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comparison ideas.xml @ 49:af8bf2b76697 draft

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Uploaded
author greg
date Wed, 23 Aug 2017 14:17:09 -0400
parents c9c90bfbeb20
children 14ac679f3c4c
comparison
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48:c9c90bfbeb20 49:af8bf2b76697
17 ##mkdir -p $ideas_input_dir && 17 ##mkdir -p $ideas_input_dir &&
18 ############################################## 18 ##############################################
19 ## Create the config file and prepare the data 19 ## Create the config file and prepare the data
20 ############################################## 20 ##############################################
21 #set input_type = $input_type_cond.input_type 21 #set input_type = $input_type_cond.input_type
22 prepMat
23 #if str($input_type) == 'datasets': 22 #if str($input_type) == 'datasets':
24 #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
25 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor 24 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
26 #if str($cell_type_epigenetic_factor) == 'extract': 25 #if str($cell_type_epigenetic_factor) == 'extract':
27 '$extract_prep_input_config' 26 #set prep_input_config = '$extract_prep_input_config'
28 #else: 27 #else:
29 '$manual_prep_input_config' 28 #set prep_input_config = '$manual_prep_input_config'
30 #end if 29 #end if
31 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 30 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
32 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 31 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
32 prepMat
33 #if str($specify_genomic_window) == 'yes': 33 #if str($specify_genomic_window) == 'yes':
34 -bed '$specify_genomic_window_cond.bed_input' 34 -bed '$specify_genomic_window_cond.bed_input'
35 #else: 35 #else:
36 -gsz '$chromInfo' 36 -gsz '$chromInfo'
37 -wsz $specify_genomic_window_cond.window_size 37 -wsz $specify_genomic_window_cond.window_size
54 $norm 54 $norm
55 ############################################## 55 ##############################################
56 ## Coerce the prepMat config output to the 56 ## Coerce the prepMat config output to the
57 ## format expected by the R matrix builder. 57 ## format expected by the R matrix builder.
58 ############################################## 58 ##############################################
59 && cut -d' ' $manual_prep_input_config -f1,2 > file1.txt 59 && cut -d' ' $prep_input_config -f1,2 > file1.txt
60 && ls tmp/*.bed.gz > file2.txt 60 && ls tmp/*.bed.gz > file2.txt
61 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config 61 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
62 ############################################## 62 ##############################################
63 ## Build the R matrix from the prepMat output 63 ## Build the R matrix from the prepMat output
64 ############################################## 64 ##############################################
115 && mv ./*.profile $output_profile 115 && mv ./*.profile $output_profile
116 && mv ./*.state $output_state 116 && mv ./*.state $output_state
117 ]]></command> 117 ]]></command>
118 <configfiles> 118 <configfiles>
119 <configfile name="manual_prep_input_config"><![CDATA[ 119 <configfile name="manual_prep_input_config"><![CDATA[
120 #for $input_items in $input_type_cond.input_repeat: 120 #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat:
121 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 121 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
122 #end for]]></configfile> 122 #end for]]></configfile>
123 <configfile name="extract_prep_input_config"><![CDATA[ 123 <configfile name="extract_prep_input_config"><![CDATA[
124 #!/bin/bash 124 #!/bin/bash
125 #set $cell_type_epigenetic_factor_cond=$input_type_cond.cell_type_epigenetic_factor_cond 125 #set $cell_type_epigenetic_factor_cond=$input_type_cond.cell_type_epigenetic_factor_cond