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06 May 08 |
olle |
1 |
<?xml version="1.0"?> |
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2 |
<?xml-stylesheet type="text/xsl" href="tandem-input-style.xsl"?> |
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3 |
<bioml> |
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06 May 08 |
olle |
4 |
<note>list path parameters</note> |
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olle |
5 |
<note type="input" label="list path, default parameters">default_input.xml</note> |
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06 May 08 |
olle |
6 |
<note>This value is ignored when it is present in the default parameter |
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06 May 08 |
olle |
7 |
list path.</note> |
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06 May 08 |
olle |
8 |
<note type="input" label="list path, taxonomy information">taxonomy.xml</note> |
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olle |
9 |
|
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06 May 08 |
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10 |
<note>spectrum parameters</note> |
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06 May 08 |
olle |
11 |
<note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note> |
| 4627 |
15 Nov 16 |
fredrik |
12 |
<note type="input" label="spectrum, parent monoisotopic mass error plus">10</note> |
| 4627 |
15 Nov 16 |
fredrik |
13 |
<note type="input" label="spectrum, parent monoisotopic mass error minus">10</note> |
| 2660 |
06 May 08 |
olle |
14 |
<note type="input" label="spectrum, parent monoisotopic mass isotope error">yes</note> |
| 2660 |
06 May 08 |
olle |
15 |
<note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note> |
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06 May 08 |
olle |
16 |
<note>The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored</note> |
| 4627 |
15 Nov 16 |
fredrik |
17 |
<note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note> |
| 2660 |
06 May 08 |
olle |
18 |
<note>The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored</note> |
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06 May 08 |
olle |
19 |
<note type="input" label="spectrum, fragment mass type">monoisotopic</note> |
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06 May 08 |
olle |
20 |
<note>values are monoisotopic|average </note> |
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olle |
21 |
|
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06 May 08 |
olle |
22 |
<note>spectrum conditioning parameters</note> |
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06 May 08 |
olle |
23 |
<note type="input" label="spectrum, dynamic range">100.0</note> |
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06 May 08 |
olle |
24 |
<note>The peaks read in are normalized so that the most intense peak |
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06 May 08 |
olle |
25 |
is set to the dynamic range value. All peaks with values of less that |
| 2660 |
06 May 08 |
olle |
26 |
1, using this normalization, are not used. This normalization has the |
| 2660 |
06 May 08 |
olle |
27 |
overall effect of setting a threshold value for peak intensities.</note> |
| 2662 |
07 May 08 |
olle |
28 |
<note type="input" label="spectrum, total peaks">50</note> |
| 2660 |
06 May 08 |
olle |
29 |
<note>If this value is 0, it is ignored. If it is greater than zero (lets say 50), |
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06 May 08 |
olle |
30 |
then the number of peaks in the spectrum with be limited to the 50 most intense |
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06 May 08 |
olle |
31 |
peaks in the spectrum. X! tandem does not do any peak finding: it only |
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06 May 08 |
olle |
32 |
limits the peaks used by this parameter, and the dynamic range parameter.</note> |
| 2660 |
06 May 08 |
olle |
33 |
<note type="input" label="spectrum, maximum parent charge">4</note> |
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06 May 08 |
olle |
34 |
<note type="input" label="spectrum, use noise suppression">yes</note> |
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06 May 08 |
olle |
35 |
<note type="input" label="spectrum, minimum parent m+h">500.0</note> |
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06 May 08 |
olle |
36 |
<note type="input" label="spectrum, maximum parent m+h">4094.0</note> |
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06 May 08 |
olle |
37 |
<note type="input" label="spectrum, minimum fragment mz">150.0</note> |
| 2662 |
07 May 08 |
olle |
38 |
<note type="input" label="spectrum, minimum peaks">15</note> |
