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comparison ideas.xml @ 176:e0d5669fee03 draft

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Uploaded
author greg
date Thu, 25 Jan 2018 13:38:14 -0500
parents 843bfa2dff2c
children 606d6d833a85
comparison
equal deleted inserted replaced
175:2b6b5e2769f5 176:e0d5669fee03
8 <requirement type="package" version="1.20">ideas</requirement> 8 <requirement type="package" version="1.20">ideas</requirement>
9 <requirement type="package" version="1.10.4">r-data.table</requirement> 9 <requirement type="package" version="1.10.4">r-data.table</requirement>
10 <requirement type="package" version="1.4.4">r-optparse</requirement> 10 <requirement type="package" version="1.4.4">r-optparse</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 ## Sylink all files from input.metadata.tmp
14 ## to the current working directory.
15 #import os 13 #import os
14 #set perform_training = $perform_training_cond.perform_training
15
16 ## Set the value of chrom_bed_input since we don't symlink it.
17 #if $input.metadata.chrom_bed is None:
18 #set chrom_bed_input = None
19 #else:
20 #set chrom_bed_input = $os.path.join($input.extra_files_path, $input.metadata.chrom_bed)
21 end if
22
23 ## Link chromosome_windows.txt if not None.
24 #set chromosome_windows $input.metadata.chrom_windows
25 #if chromosome_windows is not None:
26 #set from_path = $os.path.join($input.extra_files_path, $chromosome_windows)
27 ln -s $from_path . &&
28 #end if
29
30 ## Link IDEAS_input_config.txt which will always exist.
31 #set ideas_input_config $input.metadata.input_config
32 #set from_path = $os.path.join($input.extra_files_path, $ideas_input_config)
33 ln -s $from_path . &&
34
35 ## Link all files in the extra_files_path's tmp directory.
16 #set tmp_dir = "tmp" 36 #set tmp_dir = "tmp"
17 #set from_tmp_path = $os.path.join($input.extra_files_path, "tmp") 37 #set from_path = $os.path.join($input.extra_files_path, "tmp")
18 mkdir $tmp_dir && 38 mkdir $tmp_dir &&
19 #for f in $os.listdir($from_tmp_path): 39 #for f in $os.listdir($from_path):
20 ln -s $os.path.join($from_tmp_path, $f) $tmp_dir && 40 ln -s $os.path.join($from_path, $f) $tmp_dir &&
21 #end for 41 #end for
42
43 ## Define and create output directories.
22 #set output_pdf_dir = "output_pdf_dir" 44 #set output_pdf_dir = "output_pdf_dir"
23 #set output_txt_dir = "output_txt_dir" 45 #set output_txt_dir = "output_txt_dir"
24 #set output_training_dir = "output_training_dir" 46 #set output_training_dir = "output_training_dir"
25 #set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt"
26 #set perform_training = $perform_training_cond.perform_training
27 #if str($output_heatmaps) == "yes": 47 #if str($output_heatmaps) == "yes":
28 mkdir '$output_pdf_dir' && 48 mkdir '$output_pdf_dir' &&
29 #end if 49 #end if
30 #if str($perform_training) == "yes": 50 #if str($perform_training) == "yes":
31 #set output_dir = $output_training_dir 51 #set output_dir = $output_training_dir
32 mkdir '$output_training_dir' && 52 mkdir '$output_training_dir' &&
33 #else: 53 #else:
34 #set output_dir = $output_txt_dir 54 #set output_dir = $output_txt_dir
35 mkdir '$output_txt_dir' && 55 mkdir '$output_txt_dir' &&
36 #end if 56 #end if
57
37 Rscript '$__tool_directory__/ideas.R' 58 Rscript '$__tool_directory__/ideas.R'
38 --burnin_num $burnin_num 59 --burnin_num $burnin_num
39 #if str($bychr) == "true": 60 #if str($bychr) == "true":
40 --bychr true 61 --bychr true
41 #end if 62 #end if
42 --chrom_bed_input $input.metadata.chrom_bed 63 --chrom_bed_input $chrom_bed_input
43 --chromosome_windows $input.metadata.chrom_windows 64 --chromosome_windows $chromosome_windows
44 #if str($hp) == "true": 65 #if str($hp) == "true":
45 --hp true 66 --hp true
46 #end if 67 #end if
47 #if str($initial_states) != "0": 68 #if str($initial_states) != "0":
48 --initial_states $initial_states 69 --initial_states $initial_states
49 #end if 70 #end if
50 --input $input
51 --input_files_path $input.extra_files_path 71 --input_files_path $input.extra_files_path
52 --ideas_input_config $input.metadata.input_config 72 --ideas_input_config $ideas_input_config
53 #if str($log2) != "0.0": 73 #if str($log2) != "0.0":
54 --log2 $log2 74 --log2 $log2
55 #end if 75 #end if
56 #if str($maxerr) != "0.0": 76 #if str($maxerr) != "0.0":
57 --maxerr $maxerr 77 --maxerr $maxerr