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comparison ideas.xml @ 3:9874800487e6 draft

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Uploaded
author greg
date Thu, 10 Aug 2017 12:34:52 -0400
parents d75cbb2db2c4
children 445bafcf9a4b
comparison
equal deleted inserted replaced
2:7a77ec6342c1 3:9874800487e6
6 <requirement type="package" version="332">ucsc-bedsort</requirement> 6 <requirement type="package" version="332">ucsc-bedsort</requirement>
7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement> 7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement>
8 <requirement type="package" version="1.2.0">ideas</requirement> 8 <requirement type="package" version="1.2.0">ideas</requirement>
9 </requirements> 9 </requirements>
10 <command><![CDATA[ 10 <command><![CDATA[
11 #import os
11 mkdir -p tmp && 12 mkdir -p tmp &&
13 ##############################################
12 ## Create the config file and prepare the data 14 ## Create the config file and prepare the data
15 ##############################################
13 #set input_type = $input_type_cond.input_type 16 #set input_type = $input_type_cond.input_type
14 cp '$build_config_file' 'config_file.txt' && 17 cp '$build_config_file' 'config_file.txt' &&
15 prepMat 18 prepMat
16 #if str($input_type) == 'datasets': 19 #if str($input_type) == 'datasets':
17 '$build_config_file' 20 '$build_config_file'
44 #end if 47 #end if
45 #set standardize_datasets = $standardize_datasets_cond.standardize_datasets 48 #set standardize_datasets = $standardize_datasets_cond.standardize_datasets
46 #if str($standardize_datasets) == 'yes': 49 #if str($standardize_datasets) == 'yes':
47 -norm 50 -norm
48 #end if 51 #end if
49 ## Run IDEAS on the prepared data 52 ##############################################
53 ## Build the R matrix from the prepMat output
54 ##############################################
55 #set r_matrix_input = None
56 #for f in $os.listdir(tmp):
57 #if f.endswith('.bed.gz'):
58 #set r_matrix_input = $os.path.join(tmp, f)
59 #end if
60 #end for
61 #assert $r_matrix_input is not None and $os.path.getsize($r_matrix_input) > 0, "Output file from prepMat is missing or empty."
62 && Rscript '$__tool_directory__/build_matrix.R'
63 -i $r_matrix_input
64 -o '%s.input' % $f
65 -w 'tmp'
66 ##############################################
67 ## Run IDEAS on the R matrix
68 ##############################################
50 && mkdir -p output 69 && mkdir -p output
51 && ideas 70 && ideas
52 '$build_config_file' 71 '$build_config_file'
53 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation 72 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation
54 #if str($smoother_annotation) == 'yes': 73 #if str($smoother_annotation) == 'yes':