| 4627 |
15 Nov 16 |
fredrik |
39 |
<note type="input" label="spectrum, threads">2</note> |
| 2660 |
06 May 08 |
olle |
40 |
<note type="input" label="spectrum, sequence batch size">1000</note> |
| 2662 |
07 May 08 |
olle |
41 |
|
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06 May 08 |
olle |
42 |
<note>residue modification parameters</note> |
| 3883 |
13 Oct 10 |
olle |
43 |
<note type="input" label="residue, modification mass">57.021464@C</note> |
| 2660 |
06 May 08 |
olle |
44 |
<note>The format of this parameter is m@X, where m is the modfication |
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06 May 08 |
olle |
45 |
mass in Daltons and X is the appropriate residue to modify. Lists of |
| 2660 |
06 May 08 |
olle |
46 |
modifications are separated by commas. For example, to modify M and C |
| 2660 |
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olle |
47 |
with the addition of 16.0 Daltons, the parameter line would be |
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olle |
48 |
+16.0@M,+16.0@C |
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49 |
Positive and negative values are allowed. |
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50 |
</note> |
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olle |
51 |
<note type="input" label="residue, potential modification mass"></note> |
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olle |
52 |
<note>The format of this parameter is the same as the format |
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olle |
53 |
for residue, modification mass (see above).</note> |
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06 May 08 |
olle |
54 |
<note type="input" label="residue, potential modification motif"></note> |
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olle |
55 |
<note>The format of this parameter is similar to residue, modification mass, |
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olle |
56 |
with the addition of a modified PROSITE notation sequence motif specification. |
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06 May 08 |
olle |
57 |
For example, a value of 80@[ST!]PX[KR] indicates a modification |
| 2660 |
06 May 08 |
olle |
58 |
of either S or T when followed by P, and residue and the a K or an R. |
| 2660 |
06 May 08 |
olle |
59 |
A value of 204@N!{P}[ST]{P} indicates a modification of N by 204, if it |
| 2660 |
06 May 08 |
olle |
60 |
is NOT followed by a P, then either an S or a T, NOT followed by a P. |
| 2660 |
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olle |
61 |
Positive and negative values are allowed. |
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olle |
62 |
</note> |
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|
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64 |
<note>protein parameters</note> |
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65 |
<note type="input" label="protein, taxon">no default</note> |
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olle |
66 |
<note>This value is interpreted using the information in taxonomy.xml.</note> |
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06 May 08 |
olle |
67 |
<note type="input" label="protein, cleavage site">[RK]|{P}</note> |
| 2660 |
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olle |
68 |
<note>this setting corresponds to the enzyme trypsin. The first characters |
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olle |
69 |
in brackets represent residues N-terminal to the bond - the '|' pipe - |
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70 |
and the second set of characters represent residues C-terminal to the |
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71 |
bond. The characters must be in square brackets (denoting that only |
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72 |
these residues are allowed for a cleavage) or french brackets (denoting |
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73 |
that these residues cannot be in that position). Use UPPERCASE characters. |
| 2662 |
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olle |
74 |
To denote cleavage at any residue, use [X]|[X] and reset the |
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06 May 08 |
olle |
75 |
scoring, maximum missed cleavage site parameter (see below) to something like 50. |
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olle |
76 |
</note> |
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olle |
77 |
<note type="input" label="protein, modified residue mass file"></note> |
| 2665 |
07 May 08 |
olle |
78 |
<note type="input" label="protein, cleavage N-terminal mass change">+1.007825</note> |
| 2660 |
