per million (ppm)</option>
111 </param> 125 <option value="2">Daltons</option>
112 <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" /> 126 </param>
113 <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" /> 127 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"
128 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
129 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
130 help="Provide error value for fragment ions, based on instrument used"/>
131 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
132 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
133 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
134 <option value="a">a</option>
135 <option value="b" selected="true">b</option>
136 <option value="c">c</option>
137 </param>
138 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
139 <option value="x">x</option>
140 <option value="y" selected="true">y</option>
141 <option value="z">z</option>
142 </param>
143 <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
144 <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
145 </section>
146
147 <section name="protein_modification_options" expanded="false" title="Protein Modification Options">
148 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
149 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
150 <options from_file="searchgui_mods.loc">
151 <column name="name" index="0" />
152 <column name="value" index="0" />
153 </options>
154 </param>
155 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
156 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
157 <options from_file="searchgui_mods.loc">
158 <column name="name" index="0" />
159 <column name="value" index="0" />
160 </options>
161 </param>
162 </section>
163
114 </xml> 164 </xml>
115 165
116 <xml name="citations"> 166 <xml name="citations">
117 <citations> 167 <citations>
118 <citation type="doi">10.1186/1471-2105-12-70</citation> 168 <citation type="doi">10.1186/1471-2105-12-70</citation>