crossalign.yaml

---
title:      CROSSalign
name:       crossalign
title_styled:   >
    prova
version:    1.0
description:    >
    <p>CROSSalign predicts the structural similarities of two RNA profiles of different length. The tool is based on CROSS and a Dynamic Time Warping algorithm.</p>


description_short:    >
    Computes the similarity of RNA secondary structure

nav_links:
    -   title:  >
            CROSSalign home
        href:   >
            http://service.tartaglialab.com/new_submission/crossalign
    -   title:  >
            Documentation
        href:   >
            http://service.tartaglialab.com/static_files/algorithms/crossalign/documentation.html
    -   title:  >
            Tutorial
        href:   >
            http://service.tartaglialab.com/static_files/algorithms/crossalign/tutorial.html
#    -   title:  >
#            FAQs
#        href:   >
#            http://service.tartaglialab.com/static_files/shared/faqs.html
    -   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: sequence_one
        description: RNA Sequences 1 (FASTA format, please ensure that your sequences only contain A, C, G, T, and U. Do not use !@#$% etc.; the minimum required sequence length is 25 nucleotides.)
        required: Yes
        type: textarea
        min_length: 25
        max_length: 50000
    -   name: freetext_desc
        description: >
            This module accepts text in fasta format. There is <a href="/new_submission/crossalign_file">another version</a> available that allows submission via file upload.</a>
        type: freetext
        required: No

    -   name: feature
        description: <b>Modes of Dynamic Time Warping (DTW; see the Tutorial/Documentation for the details)</b>
        type: radio
        required: Yes
        default: normal
        entries:
            -   title:  Standard DTW
                value:  normal
                shows:
                  - sequence_two
                hides:
                  - organism
                  - sequences
            -   title:  OBE-DTW
                value:  obe
                shows:
                  - sequence_two
                hides:
                  - organism
                  - sequences
            -   title:  Fragmented OBE-DTW
                value:  fragment
                shows:
                  - sequence_two
                hides:
                  - organism
                  - sequences
            -   title:  Dataset (lincRNAs of a specific organism)
                value:  dataset
                hides:
                  - sequence_two
                  - sequences
                shows:
                  - organism
            -   title:  Custom Dataset (Upload your sequences for a custom dataset)
                value:  custom_dataset
                hides:
                  - sequence_two
                  - organism
                shows:
                  - sequences
    -   name: organism
        description: <b>Organism (all lincRNAs from Ensemble)</b>
        type: radio
        required: No
        hidden: Yes
        entries:
            -   title:  Human
                value:  human
            -   title:  Mouse
                value:  mouse
            -   title:  Macaque
                value:  macaq
            -   title:  Rat
                value:  rat
            -   title:  Zebrafish
                value:  zebra
    -   name: sequence_two
        description: RNA Sequences 2 (FASTA format, please ensure that your sequences only contain A, C, G, T, and U. Do not use !@#$% etc.; the minimum required sequence length is 25 nucleotides.)
        required: No
        hidden: No
        type: textarea
        max_length: 50000
    -   name: email
        description: Email address (optional, used for notification)
        type: email
        required: No


examples:
    -   reference_id:   117190
        title:          Xist Rep-A (Standard DTW)
        description:    The Rep-A of Orangutan against the Rep-A of Human
    -   reference_id:   117188
        title:          HOTAIR D2  (DTW-OBE)
        description:    D2 of Human against the entire HOTAIR of mouse
    -   reference_id:   117192
        title:          HIV RNA (fragmented OBE-DTW)
        description:    HIV genotype AE (2001) vs HIV genotype B (1993)

file_uploads:
    -   name: sequences
        filename: C.fasta
        hidden: Yes
        description: RNA Sequences for custom dataset (FASTA format, please ensure that your sequences only contain A, C, G, T, and U. Do not use !@#$% etc.; the minimum required sequence length is 25 nucleotides.)
        format: fasta
        required: No
        min_sequences:  1
        min_indiv_len:  25
#
#
algorithm:
    command:              "crossalign.py -text=Yes -fileA=<file0> -output_dir=<output_dir>"
    processing_timeout:   86400

# for the processing part
output:
    -