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comparison ideas.xml @ 64:19112fe6e5bd draft

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author greg
date Thu, 24 Aug 2017 07:54:16 -0400
parents 2321d1e6237d
children e29e083ebef7
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63:2321d1e6237d 64:19112fe6e5bd
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 #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" 13 #set prep_output_config = "prep_output_config.txt"
15 ############################################## 14 ##############################################
16 ## Create the config file and prepare the data 15 ## Create the config file and prepare the data
17 ############################################## 16 ##############################################
18 #set input_type = $input_type_cond.input_type 17 #set input_type = $input_type_cond.input_type
19 #if str($input_type) == "datasets": 18 #if str($input_type) == "datasets":
20 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond 19 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
21 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor 20 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
22 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 21 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
23 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 22 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
24 cp '$gen_prep_input_config' $prep_input_config && 23 cp '$gen_prep_input_config' "prep_input_config.txt" &&
25 prepMat 24 prepMat
26 $prep_input_config 25 '$gen_prep_input_config'
27 #if str($specify_genomic_window) == "yes": 26 #if str($specify_genomic_window) == "yes":
28 -bed '$specify_genomic_window_cond.bed_input' 27 -bed '$specify_genomic_window_cond.bed_input'
29 #else: 28 #else:
30 -gsz '$chromInfo' 29 -gsz '$chromInfo'
31 -wsz $specify_genomic_window_cond.window_size 30 -wsz $specify_genomic_window_cond.window_size
48 $norm 47 $norm
49 ############################################## 48 ##############################################
50 ## Coerce the prepMat config output to the 49 ## Coerce the prepMat config output to the
51 ## format expected by the R matrix builder. 50 ## format expected by the R matrix builder.
52 ############################################## 51 ##############################################
53 && cut -d' ' $prep_input_config -f1,2 > file1.txt 52 && cut -d' ' '$gen_prep_input_config' -f1,2 > file1.txt
54 && ls tmp/*.bed.gz > file2.txt 53 && ls tmp/*.bed.gz > file2.txt
55 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config 54 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
56 ############################################## 55 ##############################################
57 ## Build the R matrix from the prepMat output 56 ## Build the R matrix from the prepMat output
58 ############################################## 57 ##############################################