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comparison ideas.xml @ 104:4e3a891ca4d8 draft

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Uploaded
author greg
date Tue, 14 Nov 2017 08:50:48 -0500
parents 705c4f8fbefd
children a0e38f759ad5
comparison
equal deleted inserted replaced
103:705c4f8fbefd 104:4e3a891ca4d8
7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement> 7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement>
8 <requirement type="package" version="1.20">ideas</requirement> 8 <requirement type="package" version="1.20">ideas</requirement>
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 detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #set output_dir = "output_dir"
12 #set tmp_dir = "tmp" 13 #set tmp_dir = "tmp"
13 #set prep_input_config = "prep_input_config.txt" 14 #set prep_input_config = "prep_input_config.txt"
14 #set prep_output_config = "prep_output_config.txt" 15 #set prep_output_config = "prep_output_config.txt"
15 ############################################## 16 ##############################################
16 ## Create the config file and prepare the data 17 ## Create the config file and prepare the data
90 #if str($save_ideas_log) == "yes": 91 #if str($save_ideas_log) == "yes":
91 > $output_log 92 > $output_log
92 #else: 93 #else:
93 > /dev/null 94 > /dev/null
94 #end if 95 #end if
95 && mv ./*.cluster output_dir 96 && mv ./*.cluster '$output_dir'
96 && mv ./*.para output_dir 97 && mv ./*.para '$output_dir'
97 && mv ./*.profile output_dir 98 && mv ./*.profile '$output_dir'
98 && mv ./*.state output_dir 99 && mv ./*.state '$output_dir'
99 ]]></command> 100 ]]></command>
100 <configfiles> 101 <configfiles>
101 <configfile name="gen_prep_input_config"><![CDATA[#import os 102 <configfile name="gen_prep_input_config"><![CDATA[#import os
102 #if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 103 #if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
103 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 104 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions