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comparison ideas.xml @ 60:ec0e85a08def draft

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Uploaded
author greg
date Wed, 23 Aug 2017 15:03:40 -0400
parents 9fbd77da3043
children d89f1a065d5c
comparison
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59:9fbd77da3043 60:ec0e85a08def
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 <requirement type="package" version="1.3.2">r-optparse</requirement> 9 <requirement type="package" version="1.3.2">r-optparse</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #import os
13 #set tmp_dir = 'tmp' 12 #set tmp_dir = 'tmp'
13 #set prep_input_config = "prep_input_config.txt"
14 #set prep_output_config = 'prep_output_config.txt' 14 #set prep_output_config = 'prep_output_config.txt'
15 ##set ideas_input_dir = 'ideas_input'
16 ##set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt')
17 ##mkdir -p $ideas_input_dir &&
18 ############################################## 15 ##############################################
19 ## Create the config file and prepare the data 16 ## Create the config file and prepare the data
20 ############################################## 17 ##############################################
21 #set input_type = $input_type_cond.input_type 18 #set input_type = $input_type_cond.input_type
22 #if str($input_type) == 'datasets': 19 #if str($input_type) == 'datasets':
23 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond 20 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
24 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor 21 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
25 #if str($cell_type_epigenetic_factor) == 'extract': 22 #if str($cell_type_epigenetic_factor) == 'extract':
26 cp '$extract_prep_input_config' "prep_input_config.txt" && 23 cp '$extract_prep_input_config' $prep_input_config &&
27 #else: 24 #else:
28 cp '$manual_prep_input_config' "prep_input_config.txt" && 25 cp '$manual_prep_input_config' $prep_input_config &&
29 #end if 26 #end if
30 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 27 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
31 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 28 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
32 prepMat 29 prepMat
33 "prep_input_config.txt" 30 $prep_input_config
34 #if str($specify_genomic_window) == 'yes': 31 #if str($specify_genomic_window) == 'yes':
35 -bed '$specify_genomic_window_cond.bed_input' 32 -bed '$specify_genomic_window_cond.bed_input'
36 #else: 33 #else:
37 -gsz '$chromInfo' 34 -gsz '$chromInfo'
38 -wsz $specify_genomic_window_cond.window_size 35 -wsz $specify_genomic_window_cond.window_size
55 $norm 52 $norm
56 ############################################## 53 ##############################################
57 ## Coerce the prepMat config output to the 54 ## Coerce the prepMat config output to the
58 ## format expected by the R matrix builder. 55 ## format expected by the R matrix builder.
59 ############################################## 56 ##############################################
60 && cut -d' ' prep_input_config.txt -f1,2 > file1.txt 57 && cut -d' ' $prep_input_config -f1,2 > file1.txt
61 && ls tmp/*.bed.gz > file2.txt 58 && ls tmp/*.bed.gz > file2.txt
62 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config 59 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
63 ############################################## 60 ##############################################
64 ## Build the R matrix from the prepMat output 61 ## Build the R matrix from the prepMat output
65 ############################################## 62 ##############################################