spsReports

This page contains information on how to use spsReport to generate reports

Usage instruction

To generate a report, a specific set of files are required. 

$ spsReports --build-tables --build-html dynamic 

Will generate the report based on the project located in the current directory.

$ spsReports --debug

Will output debug information based on the report data located in the current directory. This is extremely useful for debugging purposes.
Additionally, a parameter file may be created, containing all desired parameters and used with spsReports, using the --p option.

spsReports parameters reference

Parameter  Parameter in Parameters File Accepted values Default Description
--build-tables buildTables=1
- - Build report data tables
--build-html TYPE REPORT_HTML_TYPE=<TYPE>
static, client, single, dynamic static Build html report.
--build-pdf REPORT_PDF=1
- - Build PDF report
--exe-dir PATH EXE_DIR=<PATH> Any valid path spsReports exec dir
Executables directory
--project-dir PATH PROJECT_DIR=<PATH> Any valid path current directory
Project directory
--tables-dir PATH TABLES_DIR=<PATH> Any valid path project directory Table files directory
--project-dir-server PATH PROJECT_DIR_SERVER=<PATH> Any valid path --project-dir
Directory for project after relocation. Used by dynamic reports.
--tables-header FILENAME TABLE_HEADER=<PATH> any filename tableHeader.txt Header table filename
--tables-protein FILENAME TABLE_PROTEIN=<PATH> any filename
tableProteins.txt Proteins table filename
--tables-contig FILENAME TABLE_CONTIG=<PATH> any filename
tableContigs.txt Contigs table filename
--tables-cluster FILENAME TABLE_CLUSTER=<PATH> any filename
tableCluster.txt Cluster consensus table filename
--tables-spectra FILENAME TABLE_SPECTRA=<PATH> any filename
tableSpectra.txt Input spectra table filename
--aa FILE AMINO_ACID_LIST=<FILE> any filename
- Amino acids file
--annotation-model FILE ANNOTATION_MODEL=<FILE>
any filename
model_cid.txt
Annotation model file
--peakmasstol NUMBER TOLERANCE_PEAK=<NUMBER>
any number 0.45 Amino acid peak mass tolerance
--parentmasstol NUMBER TOLERANCE_PM=<NUMBER>
any number
  Parent mass tolerance
--resolution NUMBER RESOLUTION=<NUMBER>
any number
  Resolution
--shift-value VALUE SHIFT_VALUE=<VALUE>
any number
0.0 Specify and apply mass shift
--abruijn FILE FILE_COMP=<FILE> any filename
- Abruijn graph
--sps-seqs FILE FILE_SEQS=<FILE> any filename
- sps_seqs files
--contigs-mp FILE FILE_MP2=<FILE> any filename
- Contigs map to protein file
--contigs-midx FILE FILE_MIDX2=<FILE> any filename
- Contigs map to protein file
--homglue-ref-mp FILE FILE_REFMP=<FILE> any filename
- Contigs map to reference protein file
--homglue-ref-midx FILE FILE_REFMIDX=<FILE> any filename
- Contigs map to reference protein file
--stars FILE FILE_STARS=<FILE> any filename
- Star spectra file
--consensus-spectra FILE FILE_MS=<FILE> any filename
- Consensus spectra file
--input-spectra-list FILE FILE_INDEX=<FILE> any filename
- Input spectra list file
--cluster-ms FILE FILE_CLUSTERMS=<FILE> any filename
-  
--cluster-scan FILE FILE_CLUSTERSCAN=<FILE> any filename
-  
--proteins FILE FILE_FASTA=<FILE> any filename
- Fasta file containg protein information
--tool NUMBER TOOL=<NUMBER>
1, 2, 3 1 Indicates tool(s) used. 1 for SPS, 2 for GenoMS, 3 for both
--no-clusters NO_CLUSTERS=1
- - Generate reports without the cluster layer
--server URL SERVER=<URL> any URL - Path to server cgi-bin directory
--user STRING USER=<STRING> any string user User name
--job STRING JOB=<STRING> any string job job name
--cells-per-line NUMBER CELLS_PER_LINE=1 any integer 20 Specifies number of aa cells per line in protein coverage view
--no-msms-images NO_MSMS_IMAGES=1 - - Specifies that no MS/MS images are generated
--outdir PATH REPORT_DIR=<PATH>
any valid path <--project-dir>/report
Output directory
--verbose verbose=1 - - Display progress information
--p FILE PARAMETER_FILE=<FILE>
any filename - Read parameters from file
--help help=1 - - Display this help and exit
--version VERSION=1 - - Output version information and exit
--debug debug=1 - - Output debug information
--cpu-count CPUS Any integer > 0 1 Number of CPUs used to generated report pages.

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