Update version file for the web site

commands/cascade-search.html

@@ -99,7 +99,7 @@ <h3>cascade-search options</h3>
   <li class="nobullet"><code>--top-match-in &lt;integer&gt;</code> &ndash; Specify the maximum rank to allow when parsing results files. Matches with ranks higher than this value will be ignored (a value of zero allows matches with any rank). Default = <code>0</code>.</li>
   <li class="nobullet"><code>--combine-charge-states T|F</code> &ndash; Specify this parameter to T in order to combine charge states with peptide sequencesin peptide-centric search. Works only if estimation-method = peptide-level. Default = <code>false</code>.</li>
   <li class="nobullet"><code>--combine-modified-peptides T|F</code> &ndash; Specify this parameter to T in order to treat peptides carrying different or no modifications as being the same. Works only if estimation = peptide-level. Default = <code>false</code>.</li>
-  <li class="nobullet"><code>--use-tailor-calibration T|F</code> &ndash; Fast, but heuristic PSM score calibration as described in <a href="https://pubmed.ncbi.nlm.nih.gov/32175744/">this article</a>. Default = <code>false</code>.</li>
+  <li class="nobullet"><code>--mztab-output T|F</code> &ndash; Output results in mzTab file to the output directory. Default = <code>false</code>.</li>
 </ul>
 </li>
 <li class="nobullet">
@@ -122,20 +122,17 @@ <h3>Precursor selection</h3>
 <h3>Search parameters</h3>
 <ul>
   <li class="nobullet"><code>--auto-mz-bin-width false|warn|fail</code> &ndash; Automatically estimate optimal value for the mz-bin-width parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
-  <li class="nobullet"><code>--compute-sp T|F</code> &ndash; Compute the preliminary score Sp for all candidate peptides. Report this score in the output, along with the corresponding rank, the number of matched ions and the total number of ions. This option is recommended if results are to be analyzed by Percolator.If sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Note that the Sp computation requires re-processing each observed spectrum, so turning on this switch involves significant computational overhead. Default = <code>false</code>.</li>
   <li class="nobullet"><code>--deisotope &lt;float&gt;</code> &ndash; Perform a simple deisotoping operation across each MS2 spectrum. For each peak in an MS2 spectrum, consider lower m/z peaks. If the current peak occurs where an expected peak would lie for any charge state less than the charge state of the precursor, within mass tolerance, and if the current peak is of lower abundance, then the peak is removed.  The value of this parameter is the mass tolerance, in units of parts-per-million.  If set to 0, no deisotoping is performed. Default = <code>0</code>.</li>
-  <li class="nobullet"><code>--exact-p-value T|F</code> &ndash; Enable the calculation of exact p-values for the XCorr score as described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">this article</a>. Calculation of p-values increases the running time but increases the number of identifications at a fixed confidence threshold. The p-values will be reported in a new column with header "exact p-value", and the "xcorr score" column will be replaced with a "refactored xcorr" column. Note that, currently, p-values can only be computed when the mz-bin-width parameter is set to its default value. Variable and static mods are allowed on non-terminal residues in conjunction with p-value computation, but currently only static mods are allowed on the N-terminus, and no mods on the C-terminus. Default = <code>false</code>.</li>
+  <li class="nobullet"><code>--fragment-tolerance &lt;float&gt;</code> &ndash; Mass tolerance (in Da) for scoring pairs of peaks when creating the residue evidence matrix. This parameter only makes sense when score-function is 'residue-evidence' or 'both'. Default = <code>0.02</code>.</li>
   <li class="nobullet"><code>--isotope-error &lt;string&gt;</code> &ndash; List of positive, non-zero integers. Default = <code>&lt;empty&gt;</code>.</li>
   <li class="nobullet"><code>--min-peaks &lt;integer&gt;</code> &ndash; The minimum number of peaks a spectrum must have for it to be searched. Default = <code>20</code>.</li>
   <li class="nobullet"><code>--mz-bin-offset &lt;float&gt;</code> &ndash; In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). Default = <code>0.4</code>.</li>
   <li class="nobullet"><code>--mz-bin-width &lt;float&gt;</code> &ndash; Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>0.02</code>.</li>
-  <li class="nobullet"><code>--peptide-centric-search T|F</code> &ndash; Carries out a peptide-centric search. For each peptide the top-scoring spectra are reported, in contrast to the standard spectrum-centric search where the top-scoring peptides are reported. Note that in this case the "xcorr rank" column will contain the rank of the given spectrum with respect to the given candidate peptide, rather than vice versa (which is the default). Default = <code>false</code>.</li>
-  <li class="nobullet"><code>--score-function xcorr|residue-evidence|both</code> &ndash; Function used for scoring PSMs. 'xcorr' is the original scoring function used by SEQUEST; 'residue-evidence' is designed to score high-resolution MS2 spectra; and 'both' calculates both scores. The latter requires that exact-p-value=T. Default = <code>xcorr</code>.</li>
