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comparison ideas.xml @ 25:0169856fe7bb draft

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Uploaded
author greg
date Fri, 11 Aug 2017 13:24:23 -0400
parents 28201e1f1633
children 53891e4e4c63
comparison
equal deleted inserted replaced
24:28201e1f1633 25:0169856fe7bb
10 </requirements> 10 </requirements>
11 <command><![CDATA[ 11 <command><![CDATA[
12 #import os 12 #import os
13 #set tmp_dir = 'tmp' 13 #set tmp_dir = 'tmp'
14 #set prep_output_dir = 'prep_output' 14 #set prep_output_dir = 'prep_output'
15 #set prep_output_config = 'prep_output_config.txt'
15 #set ideas_input_dir = 'ideas_input' 16 #set ideas_input_dir = 'ideas_input'
16 #set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt') 17 #set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt')
17 mkdir -p $prep_output_dir && 18 mkdir -p $prep_output_dir &&
18 mkdir -p $ideas_input_dir && 19 mkdir -p $ideas_input_dir &&
19 ############################################## 20 ##############################################
20 ## Create the config file and prepare the data 21 ## Create the config file and prepare the data
21 ############################################## 22 ##############################################
22 #set input_type = $input_type_cond.input_type 23 #set input_type = $input_type_cond.input_type
23 cp '$build_config_file' 'config_file.txt' && 24 cp '$prep_input_config' 'prep_input_config.txt' &&
24 prepMat 25 prepMat
25 #if str($input_type) == 'datasets': 26 #if str($input_type) == 'datasets':
26 '$build_config_file' 27 '$prep_input_config'
27 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 28 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
28 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 29 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
29 #if str($specify_genomic_window) == 'yes': 30 #if str($specify_genomic_window) == 'yes':
30 -bed '$bed_input' 31 -bed '$bed_input'
31 #else: 32 #else:
56 -norm 57 -norm
57 #end if 58 #end if
58 ############################################## 59 ##############################################
59 ## Build the R matrix from the prepMat output 60 ## Build the R matrix from the prepMat output
60 ############################################## 61 ##############################################
61 && Rscript '$__tool_directory__/build_matrix.R' 62 ##&& Rscript '$__tool_directory__/build_matrix.R'
62 -i $tmp_dir/*.bed.gz 63 ##-i $tmp_dir/*.bed.gz
63 -o $ideas_matrix_input_file 64 ##-o $ideas_matrix_input_file
64 -w $ideas_input_dir 65 ##-w $ideas_input_dir
66 && cut -d' ' $prep_input_config -f1,2 > file1.txt
67 && ls -p tmp/ | grep ".bed.gz" > file2.txt
68 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
65 ############################################## 69 ##############################################
66 ## Run IDEAS on the R matrix 70 ## Run IDEAS on the R matrix
67 ############################################## 71 ##############################################
68 && ideas 72 && ideas
69 '$build_config_file' 73 '$prep_output_config'
70 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation 74 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation
71 #if str($smoother_annotation) == 'yes': 75 #if str($smoother_annotation) == 'yes':
72 -hp 76 -hp
73 #end if 77 #end if
74 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation 78 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation
121 && mv $prep_output_dir/*.state $output_state 125 && mv $prep_output_dir/*.state $output_state
122 && mv $prep_output_dir/*.para $output_para 126 && mv $prep_output_dir/*.para $output_para
123 && mv $prep_output_dir/*cluster $output_cluster 127 && mv $prep_output_dir/*cluster $output_cluster
124 ]]></command> 128 ]]></command>
125 <configfiles> 129 <configfiles>
126 <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat: 130 <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat:
127 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 131 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
128 #end for ]]></configfile> 132 #end for ]]></configfile>
129 </configfiles> 133 </configfiles>
130 <inputs> 134 <inputs>
131 <conditional name="input_type_cond"> 135 <conditional name="input_type_cond">