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comparison ideas.xml @ 7:00b59afd9fbd draft

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author greg
date Thu, 10 Aug 2017 12:50:54 -0400
parents 8c6de654737b
children 129b880ba2ea
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6:8c6de654737b 7:00b59afd9fbd
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 = ($os.path.join($os.getcwd(), 'tmp') 12 #set tmp_dir = $os.path.join($os.getcwd(), 'tmp')
13 #set prep_output_dir = $os.path.join($os.getcwd(), 'prep_output')
13 mkdir -p $tmp_dir && 14 mkdir -p $tmp_dir &&
15 mkdir -p $prep_output_dir &&
14 ############################################## 16 ##############################################
15 ## Create the config file and prepare the data 17 ## Create the config file and prepare the data
16 ############################################## 18 ##############################################
17 #set input_type = $input_type_cond.input_type 19 #set input_type = $input_type_cond.input_type
18 cp '$build_config_file' 'config_file.txt' && 20 cp '$build_config_file' 'config_file.txt' &&
65 -o '%s.input' % $f 67 -o '%s.input' % $f
66 -w $tmp_dir 68 -w $tmp_dir
67 ############################################## 69 ##############################################
68 ## Run IDEAS on the R matrix 70 ## Run IDEAS on the R matrix
69 ############################################## 71 ##############################################
70 && mkdir -p output
71 && ideas 72 && ideas
72 '$build_config_file' 73 '$build_config_file'
73 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation 74 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation
74 #if str($smoother_annotation) == 'yes': 75 #if str($smoother_annotation) == 'yes':
75 -hp 76 -hp
118 #set set_max_standard_dev = $set_max_standard_dev_cond.set_max_standard_dev 119 #set set_max_standard_dev = $set_max_standard_dev_cond.set_max_standard_dev
119 #if str($set_max_standard_dev) == 'yes': 120 #if str($set_max_standard_dev) == 'yes':
120 -maxerr $set_max_standard_dev_cond.max_standard_dev 121 -maxerr $set_max_standard_dev_cond.max_standard_dev
121 #end if 122 #end if
122 -thread \${GALAXY_SLOTS:-4} 123 -thread \${GALAXY_SLOTS:-4}
123 -o output 124 -o $prep_output_dir
124 && mv output/*.state $output_state 125 && mv $prep_output_dir/*.state $output_state
125 && mv output/*.para $output_para 126 && mv $prep_output_dir/*.para $output_para
126 && mv output/*cluster $output_cluster 127 && mv $prep_output_dir/*cluster $output_cluster
127 ]]></command> 128 ]]></command>
128 <configfiles> 129 <configfiles>
129 <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat: 130 <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat:
130 ${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}
131 #end for ]]></configfile> 132 #end for ]]></configfile>