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# Line 184 | Line 184
184   emerge, the code that interfaces with the instrument software need not
185   change.
186   <P>
187 + <quote>
188 + <b>NOTE!</b>
189 + <P>
190 + The vendor software (Analyst for .wiff
191 + files, Data Explorer for .t2d files) be installed on the same computer
192 + as <b>PyMsXML</b>. These binary formats cannot be read without the
193 + vendor support libraries.
194 + </quote>
195 + <P>
196   <h3>Installation</h3>
197   <P>
198   <ol>
# Line 222 | Line 231
231   </code>
232   <P>
233   <li> Download and unpack the <b>PyMsXML</b> scripts and examples. <A
234 < href="http://bioinformatics.org/project/filelist.php?group_id=701">Download
234 > href="http://www.umiacs.umd.edu/~nedwards/research/downloads/PyMsXML.zip">Download
235   <b>PyMsXML</b></A>. After unzipping <b>PyMsXML</b>, edit the file pymsxml.cmd to
236   point to your Python installation (usually C:\Python24\python.exe)
237   and your <b>PyMsXML</b> installation.
# Line 241 | Line 250
250   <dl>
251   <dt>-R <i>raw-format</i>, --rawdata <i>raw-format</i></dt>
252   <dd>Valid <i>raw-format</i> values: <tt>wiff</tt>, <tt>qstar</tt>, <tt>t2d</tt>, <tt>ab4700</tt>, <tt>voyager</tt>, <tt>mariner</tt>, <tt>mzXML</tt>. Optional if <i>raw-spectra-data-file</i> ends in <tt>.wiff</tt>, <tt>.t2m</tt>, or <tt>.mzXML</tt>.
244 </dd>
253   <P>
254   <dt>-X <i>xml-format</i>, --xmlformat <i>xml-format</i></dt>
255   <dd>Valid <i>xml-format</i> values: <tt>mzXML</tt> (ISB), <tt>mzData</tt> (HUPO). Optional if <i>output-file</i> ends in <tt>.mzXML</tt> or <tt>.mzData</TT>.
248 </dd>
256   <P>
257   <dt>-o <i>output-file</i>, --output <i>output-file</i></dt>
258   <dd>Name of output file. If omitted, and <i>xml-format</i> is supplied, then the output file is inferred by changing the file extention of <i>raw-spectra-data-file</i> to <i>xml-format</i>.
252 </dd>
259   <P>
260   <dt>-p <i>ms-levels</i>, --peaks <i>ms-levels</i></dt>
261   <dd> Apply (vendor library) peak detetion to spectra with level in <i>ms-levels</i> (comma separated). QStar (MS/MS spectra only) raw format, 4700 raw format only. Default: 2.
256 </dd>
262   <P>
263   <dt>-f <i>filter-spec</i>, --filter <i>filter-spec</i></dt> <dd>
264   Filter output scans by their meta-data. Filters are specified as a
# Line 263 | Line 268
268   <tt>eq</tt>, <tt>ne</tt>, <tt>lt</tt>, <tt>le</tt>, <tt>gt</tt>, or
269   <tt>ge</tt>, specifying =, &ne;, &lt;, &le;, &gt;, and &ge;
270   respectively.
266 </dd>
267 <P>
268 <dt>-V <i>xml-version</i>, --version <i>xml-version</i></dt>
269 <dd>
270 XML version. mzXML only. Valid values: <tt>2.1</tt>, <tt>2.2</tt>, and <tt>3.0</tt>. Default: <tt>3.0</tt>
271 </dd>
272 <P>
273 <dt>-z, --compress_peaks</dt>
274 <dd> Compress mzXML peaks data using zlib. mzXML version &ge; 3.0 only. Default: False.
275 </dd>
271   <P>
272   <dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt>
273 < <dd> Compress output file. Valid values: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>.
279 < </dd>
273 > <dd> Compress output file. Valid options: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>.
274   <P>
275   <dt>-d, --debug</dt>
276   <dd>Debug. Output XML for first 10 spectra only. Truncate spectral data, too. Useful to verify that the output is formatted correctly.</dd>

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