06 May 08 |
olle |
79 |
<note type="input" label="protein, cleavage C-terminal mass change">+17.002735</note> |
| 2660 |
06 May 08 |
olle |
80 |
<note type="input" label="protein, N-terminal residue modification mass">0.0</note> |
| 2660 |
06 May 08 |
olle |
81 |
<note type="input" label="protein, C-terminal residue modification mass">0.0</note> |
| 2660 |
06 May 08 |
olle |
82 |
<note type="input" label="protein, homolog management">no</note> |
| 2660 |
06 May 08 |
olle |
83 |
<note>if yes, an upper limit is set on the number of homologues kept for a particular spectrum</note> |
| 2660 |
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olle |
84 |
|
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olle |
85 |
<note>model refinement parameters</note> |
| 2660 |
06 May 08 |
olle |
86 |
<note type="input" label="refine">yes</note> |
| 2660 |
06 May 08 |
olle |
87 |
<note type="input" label="refine, modification mass"></note> |
| 2660 |
06 May 08 |
olle |
88 |
<note type="input" label="refine, sequence path"></note> |
| 2660 |
06 May 08 |
olle |
89 |
<note type="input" label="refine, tic percent">20</note> |
| 2660 |
06 May 08 |
olle |
90 |
<note type="input" label="refine, spectrum synthesis">yes</note> |
| 2660 |
06 May 08 |
olle |
91 |
<note type="input" label="refine, maximum valid expectation value">0.1</note> |
| 2660 |
06 May 08 |
olle |
92 |
<note type="input" label="refine, potential N-terminus modifications">+42.010565@[</note> |
| 2660 |
06 May 08 |
olle |
93 |
<note type="input" label="refine, potential C-terminus modifications"></note> |
| 2660 |
06 May 08 |
olle |
94 |
<note type="input" label="refine, unanticipated cleavage">yes</note> |
| 2660 |
06 May 08 |
olle |
95 |
<note type="input" label="refine, potential modification mass"></note> |
| 2660 |
06 May 08 |
olle |
96 |
<note type="input" label="refine, point mutations">no</note> |
| 2660 |
06 May 08 |
olle |
97 |
<note type="input" label="refine, use potential modifications for full refinement">no</note> |
| 2660 |
06 May 08 |
olle |
98 |
<note type="input" label="refine, potential modification motif"></note> |
| 2664 |
07 May 08 |
olle |
99 |
<note>The format of this parameter is similar to residue, modification mass, |
| 2660 |
06 May 08 |
olle |
100 |
with the addition of a modified PROSITE notation sequence motif specification. |
| 2660 |
06 May 08 |
olle |
101 |
For example, a value of 80@[ST!]PX[KR] indicates a modification |
| 2660 |
06 May 08 |
olle |
102 |
of either S or T when followed by P, and residue and the a K or an R. |
| 2660 |
06 May 08 |
olle |
103 |
A value of 204@N!{P}[ST]{P} indicates a modification of N by 204, if it |
| 2660 |
06 May 08 |
olle |
104 |
is NOT followed by a P, then either an S or a T, NOT followed by a P. |
| 2660 |
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olle |
105 |
Positive and negative values are allowed. |
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06 May 08 |
olle |
106 |
</note> |
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olle |
107 |
|
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108 |
<note>scoring parameters</note> |
| 2660 |
06 May 08 |
olle |
109 |
<note type="input" label="scoring, minimum ion count">4</note> |
| 2660 |
06 May 08 |
olle |
110 |
<note type="input" label="scoring, maximum missed cleavage sites">1</note> |
| 2660 |
06 May 08 |
olle |
111 |
<note type="input" label="scoring, x ions">no</note> |
| 2660 |
06 May 08 |
olle |
112 |
<note type="input" label="scoring, y ions">yes</note> |
| 2660 |
06 May 08 |
olle |
113 |
<note type="input" label="scoring, z ions">no</note> |
| 2660 |
06 May 08 |
olle |
114 |
<note type="input" label="scoring, a ions">no</note> |
| 2660 |
06 May 08 |
olle |
115 |
<note type="input" label="scoring, b ions">yes</note> |
| 2660 |
06 May 08 |
olle |
116 |
<note type="input" label="scoring, c ions">no</note> |
| 2660 |
06 May 08 |
olle |
117 |
<note type="input" label="scoring, cyclic permutation">no</note> |
| 2660 |
06 May 08 |
olle |
118 |
<note>if yes, cyclic peptide sequence permutation is used to pad the scoring histograms</note> |
| 2660 |
06 May 08 |
olle |
119 |
<note type="input" label="scoring, include reverse">no</note> |
| 2660 |
06 May 08 |
olle |
120 |
<note>if yes, then reversed sequences are searched at the same time as forward sequences</note> |
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olle |
121 |
|
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olle |
122 |
<note>output parameters</note> |
| 2660 |
06 May 08 |
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123 |
<note type="input" label="output, log path"></note> |
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06 May 08 |
olle |
124 |
