diff --git a/Readme.md b/Readme.md index 0900ceb..7b9dc1a 100644 --- a/Readme.md +++ b/Readme.md @@ -2,17 +2,17 @@ ## Overview -Converts an .mzid file created by MS-GF+ to a tab-delimited text file. +Converts a [mzIdentML](http://www.psidev.info/mzidentml) file (.mzid) created by MS-GF+ to a tab-delimited text file. Although MS-GF+ has this option (see [MzidToTsv.html](https://msgfplus.github.io/msgfplus/MzidToTsv.html) ), MzidToTsvConverter.exe can convert the .mzid file faster, using less memory. ## Details -MzidToTsvConverter reads in the .mzid file created by MS-GF+ and creates a tsv file with the peptide identifications. +MzidToTsvConverter reads in the .mzid file created by MS-GF+ and creates a [tsv file](https://en.wikipedia.org/wiki/Tab-separated_values) with the peptide identifications. The program can also read .mzid.gz files, and it includes other options for how to handle peptides that are associated with multiple proteins. -The MzidToTsvConverter uses [PSI_Interface.dll](https://github.com/PNNL-Comp-Mass-Spec/PSI-Interface) to read the mzid file. +The MzidToTsvConverter uses [PSI_Interface.dll](https://github.com/PNNL-Comp-Mass-Spec/PSI-Interface) to read the .mzid file. ## Syntax @@ -34,16 +34,16 @@ MzidToTsvConverter -mzid:"mzid path" [-tsv:"tsv output path"] ### Optional parameters: `-tsv:path` -* Path to tab-separated-value file to be written +* Path to tab-separated values file to be written * Can be a filename, a directory path, or a file path -* If not specified, will be output to the same location as the mzid. +* If not specified, will be output to the same location as the mzid * If mzid path is a directory, this will be treated as a directory path `-unroll` or `-u` * Signifies that results should be unrolled, giving one line per unique peptide/protein combination in each spectrum identification `-showDecoy` or `-sd` -* Signifies that decoy results should be included in the output .tsv file. +* Signifies that decoy results should be included in the output .tsv file * Decoy results have protein names that start with XXX_ `-noExtended` or `-ne` @@ -64,10 +64,10 @@ MzidToTsvConverter -mzid:"mzid path" [-tsv:"tsv output path"] * For example, -qvalue:0.001 `-recurse` or `-r` -* If mzid path is a directory, specifying this will cause mzid files in subdirectories to also be converted. +* If mzid path is a directory, specifying this will cause .mzid files in subdirectories to also be converted `-skipDupIds` -* If there are issues converting a file due to \"duplicate ID\" errors, specifying this will cause the duplicate IDs to be ignored, at the likely cost of some correctness. +* If there are issues converting a file due to \"duplicate ID\" errors, specifying this will cause the duplicate IDs to be ignored, at the likely cost of some correctness `-geneId` * If specified, adds a 'GeneID' column to the output for non-decoy identifications