Mercurial > repos > greg > ideas

comparison ideas.xml @ 27:0cf199863400 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Mon, 14 Aug 2017 09:02:58 -0400
parents 53891e4e4c63
children 91dc2a532890
comparison
equal deleted inserted replaced
26:53891e4e4c63 27:0cf199863400
9 <requirement type="package" version="1.3.2">r-optparse</requirement> 9 <requirement type="package" version="1.3.2">r-optparse</requirement>
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'
15 #set prep_output_config = 'prep_output_config.txt' 14 #set prep_output_config = 'prep_output_config.txt'
16 #set ideas_input_dir = 'ideas_input' 15 ##set ideas_input_dir = 'ideas_input'
17 #set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt') 16 ##set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt')
18 mkdir -p $prep_output_dir && 17 ##mkdir -p $ideas_input_dir &&
19 mkdir -p $ideas_input_dir &&
20 ############################################## 18 ##############################################
21 ## Create the config file and prepare the data 19 ## Create the config file and prepare the data
22 ############################################## 20 ##############################################
23 #set input_type = $input_type_cond.input_type 21 #set input_type = $input_type_cond.input_type
24 cp '$prep_input_config' 'prep_input_config.txt' && 22 cp '$prep_input_config' 'prep_input_config.txt' &&
124 #set set_max_standard_dev = $set_max_standard_dev_cond.set_max_standard_dev 122 #set set_max_standard_dev = $set_max_standard_dev_cond.set_max_standard_dev
125 #if str($set_max_standard_dev) == 'yes': 123 #if str($set_max_standard_dev) == 'yes':
126 -maxerr $set_max_standard_dev_cond.max_standard_dev 124 -maxerr $set_max_standard_dev_cond.max_standard_dev
127 #end if 125 #end if
128 -thread \${GALAXY_SLOTS:-4} 126 -thread \${GALAXY_SLOTS:-4}
129 -o $prep_output_dir 127 && mv *.cluster $output_cluster
130 && mv $prep_output_dir/*cluster $output_cluster 128 && mv *.para $output_para
131 && mv $prep_output_dir/*.para $output_para 129 && mv *.profile $output_profile
132 && mv $prep_output_dir/*.profile $output_profile 130 && mv *.state $output_state
133 && mv $prep_output_dir/*.state $output_state
134 ]]></command> 131 ]]></command>
135 <configfiles> 132 <configfiles>
136 <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat: 133 <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat:
137 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 134 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
138 #end for ]]></configfile> 135 #end for ]]></configfile>