omixcore.yaml

---
title:      OmiXcore
name:       omixcore
title_styled:   >
    <i>omiXcore</i>
version:    1.0
description:    >
    <p><i>OmiXcore</i> predicts protein interactions with large RNA and is trained on eCLIP data, with proteins of length 150-2500 aa and RNAs of length  500-20000 nt.
    <i>OmiXcore</i> allows the quantitative prediction of binding site location on >15.000 long intergenic non-coding RNAs (lincRNAs), facilitating experimental design and analysis.</p>
description_short:    >
    The algorithm has been calibrated on RBP interactomes studied by eCLIP assays <a href="https://www.ncbi.nlm.nih.gov/pubmed/27018577">(Van Nostrand et al. 2016)</a> and allows high-throughput predictions on long intergenic non-coding RNAs.
nav_links:
    -   title:  >
            OmiXcore home
        href:   >
            http://service.tartaglialab.com/new_submission/omixcore
    -   title:  >
            Tutorial
        href:   >
            http://service.tartaglialab.com/static_files/shared/tutorial_omixcore.html
    -   title:  >
            Documentation
        href:   >
            http://service.tartaglialab.com/static_files/shared/documentation_omixcore.html#8
    -   title:  >
            Group page @ CRG
        href:   >
            http://pasteur.crg.es/portal/page/portal/827A462EAB6802B3E04012AC0E01291B

form_fields:
    -   name: title
        description: Submission label (optional)
        required: No
        type: text
    -   name: protein_seq
        description: Protein sequence (FASTA format - length in the range 150-2500 aa)
        # based on statistics on training and testing sets.
        required: Yes
        type: textarea
        min_length: 150
        max_length: 5000
    -   name: mode
        description: Run against lincRNAs database or custom RNA sequences
        type: radio
        hidden: No
        required: Yes
        default: custom
        entries:
            -   title:  Custom
                value:  custom
                shows:
                  - rna_seq
            -   title:  lincRNA library
                value:  lincrnas
                hides:
                  - rna_seq
    -   name: rna_seq
        description: RNA sequences (FASTA format - length in the range 500-20000 nt)
        # based on statistics on training and testing sets.
        required: No
        type: textarea
        hidden: No
        max_length: 30000
    -   name: email
        description: Email address (optional, used for notification)
        type: email
        required: No

examples:
    #-   reference_id:   55985
    #    title:          <br>CELF1
    #    description:    a canonical RNA-binding protein ( from <a href="http://www.sciencedirect.com/science/article/pii/S0300908405002634" target="_blank">Biochimie 2006</a>)
    -   reference_id: 96669
        title: P16989 and NM_006312 (NCOR2)
        description: a positive protein-RNA pair, validated by eCLIP assay.
    #-   reference_id: 96538
    #    title: P78344 NR_036527
    #    description: a negative protein-RNA pair, validated by eCLIP assay.

algorithm:
    command:              "omixcore.py -output_dir=<output_dir>"
    processing_timeout: 72000

# for the processing part
output:
    -