Mercurial > repos > greg > ideas_preprocessor

comparison ideas_preprocessor.xml @ 6:6fe65d1379a8 draft

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Uploaded
author greg
date Wed, 24 Jan 2018 09:55:21 -0500
parents f577a83e86c4
children 860b59cae5df
comparison
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5:2b4e1bd725f7 6:6fe65d1379a8
29 cp '$gen_ideaspre_input_config' $ideaspre_input_config && 29 cp '$gen_ideaspre_input_config' $ideaspre_input_config &&
30 sort $ideaspre_input_config -o $ideaspre_input_config && 30 sort $ideaspre_input_config -o $ideaspre_input_config &&
31 Rscript '$__tool_directory__/ideas_preprocessor.R' 31 Rscript '$__tool_directory__/ideas_preprocessor.R'
32 --ideaspre_input_config '$ideaspre_input_config' 32 --ideaspre_input_config '$ideaspre_input_config'
33 #if str($specify_chrom_window) == "yes": 33 #if str($specify_chrom_window) == "yes":
34 --chrom_bed_input '$specify_chrom_window_cond.chrom_bed_input'
35 --chromosome_windows '$chromosome_windows'
34 --ideas_input_config '$ideas_input_config' 36 --ideas_input_config '$ideas_input_config'
35 --chromosome_windows '$chromosome_windows'
36 #end if
37 #if str($specify_chrom_window) == "yes":
38 --chrom_bed_input '$specify_chrom_window_cond.chrom_bed_input'
39 #else: 37 #else:
40 --chrom_len_file '$chromInfo' 38 --chrom_len_file '$chromInfo'
41 --window_size $specify_chrom_window_cond.window_size 39 --window_size $specify_chrom_window_cond.window_size
42 #set restrict_chromosomes = $specify_chrom_window_cond.restrict_chromosomes_cond.restrict_chromosomes 40 #set restrict_chromosomes = $specify_chrom_window_cond.restrict_chromosomes_cond.restrict_chromosomes
43 #if str($restrict_chromosomes) == "yes": 41 #if str($restrict_chromosomes) == "yes":