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comparison ideas.xml @ 11:6f486284731d draft

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Uploaded
author greg
date Thu, 10 Aug 2017 13:13:15 -0400
parents 694d13d8b473
children 5b5733e09344
comparison
equal deleted inserted replaced
10:694d13d8b473 11:6f486284731d
7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement> 7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement>
8 <requirement type="package" version="1.2.0">ideas</requirement> 8 <requirement type="package" version="1.2.0">ideas</requirement>
9 </requirements> 9 </requirements>
10 <command><![CDATA[ 10 <command><![CDATA[
11 #import os 11 #import os
12 #set tmp_dir = 'tmp' 12 mkdir -p tmp &&
13 #set prep_output_dir = 'prep_output' 13 mkdir -p prep_output &&
14 mkdir -p $tmp_dir &&
15 mkdir -p $prep_output_dir &&
16 echo "#############################################" &&
17 echo $tmp_dir &&
18 echo $output_dir &&
19 ############################################## 14 ##############################################
20 ## Create the config file and prepare the data 15 ## Create the config file and prepare the data
21 ############################################## 16 ##############################################
22 #set input_type = $input_type_cond.input_type 17 #set input_type = $input_type_cond.input_type
23 cp '$build_config_file' 'config_file.txt' && 18 cp '$build_config_file' 'config_file.txt' &&
57 #end if 52 #end if
58 ############################################## 53 ##############################################
59 ## Build the R matrix from the prepMat output 54 ## Build the R matrix from the prepMat output
60 ############################################## 55 ##############################################
61 #set r_matrix_input = None 56 #set r_matrix_input = None
62 #for f in $os.listdir($tmp_dir): 57 #for f in $os.listdir('tmp'):
63 #if f.endswith('.bed.gz'): 58 #if f.endswith('.bed.gz'):
64 #set r_matrix_input = $os.path.join($tmp_dir, $f) 59 #set r_matrix_input = $os.path.join('tmp', $f)
65 #end if 60 #end if
66 #end for 61 #end for
67 #assert $r_matrix_input is not None and $os.path.getsize($r_matrix_input) > 0, "Output file from prepMat is missing or empty." 62 #assert $r_matrix_input is not None and $os.path.getsize($r_matrix_input) > 0, "Output file from prepMat is missing or empty."
68 && Rscript '$__tool_directory__/build_matrix.R' 63 && Rscript '$__tool_directory__/build_matrix.R'
69 -i $r_matrix_input 64 -i $r_matrix_input
70 -o '%s.input' % $f 65 -o '%s.input' % $f
71 -w $tmp_dir 66 -w 'tmp'
72 ############################################## 67 ##############################################
73 ## Run IDEAS on the R matrix 68 ## Run IDEAS on the R matrix
74 ############################################## 69 ##############################################
75 && ideas 70 && ideas
76 '$build_config_file' 71 '$build_config_file'
122 #set set_max_standard_dev = $set_max_standard_dev_cond.set_max_standard_dev 117 #set set_max_standard_dev = $set_max_standard_dev_cond.set_max_standard_dev
123 #if str($set_max_standard_dev) == 'yes': 118 #if str($set_max_standard_dev) == 'yes':
124 -maxerr $set_max_standard_dev_cond.max_standard_dev 119 -maxerr $set_max_standard_dev_cond.max_standard_dev
125 #end if 120 #end if
126 -thread \${GALAXY_SLOTS:-4} 121 -thread \${GALAXY_SLOTS:-4}
127 -o $prep_output_dir 122 -o 'prep_output'
128 && mv $prep_output_dir/*.state $output_state 123 && mv prep_output/*.state $output_state
129 && mv $prep_output_dir/*.para $output_para 124 && mv prep_output/*.para $output_para
130 && mv $prep_output_dir/*cluster $output_cluster 125 && mv prep_output/*cluster $output_cluster
131 ]]></command> 126 ]]></command>
132 <configfiles> 127 <configfiles>
133 <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat: 128 <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat:
134 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 129 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
135 #end for ]]></configfile> 130 #end for ]]></configfile>