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comparison ideas.xml @ 125:5e545c9030a0 draft

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Uploaded
author greg
date Tue, 21 Nov 2017 14:39:31 -0500
parents e2995f2f127f
children dcc642e255ec
comparison
equal deleted inserted replaced
124:7a5b618675a6 125:5e545c9030a0
7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement> 7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement>
8 <requirement type="package" version="1.20">ideas</requirement> 8 <requirement type="package" version="1.20">ideas</requirement>
9 <requirement type="package" version="1.4.4">r-optparse</requirement> 9 <requirement type="package" version="1.4.4">r-optparse</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #set window_positions_by_chrom = "window.inv"
12 #set output_pdf_dir = "output_pdf_dir" 13 #set output_pdf_dir = "output_pdf_dir"
13 #set output_txt_dir = "output_txt_dir" 14 #set output_txt_dir = "output_txt_dir"
14 #set tmp_dir = "tmp" 15 #set tmp_dir = "tmp"
15 #set prep_input_config = "prep_input_config.txt" 16 #set prep_input_config = "prep_input_config.txt"
16 #set prep_output_config = "prep_output_config.txt" 17 #set prep_output_config = "prep_output_config.txt"
50 ############################################## 51 ##############################################
51 && cut -d' ' $prep_input_config -f1,2 > file1.txt 52 && cut -d' ' $prep_input_config -f1,2 > file1.txt
52 && ls tmp/*.bed.gz > file2.txt 53 && ls tmp/*.bed.gz > file2.txt
53 && paste <(cat file1.txt) <(cat file2.txt) -d' ' > $prep_output_config 54 && paste <(cat file1.txt) <(cat file2.txt) -d' ' > $prep_output_config
54 ############################################## 55 ##############################################
56 ## If using a genomic window bed file, then
57 ## generate a text file that categorizes the
58 ## window positions by chromosome to enable
59 ## the IDEAS -inv option.
60 ##############################################
61 #if str($specify_genomic_window) == "yes":
62 && python '$__tool_directory__/create_window_positions_by_chrome.py'
63 --input '$specify_genomic_window_cond.bed_input'
64 --output $window_positions_by_chrom
65 #end if
66 ##############################################
55 ## Run IDEAS 67 ## Run IDEAS
56 ############################################## 68 ##############################################
57 && ideas 69 && ideas
58 '$prep_output_config' 70 '$prep_output_config'
59 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 71 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
60 #if str($specify_genomic_window) == "yes": 72 #if str($specify_genomic_window) == "yes":
61 '$specify_genomic_window_cond.bed_input' 73 '$specify_genomic_window_cond.bed_input'
74 -inv $window_positions_by_chrom
62 #else: 75 #else:
63 $tmp_dir/*.bed 76 $tmp_dir/*.bed
64 #end if 77 #end if
65 $hp 78 $hp
66 #if str($log2) != "0.0": 79 #if str($log2) != "0.0":