Mercurial > repos > galaxyp > msconvert

comparison msconvert.xml @ 0:ab59b1826345 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
author galaxyp
date Thu, 22 Oct 2015 14:00:58 -0400
parents
children 8e2e7ff2b6bd
comparison
equal deleted inserted replaced
-1:000000000000 0:ab59b1826345
1 <tool id="msconvert" name="msconvert" version="0.3.0">
2 <description>Convert and/or filter mass spectrometry files</description>
3
4 <requirements>
5 <requirement type="package" version="3_0_9016">proteowizard</requirement>
6 </requirements>
7
8 <macros>
9 <import>msconvert_macros.xml</import>
10 </macros>
11
12 <expand macro="msconvertCommand" />
13
14 <inputs>
15 <param format="mzml,mzxml,mz5,mgf,ms2" name="input" type="data" label="Input unrefined MS data" />
16
17 <expand macro="msconvertInputParameters" />
18 </inputs>
19
20 <expand macro="msconvertOutput" />
21
22 <tests>
23 <test>
24 <param name="input" value="small.mzML" />
25 <param name="output_type" value="mzML" />
26 <param name="pick_peaks" value="true" />
27 <param name="pick_peaks_algorithm" value="cwt" />
28 <param name="pick_peaks_ms_levels" value="1-" />
29 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
30 </test>
31
32 <!-- this data file only has profile MS1, so the result is the same -->
33 <test>
34 <param name="input" value="small.mzML" />
35 <param name="output_type" value="mzML" />
36 <param name="pick_peaks" value="true" />
37 <param name="pick_peaks_algorithm" value="cwt" />
38 <param name="pick_peaks_ms_levels" value="1" />
39 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
40 </test>
41 <test>
42 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
43 <param name="output_type" value="mz5" />
44 <param name="mz_encoding" value="64" />
45 <param name="intensity_encoding" value="64" />
46 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" />
47 </test>
48 <test>
49 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
50 <param name="output_type" value="mzXML" />
51 <param name="mz_encoding" value="32" />
52 <param name="intensity_encoding" value="32" />
53 <output name="output" file="small-zlib-32.mzXML" />
54 </test>
55 <!-- TODO: how to test gzipped output?
56 <test>
57 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
58 <param name="output_type" value="mzXML" />
59 <param name="mz_encoding" value="32" />
60 <param name="intensity_encoding" value="32" />
61 <param name="binary_compression" value="false" />
62 <param name="gzip_compression" value="true" />
63 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
64 </test>
65 <test>
66 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
67 <param name="output_type" value="mzML" />
68 <param name="mz_encoding" value="32" />
69 <param name="intensity_encoding" value="32" />
70 <param name="binary_compression" value="false" />
71 <param name="gzip_compression" value="true" />
72 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
73 </test>-->
74
75 <test>
76 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
77 <param name="output_type" value="mzML" />
78 <param name="binary_compression" value="numpressLinearPic" />
79 <output name="output" file="small-numpressLP.mzML" />
80 </test>
81
82 <test>
83 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
84 <param name="output_type" value="mzML" />
85 <param name="binary_compression" value="numpressLinearSlof" />
86 <output name="output" file="small-numpressLS.mzML" />
87 </test>
88
89 <test>
90 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
91 <param name="output_type" value="mzML" />
92 <param name="binary_compression" value="numpressLinear" />
93 <output name="output" file="small-numpressL.mzML" />
94 </test>
95
96 <test>
97 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
98 <param name="output_type" value="mzML" />
99 <param name="binary_compression" value="numpressPic" />
100 <output name="output" file="small-numpressP.mzML" />
101 </test>
102
103 <test>
104 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
105 <param name="output_type" value="mzML" />
106 <param name="binary_compression" value="numpressSlof" />
107 <output name="output" file="small-numpressS.mzML" />
108 </test>
109
110 <test>
111 <param name="input" value="Rpal_01.mz5" />
112 <param name="output_type" value="mzML" />
113 <param name="binary_compression" value="numpressLinearPic" />
114 <param name="use_mzrefinement" value="true" />
115 <param name="input_ident" value="Rpal_01.pepXML.gz" />
116 <param name="thresholdScore" value="mvh" />
117 <param name="thresholdValue" value="40-" />
118 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
119 <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
120 </test>
121
122 <test>
123 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
124 <param name="output_type" value="mzML" />
125 <param name="binary_compression" value="numpressLinearPic" />
126 <param name="charge_state_calculation_method" value="predictor" />
127 <param name="predictor_overrideExistingCharge" value="true" />
128 <param name="minMultipleCharge" value="2" />
129 <param name="maxMultipleCharge" value="5" />
130 <param name="singleChargeFractionTIC" value="0.95" />
131 <param name="maxKnownCharge" value="8" />
132 <output name="output" file="small-chargeStatePredictor.mzML" />
133 </test>
134 <test>
135 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
136 <param name="output_type" value="mzML" />
137 <param name="binary_compression" value="numpressLinearPic" />
138 <param name="charge_state_calculation_method" value="turbocharger" />
139 <param name="minCharge" value="1" />
140 <param name="maxCharge" value="5" />
141 <param name="precursorsBefore" value="1" />
142 <param name="precursorsAfter" value="1" />
143 <param name="halfIsoWidth" value="1.5" />
144 <param name="defaultMinCharge" value="1" />
