From d9e37be2c76d018c6c08ef254c12264672ee00c9 Mon Sep 17 00:00:00 2001 From: Beibei Chen <beibei.chen@utsouthwestern.edu> Date: Wed, 15 Mar 2017 13:04:52 -0500 Subject: [PATCH] update xml file --- astrocyte_pkg.yml | 46 ++++++++++++++++++++++++++++++---------------- 1 file changed, 30 insertions(+), 16 deletions(-) diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml index 2e14860..686e4e4 100644 --- a/astrocyte_pkg.yml +++ b/astrocyte_pkg.yml @@ -76,29 +76,43 @@ workflow_modules: workflow_parameters: + - id: bams + type: files + required: true + description: | + Bam files of all samples + + - id: peaks + type: files + required: true + description: | + Peak files of all samples. Bed format + - id: design type: files required: true regex: ".*(csv)" description: | - A design file listing pairs of sample name and sample group. + A design file listing pairs of sample name and sample group. Must be in csv format Columns must include: SampleID,Tissue, Factor, Condition, Replicate, Peaks, bamReads, bamControl, ControlID, PeakCaller -# - id: genome -# type: select -# choices: -# - [ '/project/shared/bicf_workflow_ref/GRCh38', 'Human GRCh38'] -# - [ '/project/shared/bicf_workflow_ref/GRCh37', 'Human GRCh37'] -# - [ '/project/shared/bicf_workflow_ref/GRCm38', 'Mouse GRCh38'] -# required: true -# description: | -# Reference genome for annotation - -# - id: toppeak -# type: integer -# required: true -# description: | -# The number of top peaks to use for motif discovery. + - id: genome + type: select + choices: + - [ '/project/shared/bicf_workflow_ref/GRCh38', 'hg38'] + - [ '/project/shared/bicf_workflow_ref/GRCh37', 'hg19'] + - [ '/project/shared/bicf_workflow_ref/GRCm38', 'mm10'] + required: true + description: | + Reference genome for annotation + + - id: toppeak + type: integer + required: true + description: | + The number of top peaks to use for motif discovery. + + # ----------------------------------------------------------------------------- # SHINY APP CONFIGURATION # ----------------------------------------------------------------------------- -- GitLab