-  <li class="nobullet"><code>--fragment-tolerance &lt;float&gt;</code> &ndash; Mass tolerance (in Da) for scoring pairs of peaks when creating the residue evidence matrix. This parameter only makes sense when score-function is 'residue-evidence' or 'both'. Default = <code>0.02</code>.</li>
-  <li class="nobullet"><code>--evidence-granularity &lt;integer&gt;</code> &ndash; This parameter controls the granularity of the entries in the dynamic programming matrix used in residue-evidence scoring.Smaller values make the program run faster but give less accurate p-values; larger values make the program run more slowly but give more accurate p-values. Default = <code>25</code>.</li>
+  <li class="nobullet"><code>--override-charges T|F</code> &ndash; If this is set to T, then all spectra are searched in all charge states from min-charge to max-charge. Otherwise, the default behavior is to search with all charge states only if a spectrum has no charge or charge=0. Default = <code>false</code>.</li>
   <li class="nobullet"><code>--remove-precursor-peak T|F</code> &ndash; If true, all peaks around the precursor m/z will be removed, within a range specified by the --remove-precursor-tolerance option. Default = <code>false</code>.</li>
   <li class="nobullet"><code>--remove-precursor-tolerance &lt;float&gt;</code> &ndash; This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the --remove-precursor-peak option is invoked. Default = <code>1.5</code>.</li>
   <li class="nobullet"><code>--scan-number &lt;string&gt;</code> &ndash; A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code>&lt;empty&gt;</code>.</li>
+  <li class="nobullet"><code>--score-function xcorr|combined-p-values|hyperscore|hyperscore-la</code> &ndash; Function used for scoring PSMs. 'xcorr' is the original scoring function used by SEQUEST;`combined-p-values` combined (1) exact-p-value: a calibrated version of XCorr that uses dynamic programming and (2) residue-evidence-pvalue: a valibarated version of the  ResEV that considers pairs of peaks, rather than single peaks; `hyperscore` is the score function used in X!Tandem; `hyperscore-la` is a variant of the hyperscore designed for open modification searching. Default = <code>xcorr</code>.</li>
   <li class="nobullet"><code>--skip-preprocessing T|F</code> &ndash; Skip preprocessing steps on spectra. Default = F. Default = <code>false</code>.</li>
   <li class="nobullet"><code>--spectrum-max-mz &lt;float&gt;</code> &ndash; The highest spectrum m/z to search in the ms2 file. Default = <code>1e+09</code>.</li>
   <li class="nobullet"><code>--spectrum-min-mz &lt;float&gt;</code> &ndash; The lowest spectrum m/z to search in the ms2 file. Default = <code>0</code>.</li>
@@ -177,7 +174,6 @@ <h3>Input and output</h3>
   <li class="nobullet"><code>--list-of-files T|F</code> &ndash; Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
   <li class="nobullet"><code>--fileroot &lt;string&gt;</code> &ndash; The fileroot string will be added as a prefix to all output file names. Default = <code>&lt;empty&gt;</code>.</li>
   <li class="nobullet"><code>--concat T|F</code> &ndash; When set to T, target and decoy search results are reported in a single file, and only the top-scoring N matches (as specified via --top-match) are reported for each spectrum, irrespective of whether the matches involve target or decoy peptides. Default = <code>false</code>.</li>
-  <li class="nobullet"><code>--file-column T|F</code> &ndash; Include the file column in tab-delimited output. Default = <code>true</code>.</li>
   <li class="nobullet"><code>--mass-precision &lt;integer&gt;</code> &ndash; Set the precision for masses and m/z written to sqt and text files. Default = <code>4</code>.</li>
   <li class="nobullet"><code>--mzid-output T|F</code> &ndash; Output an mzIdentML results file to the output directory. Default = <code>false</code>.</li>
   <li class="nobullet"><code>--pepxml-output T|F</code> &ndash; Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
@@ -189,7 +185,6 @@ <h3>Input and output</h3>
   <li class="nobullet"><code>--store-index &lt;string&gt;</code> &ndash; When providing a FASTA file as the index, the generated binary index will be stored at the given path. This option has no effect if a binary index is provided as the index. Default = <code>&lt;empty&gt;</code>.</li>
   <li class="nobullet"><code>--store-spectra &lt;string&gt;</code> &ndash; Specify the name of the file where the binarized fragmentation spectra will be stored. Subsequent runs of crux tide-search will execute more quickly if provided with the spectra in binary format. The filename is specified relative to the current working directory, not the Crux output directory (as specified by --output-dir). This option is not valid if multiple input spectrum files are given. Default = <code>&lt;empty&gt;</code>.</li>
   <li class="nobullet"><code>--txt-output T|F</code> &ndash; Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
-  <li class="nobullet"><code>--brief-output T|F</code> &ndash; Output in tab-delimited text only the file name, scan number, charge, score and peptide.Incompatible with mzid-output=T, pin-output=T, pepxml-output=T or txt-output=F. Default = <code>false</code>.</li>
   <li class="nobullet"><code>--use-z-line T|F</code> &ndash; Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line.  Default = <code>true</code>.</li>
 </ul>
 </li>

