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comparison ideas_preprocessor.xml @ 2:248b5f72fc02 draft

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Uploaded
author greg
date Tue, 23 Jan 2018 10:48:31 -0500
parents f060a0fbd4fe
children f577a83e86c4
comparison
equal deleted inserted replaced
1:91c5dbb14a13 2:248b5f72fc02
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #set tmp_dir = "tmp" 11 #set tmp_dir = "tmp"
12 #set prep_input_config = "prep_input_config.txt" 12 #set prep_input_config = "prep_input_config.txt"
13 #set prep_output_config = "prep_output_config.txt" 13 #set prep_output_config = "prep_output_config.txt"
14 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 14 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
15 #set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt" 15 mkdir $tmp_dir &&
16 mkdir $output.files_path &&
17 #if str($specify_genomic_window) == "yes":
18 ##############################################
19 ## Using a genomic window bed file, so categorize
20 ## the window positions by chromosome to enable
21 ## the IDEAS -inv option.
22 ##############################################
23 #set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt"
24 cp '$gen_windows_positions_by_chroms_config' $windows_positions_by_chroms_config &&
25 #end if
16 ############################################## 26 ##############################################
17 ## Create the config file and prepare the data 27 ## Create the config file and prepare the data
18 ############################################## 28 ##############################################
19 #set output_dir = $output_txt_dir
20 #set tmp_dir = "tmp"
21 mkdir '$output_txt_dir' &&
22 cp '$gen_prep_input_config' $prep_input_config && 29 cp '$gen_prep_input_config' $prep_input_config &&
23 sort $prep_input_config -o $prep_input_config && 30 sort $prep_input_config -o $prep_input_config &&
24 Rscript '$__tool_directory__/ideas_preprocessor.R' 31 Rscript '$__tool_directory__/ideas_preprocessor.R'
25 --prep_input_config '$prep_input_config' 32 --prep_input_config '$prep_input_config'
33 #if str($specify_genomic_window) == "yes":
34 --prep_output_config '$prep_output_config'
35 --windows_positions_by_chroms_config '$windows_positions_by_chroms_config'
36 #end if
26 #if str($specify_genomic_window) == "yes": 37 #if str($specify_genomic_window) == "yes":
27 --bed_input '$specify_genomic_window_cond.bed_input' 38 --bed_input '$specify_genomic_window_cond.bed_input'
28 #else: 39 #else:
29 --chrom_len_file '$chromInfo' 40 --chrom_len_file '$chromInfo'
30 --window_size $specify_genomic_window_cond.window_size 41 --window_size $specify_genomic_window_cond.window_size
37 #end for 48 #end for
38 --restrict_to_chroms ",".join(chroms) 49 --restrict_to_chroms ",".join(chroms)
39 #end if 50 #end if
40 #end if 51 #end if
41 --reads_per_bp $reads_per_bp 52 --reads_per_bp $reads_per_bp
42 #if str($blacklist_input) not in ["None", ""]: 53 #if str($exclude_input) not in ["None", ""]:
43 --exclude_input '$exclude_input' 54 --exclude_input '$exclude_input'
44 #end if 55 #end if
45 --output '$output' 56 --output '$output'
46 --output_files_path '$output.files_path' 57 --output_files_path '$output.files_path'
47 &> ideas_preprocessor_log.txt; 58 &> ideas_preprocessor_log.txt;
48 if [[ $? -ne 0 ]]; then 59 if [[ $? -ne 0 ]]; then
49 cp ideas_preprocessor_log.txt '$output'; 60 cp ideas_preprocessor_log.txt '$output';
50 exit 1; 61 exit 1;
51 fi 62 fi
52 ##############################################
53 ## Coerce the prepMat config output to the
54 ## format expected by IDEAS.
55 ##############################################
56 && cut -d' ' $prep_input_config -f1,2 > file1.txt
57 && ls $tmp_dir/*.bed.gz > file2.txt
58 && paste <(cat file1.txt) <(cat file2.txt) -d' ' > $prep_output_config
59 #if str($specify_genomic_window) == "yes":
60 ##############################################
61 ## Using a genomic window bed file, so categorize
62 ## the window positions by chromosome to enable
63 ## the IDEAS -inv option.
64 ##############################################
65 && cp '$gen_windows_positions_by_chroms_config' $windows_positions_by_chroms_config
66 #end if
67 ]]></command> 63 ]]></command>
68 <configfiles> 64 <configfiles>
69 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 65 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
70 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 66 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
71 #for $i in $cell_type_epigenetic_factor_cond.input: 67 #for $i in $cell_type_epigenetic_factor_cond.input:
80 #set epigenetic_factor_name = $file_name.split("-")[1] 76 #set epigenetic_factor_name = $file_name.split("-")[1]
81 #else: 77 #else:
82 #set cell_type_name = $file_name.split("-")[1] 78 #set cell_type_name = $file_name.split("-")[1]
83 #set epigenetic_factor_name = $file_name.split("-")[0] 79 #set epigenetic_factor_name = $file_name.split("-")[0]
84 #end if 80 #end if
85 ${cell_type_name} ${epigenetic_factor_name} ${i} ${i.filename} ${i.ext} 81 ${cell_type_name} ${epigenetic_factor_name} ${i} ${file_name} ${i.ext}
86 #end for 82 #end for
87 #else: 83 #else:
88 #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat: 84 #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat:
89 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} ${input_items.input.filename} ${input_items.input.ext} 85 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} ${file_name} ${input_items.input.ext}
90 #end for 86 #end for
91 #end if]]></configfile> 87 #end if]]></configfile>
92 <configfile name="gen_windows_positions_by_chroms_config"><![CDATA[#if str($specify_genomic_window_cond.specify_genomic_window) == "yes": 88 <configfile name="gen_windows_positions_by_chroms_config"><![CDATA[#if str($specify_genomic_window_cond.specify_genomic_window) == "yes":
93 #import collections 89 #import collections
94 #set window_positions_by_chroms_odict = $collections.OrderedDict() 90 #set window_positions_by_chroms_odict = $collections.OrderedDict()