Mercurial > repos > galaxyp > peptideshaker
comparison macros.xml @ 20:2cafc729b2ae draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
author | iracooke |
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date | Sun, 31 May 2015 09:05:57 -0400 |
parents | |
children | 815f93bb3e1b |
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19:7e61179c5952 | 20:2cafc729b2ae |
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1 <macros> | |
2 <xml name="stdio"> | |
3 <stdio> | |
4 <exit_code range="1:" level="fatal" description="Job Failed" /> | |
5 <regex match="java.*Exception" level="fatal" description="Java Exception"/> | |
6 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> | |
7 </stdio> | |
8 </xml> | |
9 <token name="@GENERAL_PARAMETERS@"> | |
10 -frag_tol "${fragment_tol}" | |
11 -prec_tol "${precursor_ion_tol}" | |
12 -prec_ppm "${precursor_ion_tol_units}" | |
13 -enzyme "${enzyme}" | |
14 #set $fixed_mods_str = $fixed_modifications or '' | |
15 #set $variable_mods_str = $variable_modifications or '' | |
16 #if $fixed_mods_str | |
17 -fixed_mods "$fixed_mods_str" | |
18 #end if | |
19 #if $variable_mods_str | |
20 -variable_mods "$variable_mods_str" | |
21 #end if | |
22 -min_charge $min_charge | |
23 -max_charge $max_charge | |
24 -mc $missed_cleavages | |
25 -fi $forward_ion | |
26 -ri $reverse_ion | |
27 </token> | |
28 | |
29 <xml name="general_options"> | |
30 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" | |
31 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> | |
32 <option value="1">Parts per million (ppm)</option> | |
33 <option value="2">Daltons</option> | |
34 </param> | |
35 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" | |
36 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> | |
37 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" | |
38 help="Provide error value for fragment ions, based on instrument used"/> | |
39 <param name="enzyme" type="select" label="Enzyme" | |
40 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> | |
41 <option value="Trypsin">Trypsin</option> | |
42 <option value="Arg-C">Arg-C</option> | |
43 <option value="CNBr">CNBr</option> | |
44 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> | |
45 <option value="Formic Acid">Formic Acid</option> | |
46 <option value="Lys-C">Lys-C</option> | |
47 <option value="Lys-C, no P rule">Lys-C, no P rule</option> | |
48 <option value="Pepsin A">Pepsin A</option> | |
49 <option value="Trypsin + CNBr">Trypsin + CNBr</option> | |
50 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> | |
51 <option value="Trypsin, no P rule">Trypsin, no P rule</option> | |
52 <option value="whole protein">whole protein</option> | |
53 <option value="Asp-N">Asp-N</option> | |
54 <option value="Glu-C">Glu-C</option> | |
55 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> | |
56 <option value="Top-Down">Top-Down</option> | |
57 <option value="Semi-Tryptic">Semi-Tryptic</option> | |
58 <option value="No enzyme">No enzyme</option> | |
59 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> | |
60 <option value="Asp-N (DE)">Asp-N (DE)</option> | |
61 <option value="Glu-C (DE)">Glu-C (DE)</option> | |
62 <option value="Lys-N (K)">Lys-N (K)</option> | |
63 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> | |
64 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> | |
65 <option value="Semi-Glu-C">Semi-Glu-C</option> | |
66 </param> | |
67 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" | |
68 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> | |
69 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" | |
70 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> | |
71 <options from_file="searchgui_mods.loc"> | |
72 <column name="name" index="0" /> | |
73 <column name="value" index="0" /> | |
74 </options> | |
75 </param> | |
76 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" | |
77 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> | |
78 <options from_file="searchgui_mods.loc"> | |
79 <column name="name" index="0" /> | |
80 <column name="value" index="0" /> | |
81 </options> | |
82 </param> | |
83 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> | |
84 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> | |
85 <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"> | |
86 <option value="a">a</option> | |
87 <option value="b" selected="true">b</option> | |
88 <option value="c">c</option> | |
89 </param> | |
90 <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"> | |
91 <option value="x">x</option> | |
92 <option value="y" selected="true">y</option> | |
93 <option value="z">z</option> | |
94 </param> | |
95 </xml> | |
96 | |
97 <xml name="citations"> | |
98 <citations> | |
99 <citation type="doi">10.1186/1471-2105-12-70</citation> | |
100 <citation type="doi">10.1002/pmic.201000595</citation> | |
101 <citation type="doi">doi:10.1038/nbt.3109</citation> | |
102 </citations> | |
103 </xml> | |
104 | |
105 </macros> |