commands/default.params

@@ -8,7 +8,7 @@
 #
 ################################################################################
 
-# Crux parameter file (generated by Crux version 4.2-a532fee-2024-10-15)
+# Crux parameter file (generated by Crux version 4.2-1efee64-2024-10-18)
 # Full documentation available at http://cruxtoolkit.sourceforge.net/
 # comet_version 2016.01 rev. 1
 # Everything following the '#' symbol is treated as a comment.
@@ -191,12 +191,16 @@ mzid-output=false
 # Available for tide-search.
 pin-output=false
 
+# Output results in mzTab file to the output directory.
+# Available for tide-search.
+mztab-output=false
+
 # Output a Percolator pout.xml format results file to the output directory.
 # Available for percolator.
 pout-output=false
 
 # Output a pepXML results file to the output directory.
-# Available for tide-search.
+# Available for tide-search, percolator.
 pepxml-output=false
 
 # Output a tab-delimited results file to the output directory.
@@ -739,9 +743,12 @@ peptide-centric-search=false
 skip-preprocessing=false
 
 # Function used for scoring PSMs. 'xcorr' is the original scoring function used
-# by SEQUEST; 'residue-evidence' is designed to score high-resolution MS2
-# spectra; and 'both' calculates both scores. The latter requires that
-# exact-p-value=T.
+# by SEQUEST;`combined-p-values` combined (1) exact-p-value: a calibrated
+# version of XCorr that uses dynamic programming and (2)
+# residue-evidence-pvalue: a valibarated version of the  ResEV that considers
+# pairs of peaks, rather than single peaks; `hyperscore` is the score function
+# used in X!Tandem; `hyperscore-la` is a variant of the hyperscore designed for
+# open modification searching.
 # Available for tide-search.
 score-function=xcorr
 
@@ -773,6 +780,12 @@ num-threads=1
 # Available for tide-search
 brief-output=false
 
+# If this is set to T, then all spectra are searched in all charge states from
+# min-charge to max-charge. Otherwise, the default behavior is to search with
+# all charge states only if a spectrum has no charge or charge=0.
+# Available for tide-search
+override-charges=false
+
 # Specify that the search results are provided as lists of files, rather than as
 # individual files.
 # Available for assign-confidence.
@@ -910,7 +923,8 @@ threshold=0.01
 
 # Specify which field to apply the threshold to. The direction of the threshold
 # (<= or >=) is governed by --custom-threshold-min. By default, the threshold
-# applies to the percolator q-value, specified by "percolator q-value".
+# applies to the q-value, specified by "percolator q-value", "decoy q-value
+# (xcorr)".
 # Available for spectral-counts.
 custom-threshold-name=