145 <param name="defaultMaxCharge" value="5" />
146 <output name="output" file="small-turbocharger.mzML" />
147 </test>
148 <test>
149 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
150 <param name="output_type" value="mzML" />
151 <param name="do_etd_filtering" value="true" />
152 <param name="remove_precursor" value="true" />
153 <param name="remove_charge_reduced" value="true" />
154 <param name="remove_neutral_loss" value="false" />
155 <param name="blanket_removal" value="false" />
156 <param name="matching_tolerance" value="50" />
157 <param name="matching_tolerance_units" value="ppm" />
158 <param name="binary_compression" value="numpressLinearPic" />
159 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
160 </test>
161 <test>
162 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
163 <param name="output_type" value="mzML" />
164 <param name="thresholds_0|threshold_type" value="count" />
165 <param name="thresholds_0|value" value="100" />
166 <param name="thresholds_0|orientation" value="most-intense" />
167 <param name="thresholds_1|threshold_type" value="absolute" />
168 <param name="thresholds_1|value" value="1" />
169 <param name="thresholds_1|orientation" value="most-intense" />
170 <param name="binary_compression" value="numpressLinearPic" />
171 <output name="output" file="small-threshold.mzML" />
172 </test>
173 <test>
174 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
175 <param name="output_type" value="mzML" />
176 <param name="do_mzwindow_filter" value="true" />
177 <param name="mz_window_from" value="420" />
178 <param name="mz_window_to" value="840" />
179 <param name="binary_compression" value="numpressLinearPic" />
180 <output name="output" file="small-mzWindow.mzML" />
181 </test>
182 <test>
183 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
184 <param name="output_type" value="mzML" />
185 <param name="denoise" value="true" />
186 <param name="num_peaks" value="10" />
187 <param name="window_width" value="40" />
188 <param name="relax" value="false" />
189 <param name="binary_compression" value="numpressLinearPic" />
190 <output name="output" file="small-denoise.mzML" />
191 </test>
192 <test>
193 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
194 <param name="output_type" value="mzML" />
195 <param name="ms2deisotope" value="true" />
196 <param name="binary_compression" value="numpressLinearPic" />
197 <output name="output" file="small-deisotope.mzML" />
198 </test>
199 <test>
200 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
201 <param name="output_type" value="mzML" />
202 <param name="activation" value="CID" />
203 <param name="binary_compression" value="numpressLinearPic" />
204 <output name="output" file="small-activation.mzML" />
205 </test>
206 <test>
207 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
208 <param name="output_type" value="mzML" />
209 <param name="indices_0|from" value="2" />
210 <param name="indices_0|to" value="4" />
211 <param name="indices_1|from" value="10" />
212 <param name="indices_1|to" value="10" />
213 <param name="indices_2|from" value="13" />
214 <param name="indices_2|to" value="15" />
215 <param name="binary_compression" value="numpressLinearPic" />
216 <output name="output" file="small-index-filter.mzML" />
217 </test>
218 <test>
219 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
220 <param name="output_type" value="mzML" />
221 <param name="strip_it" value="true" />
222 <param name="binary_compression" value="numpressLinearPic" />
223 <output name="output" file="small-strip-it.mzML" />
224 </test>
225 <test>
226 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
227 <param name="output_type" value="mzML" />
228 <param name="do_ms_level_filter" value="true" />
229 <param name="ms_level_from" value="2" />
230 <param name="ms_level_to" value="2" />
231 <param name="binary_compression" value="numpressLinearPic" />
232 <output name="output" file="small-ms-level-filter.mzML" />
233 </test>
234 <test>
235 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
236 <param name="output_type" value="mzML" />
237 <param name="polarity" value="positive" />
238 <param name="binary_compression" value="numpressLinearPic" />
239 <output name="output" file="small-polarity-filter.mzML" />
240 </test>
241 <test>
242 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
243 <param name="output_type" value="mzML" />
244 <param name="analyzer" value="IT" />
245 <param name="binary_compression" value="numpressLinearPic" />
246 <output name="output" file="small-analyzer-filter.mzML" />
247 </test>
248 <test>
249 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
250 <param name="output_type" value="mzML" />
251 <param name="scan_numbers_0|from" value="3" />
252 <param name="scan_numbers_0|to" value="5" />
253 <param name="scan_numbers_1|from" value="11" />
254 <param name="scan_numbers_1|to" value="11" />
255 <param name="scan_numbers_2|from" value="14" />
256 <param name="scan_numbers_2|to" value="16" />
257 <param name="binary_compression" value="numpressLinearPic" />
258 <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
259 </test>
260 <!--<test>
261 <param name="input" value="small.mzML" />
262 <param name="output_type" value="mzML" />
263 <param name="binary_compression" value="numpressLinearPic" />
264 <output name="output" file="small-deisotope-poisson.mzML" />
265 </test>-->
266 </tests>
267 <help>
268 **What it does**
269
270 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
271
272 You can view the original documentation here_.
273
274 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
275 </help>
276 <citations>
277 <citation type="doi">10.1093/bioinformatics/btn323</citation>
278 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
279 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
280 </citations>
281 </tool>