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comparison ideas.xml @ 54:7abcf1870e39 draft

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Uploaded
author greg
date Wed, 23 Aug 2017 14:36:30 -0400
parents 7d5b11f4d00d
children fa1e5f44d79e
comparison
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53:7d5b11f4d00d 54:7abcf1870e39
21 #set input_type = $input_type_cond.input_type 21 #set input_type = $input_type_cond.input_type
22 #if str($input_type) == 'datasets': 22 #if str($input_type) == 'datasets':
23 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond 23 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
24 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor 24 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
25 #if str($cell_type_epigenetic_factor) == 'extract': 25 #if str($cell_type_epigenetic_factor) == 'extract':
26 #set prep_input_config = '$extract_prep_input_config' 26 '$extract_prep_input_config' &&
27 #else: 27 cp '$extract_prep_input_config' "prep_input_config.txt" &&
28 #set prep_input_config = '$manual_prep_input_config' 28 #else:
29 '$manual_prep_input_config' &&
30 cp '$manual_prep_input_config' "prep_input_config.txt" &&
29 #end if 31 #end if
30 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 32 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
31 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 33 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
32 cp $prep_input_config "prep_input_config.txt" &&
33 prepMat 34 prepMat
34 #if str($specify_genomic_window) == 'yes': 35 #if str($specify_genomic_window) == 'yes':
35 -bed '$specify_genomic_window_cond.bed_input' 36 -bed '$specify_genomic_window_cond.bed_input'
36 #else: 37 #else:
37 -gsz '$chromInfo' 38 -gsz '$chromInfo'
55 $norm 56 $norm
56 ############################################## 57 ##############################################
57 ## Coerce the prepMat config output to the 58 ## Coerce the prepMat config output to the
58 ## format expected by the R matrix builder. 59 ## format expected by the R matrix builder.
59 ############################################## 60 ##############################################
60 && cut -d' ' $prep_input_config -f1,2 > file1.txt 61 && cut -d' ' prep_input_config.txt -f1,2 > file1.txt
61 && ls tmp/*.bed.gz > file2.txt 62 && ls tmp/*.bed.gz > file2.txt
62 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config 63 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
63 ############################################## 64 ##############################################
64 ## Build the R matrix from the prepMat output 65 ## Build the R matrix from the prepMat output
65 ############################################## 66 ##############################################