SPS docs - analysis

compared with
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| REPORT_DIR_SERVER \\ | Any valid path \\ | PROJECT_DIR | Project data files location in the report server. Used to specify the directory where the project is after relocation. \\
Paths starting with ~ should be avoided as they may default to the Apache process' home directory. |
| REPORT_PWD | any string | | Report password. |

h4. Optional parameters
| INPUT_SPEC_IDS | file | | Path to peptide-spectrum-matches file containing IDs for INPUT_SPECS_MS. Used to generate sequencing statistics after reports, see [statprotseqs description|specnets:Sequencing Statistics (statprotseqs output)]\\ |
| SPEC_ID_FORMAT | msgfdb/inspect | msgfdb | see [statprotseqs description|specnets:Sequencing Statistics (statprotseqs output)]\\ |
| STATS_MIN_CONTIG_AA_TAG \\ | integer >= 0 | 0 | see [statprotseqs description|specnets:Sequencing Statistics (statprotseqs output)]\\ |
| STATS_MIN_CONTIG_DB_MP \\ | integer >= 0 | 0 | see [statprotseqs description|specnets:Sequencing Statistics (statprotseqs output)]\\ |
| STATS_ENDS_CHOP \\ | integer >= 0 | 0 | see [statprotseqs description|specnets:Sequencing Statistics (statprotseqs output)]\\ |

h4. Optional SILAC Parameters