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comparison ideas.xml @ 6:8c6de654737b draft

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Uploaded
author greg
date Thu, 10 Aug 2017 12:46:17 -0400
parents 4b0f64ae5923
children 00b59afd9fbd
comparison
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5:4b0f64ae5923 6:8c6de654737b
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 #import os
12 mkdir -p tmp && 12 #set tmp_dir = ($os.path.join($os.getcwd(), 'tmp')
13 mkdir -p $tmp_dir &&
13 ############################################## 14 ##############################################
14 ## Create the config file and prepare the data 15 ## Create the config file and prepare the data
15 ############################################## 16 ##############################################
16 #set input_type = $input_type_cond.input_type 17 #set input_type = $input_type_cond.input_type
17 cp '$build_config_file' 'config_file.txt' && 18 cp '$build_config_file' 'config_file.txt' &&
51 #end if 52 #end if
52 ############################################## 53 ##############################################
53 ## Build the R matrix from the prepMat output 54 ## Build the R matrix from the prepMat output
54 ############################################## 55 ##############################################
55 #set r_matrix_input = None 56 #set r_matrix_input = None
56 #for f in $os.listdir('tmp'): 57 #for f in $os.listdir($tmp_dir):
57 #if f.endswith('.bed.gz'): 58 #if f.endswith('.bed.gz'):
58 #set r_matrix_input = $os.path.join('tmp', f) 59 #set r_matrix_input = $os.path.join($tmp_dir, $f)
59 #end if 60 #end if
60 #end for 61 #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 #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 '$__tool_directory__/build_matrix.R' 63 && Rscript '$__tool_directory__/build_matrix.R'
63 -i $r_matrix_input 64 -i $r_matrix_input
64 -o '%s.input' % $f 65 -o '%s.input' % $f
65 -w 'tmp' 66 -w $tmp_dir
66 ############################################## 67 ##############################################
67 ## Run IDEAS on the R matrix 68 ## Run IDEAS on the R matrix
68 ############################################## 69 ##############################################
69 && mkdir -p output 70 && mkdir -p output
70 && ideas 71 && ideas