<note type="input" label="output, message"></note> |
| 2660 |
06 May 08 |
olle |
125 |
<note type="input" label="output, sequence path"></note> |
| 2660 |
06 May 08 |
olle |
126 |
<note type="input" label="output, path">output.xml</note> |
| 2660 |
06 May 08 |
olle |
127 |
<note type="input" label="output, sort results by">protein</note> |
| 2660 |
06 May 08 |
olle |
128 |
<note>values = protein|spectrum (spectrum is the default)</note> |
| 2660 |
06 May 08 |
olle |
129 |
<note type="input" label="output, path hashing">yes</note> |
| 2660 |
06 May 08 |
olle |
130 |
<note>values = yes|no</note> |
| 2660 |
06 May 08 |
olle |
131 |
<note type="input" label="output, xsl path">tandem-style.xsl</note> |
| 2660 |
06 May 08 |
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132 |
<note type="input" label="output, parameters">yes</note> |
| 2660 |
06 May 08 |
olle |
133 |
<note>values = yes|no</note> |
| 2660 |
06 May 08 |
olle |
134 |
<note type="input" label="output, performance">yes</note> |
| 2660 |
06 May 08 |
olle |
135 |
<note>values = yes|no</note> |
| 2660 |
06 May 08 |
olle |
136 |
<note type="input" label="output, spectra">yes</note> |
| 2660 |
06 May 08 |
olle |
137 |
<note>values = yes|no</note> |
| 2660 |
06 May 08 |
olle |
138 |
<note type="input" label="output, histograms">yes</note> |
| 2660 |
06 May 08 |
olle |
139 |
<note>values = yes|no</note> |
| 2660 |
06 May 08 |
olle |
140 |
<note type="input" label="output, proteins">yes</note> |
| 2660 |
06 May 08 |
olle |
141 |
<note>values = yes|no</note> |
| 2660 |
06 May 08 |
olle |
142 |
<note type="input" label="output, sequences">yes</note> |
| 2660 |
06 May 08 |
olle |
143 |
<note>values = yes|no</note> |
| 2660 |
06 May 08 |
olle |
144 |
<note type="input" label="output, one sequence copy">no</note> |
| 2660 |
06 May 08 |
olle |
145 |
<note>values = yes|no, set to yes to produce only one copy of each protein sequence in the output xml</note> |
| 2660 |
06 May 08 |
olle |
146 |
<note type="input" label="output, results">valid</note> |
| 2660 |
06 May 08 |
olle |
147 |
<note>values = all|valid|stochastic</note> |
| 3884 |
13 Oct 10 |
olle |
148 |
<note type="input" label="output, maximum valid expectation value">1</note> |
| 2660 |
06 May 08 |
olle |
149 |
<note>value is used in the valid|stochastic setting of output, results</note> |
| 2660 |
06 May 08 |
olle |
150 |
<note type="input" label="output, histogram column width">30</note> |
| 2660 |
06 May 08 |
olle |
151 |
<note>values any integer greater than 0. Setting this to '1' makes cutting and pasting histograms |
| 2660 |
06 May 08 |
olle |
152 |
into spread sheet programs easier.</note> |
| 2660 |
06 May 08 |
olle |
153 |
<note type="description">ADDITIONAL EXPLANATIONS</note> |
| 2660 |
06 May 08 |
olle |
154 |
<note type="description">Each one of the parameters for X! tandem is entered as a labeled note |
| 2660 |
06 May 08 |
olle |
155 |
node. In the current version of X!, keep those note nodes |
| 2660 |
06 May 08 |
olle |
156 |
on a single line. |
| 2660 |
06 May 08 |
olle |
157 |
</note> |
| 2660 |
06 May 08 |
olle |
158 |
<note type="description">The presence of the type 'input' is necessary if a note is to be considered |
| 2660 |
06 May 08 |
olle |
159 |
an input parameter. |
| 2660 |
06 May 08 |
olle |
160 |
</note> |
| 2662 |
07 May 08 |
olle |
161 |
<note type="description">Any of the parameters that are paths to files may require alteration for a |
| 2660 |
06 May 08 |
olle |
162 |
particular installation. Full path names usually cause the least trouble, |
| 2660 |
06 May 08 |
olle |
163 |
but there is no reason not to use relative path names, if that is the |
| 2660 |
06 May 08 |
olle |
164 |
most convenient. |
| 2660 |
06 May 08 |
olle |
165 |
</note> |
| 2660 |
06 May 08 |
olle |
166 |
<note type="description">Any parameter values set in the 'list path, default parameters' file are |
| 2660 |
06 May 08 |
olle |
167 |
reset by entries in the normal input file, if they are present. Otherwise, |
| 2660 |
06 May 08 |
olle |
168 |
the default set is used. |
| 2660 |
06 May 08 |
olle |
169 |
</note> |
| 2660 |
06 May 08 |
olle |
170 |
<note type="description">The 'list path, taxonomy information' file must exist. |
| 2660 |
06 May 08 |
olle |
171 |
</note> |
| 2660 |
06 May 08 |
olle |
172 |
<note type="description">The directory containing the 'output, path' file must exist: it will not be created. |
| 2660 |
06 May 08 |
olle |
173 |
</note> |
| 2660 |
06 May 08 |
olle |
174 |
<note type="description">The 'output, xsl path' is optional: it is only of use if a good XSLT style sheet exists. |
| 2660 |
06 May 08 |
olle |
175 |
</note> |
| 2660 |
06 May 08 |
olle |
176 |
|
| 2660 |
06 May 08 |
olle |
177 |
</bioml> |