Help

This recipe is a demonstration of all parameter types that the system recognizes.

You need write access to the original recipe to edit.

#
# A recipe demonstrating the use of parameters.
#

#
# Access parameters.
#
echo "Instrument: {{instrument.value}}"
echo "Protocol: {{protocol.value}}"
echo "Cutoff: {{cutoff.value}}"
echo "Validate: {{validate.value}}"
echo "Read length: {{readlen.value}}"

#
# The files to be used.
#
echo "Reads: {{reference.value}}"
echo "SRR: {{accession.value}}"

#
# Make a nested directory structure
#
mkdir -p data/store/

#
# Create a few files.
#
cat {{reference.value}} | grep  ">"  > data/store/sequence-names.txt
cat {{accession.value}} > data/store/srr.txt

#
# Generate a table of contents.
#
find . -name '*' > contents.txt

#
# Print the contents to the screen
#
cat contents.txt

You need write access to the original recipe to edit.

Click the buttons on the right to create new fields.

Add text field Add float field Add data field Add checkbox Add dropdown Add upload field Add integer field Add radio button

Edit the content of each interface element.

[readlen]
label = "Read Length"
display = "INTEGER"
value = 250
range = [ 70, 100000,]

[validate]
label = "Cross Validate"
display = "CHECKBOX"
value = true

[cutoff]
label = "P-Value Cutoff"
display = "FLOAT"
value = 0.05
range = [ 0, 1,]

[protocol]
label = "Sequencing Protocol"
display = "RADIO"
choices = [ [ "single", "Single End",], [ "paired", "Paired End",],]
value = "single"

[instrument]
label = "Select Instrument"
display = "DROPDOWN"
choices = [ [ "hiseq", "Illumina Hiseq",], [ "pacbio", "Pacific BioSciences Sequel",], [ "minion", "Oxford Nanopor Minion",],]
value = "pacbio"

[reference]
label = "Reference Genome"
display = "DROPDOWN"
type = "FASTA"
source = "PROJECT"
value = "Genome.fa"

[accession]
label = "SRR Accesion Numbers"
display = "DROPDOWN"
source = "PROJECT"
type = "SRR"
value = "SRR numbers.txt"

[settings]
name = "Interface Elements"
image = "Interface_Elements_tutorials_47.png"
summary = "This recipe demonstrates the use of different parameter types."
help = "This recipe demonstrates the use of different parameter types.\n# Help\n\nThis recipe is a demonstration of all parameter types that the system recognizes."
template = "Interface_Elements_tutorials_47.sh"
id = 47
recipe_uid = "314ef846"
uid = "314ef846"
url = "http://localhost8000"

You need write access to the original recipe to edit.

Name

Recipe display name

Identifier

Unique identifier for the recipe.

Authorization

Determines who can run a recipe.

Image :

Optional image for the recipe ( 500px Maximum ).

Rank:

Used to order recipes (optional).

Insert Image

From the web

From your computer

Cancel

Back