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comparison ideas.xml @ 38:3421fff414de draft

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Uploaded
author greg
date Tue, 22 Aug 2017 13:10:57 -0400
parents 9298fd6e7443
children 460577fdb0dc
comparison
equal deleted inserted replaced
37:9298fd6e7443 38:3421fff414de
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 <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 shopt -s nullglob
13 function have_any() {
14 [ $# -gt 0 ]
15 }
12 #import os 16 #import os
13 #set tmp_dir = 'tmp' 17 #set tmp_dir = 'tmp'
14 #set prep_output_config = 'prep_output_config.txt' 18 #set prep_output_config = 'prep_output_config.txt'
15 ##set ideas_input_dir = 'ideas_input' 19 ##set ideas_input_dir = 'ideas_input'
16 ##set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt') 20 ##set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt')
102 -sample $burnin_num $mcmc_num 106 -sample $burnin_num $mcmc_num
103 -minerr $min_standard_dev 107 -minerr $min_standard_dev
104 -maxerr $max_standard_dev 108 -maxerr $max_standard_dev
105 -thread \${GALAXY_SLOTS:-4} 109 -thread \${GALAXY_SLOTS:-4}
106 > $output_log 110 > $output_log
107 && for file in ./*.cluster 111 && mv ./*.cluster $output_cluster
108 do 112 && mv ./*.para $output_para
109 if [ -f "${file}" ]; then 113 && mv ./*.profile $output_profile
110 mv "${file}" $output_cluster; 114 && mv ./*.state $output_state
111 break
112 fi
113 done
114 && for file in ./*.para
115 do
116 if [ -f "${file}" ]; then
117 mv "${file}" $output_para;
118 break
119 fi
120 done
121 && for file in ./*.profile
122 do
123 if [ -f "${file}" ]; then
124 mv "${file}" $output_profile;
125 break
126 fi
127 done
128 && for file in ./*.state
129 do
130 if [ -f "${file}" ]; then
131 mv "${file}" $output_state;
132 break
133 fi
134 done
135 ]]></command> 115 ]]></command>
136 <configfiles> 116 <configfiles>
137 <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat: 117 <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat:
138 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 118 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
139 #end for ]]></configfile> 119 #end for ]]></configfile>