annotate msconvert2_raw.xml @ 0:10f4a0356342

Uploaded
author galaxyp
date Wed, 19 Dec 2012 00:10:08 -0500
parents
children 861e3f0c2bb6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
1 <tool id="msconvert2_raw" name="msconvert2_raw" version="0.1.0">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
2 <!-- BEGIN_VERSION_RAW -->
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
3 <description>Convert and filter a Thermo Finnigan RAW file</description>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
4 <!-- END_VERSION_RAW -->
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
5
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
6 <command interpreter="python">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
7 msconvert_wrapper.py
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
8 --input=${input}
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
9 #if hasattr($input, 'display_name')
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
10 --input_name='${input.display_name}'
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
11 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
12 --output=${output}
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
13
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
14 ## BEGIN_VERSION_RAW
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
15 --fromextension=RAW
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
16 ## END_VERSION_RAW
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
17
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
18 --toextension=${output_type}
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
19
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
20 #if $settings.settingsType == "full"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
21 --binaryencoding=${settings.binary_encoding}
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
22 --mzencoding=${settings.mz_encoding}
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
23 --intensityencoding=${settings.intensity_encoding}
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
24 --zlib=${settings.zlib}
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
25 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
26
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
27 #if $filtering.filtering_use
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
28
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
29 #if $filtering.precursor_recalculation.value
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
30 --filter "precursorRecalculation"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
31 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
32
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
33 #if $filtering.peak_picking.pick_peaks
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
34 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
35 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
36
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
37 #if str($filtering.activation) != "false"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
38 --filter "activation $filtering.activation"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
39 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
40
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
41 #if len($filtering.indices) > 0
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
42 --filter "index
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
43 #for $index in $filtering.indices
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
44 [${index.from},${index.to}]
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
45 #end for
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
46 "
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
47 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
48
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
49 #if len($filtering.scan_numbers) > 0
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
50 --filter "scanNumber
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
51 #for $scan_number in $filtering.scan_numbers
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
52 [${scan_number.from},${scan_number.to}]
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
53 #end for
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
54 "
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
55 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
56
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
57 #for threshold_entry in $filtering.threshold_repeat
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
58 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
59 #end for
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
60
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
61
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
62 #if $filtering.strip_it.value
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
63 --filter "stripIT"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
64 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
65
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
66 #if $filtering.filter_mz_windows.do_filter
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
67 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
68 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
69
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
70
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
71 #if $filtering.filter_ms_levels.do_filter
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
72 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
73 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
74
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
75 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
76 --filter "ETDFilter"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
77 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
78
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
79 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
80 --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
81 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
82
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
83
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
84 #end if
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
85
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
86 </command>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
87
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
88 <inputs>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
89 <!-- BEGIN_VERSION_RAW -->
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
90 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
91 <!-- END_VERSION_RAW -->
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
92
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
93 <param name="output_type" type="select" label="Output Type">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
94 <option value="mzML">mzML (indexed)</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
95 <option value="unindexed_mzML">mzML (unindexed)</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
96 <option value="mzXML">mzXML (indexed)</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
97 <option value="unindexed_mzXML">mzXML (unindexed)</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
98 <option value="mgf">mgf</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
99 <option value="ms2">ms2</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
100 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
101 <conditional name="filtering">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
102 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
103 <when value="false" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
104 <when value="true">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
105 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
106
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
107
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
108 <conditional name="peak_picking">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
109 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
110 <when value="false" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
111 <when value="true">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
112 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
113 <option value="1">MS1 Only (1)</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
114 <option value="2">MS2 Only (2)</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
115 <option value="2-">MS2 and on (2-)</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
116 <option value="1-">All Levels (1-)</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
117 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
118 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
119 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
120 </conditional>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
121
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
122 <repeat name="threshold_repeat" title="Filter by Threshold">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
123 <conditional name="threshold">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
124 <param type="select" label="Specify threshold on" name="threshold_type" help="">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
125 <option value="count">Peak count</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
126 <option value="count-after-ties">Peak count (after ties)</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
127 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
128 <option value="bpi-relative">Percent of base peak intensity</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
129 <option value="tic-relative">Percent of total ion current</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
130 <option value="tic-fraction">Aggregate percent of total ion current</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
131 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
132 <when value="count">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
133 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
134 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
135 <when value="count-after-ties">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
136 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
137 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
138 <when value="absolute">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
139 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
140 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
141 <when value="bpi-relative">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
142 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
143 />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
144 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
145 <when value="tic-relative">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
146 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
147 />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
148 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
149 <when value="tic-fraction">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
150 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
151 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
152 </conditional>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
153 <param type="select" label="Keep" name="orientation">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
154 <option value="most-intense">Most intense peaks</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
155 <option value="least-intense">Least intense peaks</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
156 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
157 </repeat>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
158
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
159
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
160 <param name="activation" type="select" label="Filter by Activation">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
161 <option value="false" selected="true">no</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
162 <option value="ETD">ETD</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
163 <option value="CID">CID</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
164 <option value="SA">SA</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
165 <option value="HCD">HCD</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
166 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
167
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
168 <repeat name="indices" title="Filter Scan Indices">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
169 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
170 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
171 </repeat>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
172
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
173 <repeat name="scan_numbers" title="Filter Scan Numbers">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
174 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
175 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
176 </repeat>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
177
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
178 <conditional name="filter_mz_windows">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
179 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
180 <when value="false" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
181 <when value="true">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
182 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
183 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
184 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
185 </conditional>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
186
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
187 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
188
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
189 <conditional name="filter_ms_levels">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
190 <param name="do_filter" type="boolean" label="Filter MS Levels" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
191 <when value="false" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
192 <when value="true">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
193 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
194 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
195 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
196 </conditional>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
197
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
198 <conditional name="etd_filtering">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
199 <param name="do_etd_filtering" type="select" label="ETD Filtering">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
200 <option value="none" selected="true">none</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
201 <option value="default">yes (with default options)</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
202 <option value="advanced">yes (show advanced options) </option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
203 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
204 <when value="none" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
205 <when value="default" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
206 <when value="advanced">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
207 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
208 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
209 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
210 <option value="MZ" selected="true">mz</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
211 <option value="PPM">ppm</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
212 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
213 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
214 <option value="true" selected="true">yes</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
215 <option value="false">no</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
216 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
217 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
218 <option value="true" selected="true">yes</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
219 <option value="false">no</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
220 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
221 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
222 <option value="true" selected="true">yes</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
223 <option value="false">no</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
224 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
225 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
226 <option value="true" selected="true">yes</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
227 <option value="false">no</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
228 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
229 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
230 </conditional>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
231
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
232
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
233 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
234 </conditional>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
235
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
236 <conditional name="settings">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
237 <param name="settingsType" type="select" label="Advanced Settings" help="">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
238 <option value="default">Use Defaults</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
239 <option value="full">Full Parameter List</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
240 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
241 <when value="default" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
242 <when value="full">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
243 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
244 <option value="64" selected="true">64</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
245 <option value="32">32</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
246 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
247 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
248 <option value="64" selected="true">64</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
249 <option value="32">32</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
250 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
251 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
252 <option value="64">64</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
253 <option value="32" selected="true">32</option>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
254 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
255 <param type="boolean" name="zlib" label="Use zlib">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
256 </param>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
257 </when>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
258 </conditional>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
259
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
260
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
261 </inputs>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
262 <outputs>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
263 <data format="mzml" name="output">
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
264 <change_format>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
265 <when input="output_type" value="mzXML" format="mzxml" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
266 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
267 <when input="output_type" value="ms2" format="ms2" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
268 <when input="output_type" value="mgf" format="mgf" />
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
269 </change_format>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
270 </data>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
271 </outputs>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
272
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
273 <requirements>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
274 <requirement type="package">proteowizard</requirement>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
275 </requirements>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
276
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
277 <help>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
278 **What it does**
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
279
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
280 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
281
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
282 You can view the original documentation here_.
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
283
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
284 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
285
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
286 ------
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
287
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
288 **Citation**
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
289
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
290 For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
291
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
292 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
293
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
294 </help>
10f4a0356342 Uploaded
galaxyp
parents:
diff changeset
295 </tool>