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comparison ideas.xml @ 12:5b5733e09344 draft

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Uploaded
author greg
date Thu, 10 Aug 2017 14:09:11 -0400
parents 6f486284731d
children 3b3bf5196bbe
comparison
equal deleted inserted replaced
11:6f486284731d 12:5b5733e09344
4 <requirement type="package" version="2.26.0">bedtools</requirement> 4 <requirement type="package" version="2.26.0">bedtools</requirement>
5 <requirement type="package" version="332">ucsc-bedgraphtobigwig</requirement> 5 <requirement type="package" version="332">ucsc-bedgraphtobigwig</requirement>
6 <requirement type="package" version="332">ucsc-bedsort</requirement> 6 <requirement type="package" version="332">ucsc-bedsort</requirement>
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="1.3.0">r-optparse</requirement>
9 </requirements> 10 </requirements>
10 <command><![CDATA[ 11 <command><![CDATA[
11 #import os 12 #import os
12 mkdir -p tmp && 13 #set tmp_dir = 'tmp'
13 mkdir -p prep_output && 14 #set prep_output_dir = 'prep_output'
15 #set ideas_input_dir = 'ideas_input'
16 #set ideas_matrix_input_file = $ideas_input_dir/r_matrix.txt
17 mkdir -p $prep_output_dir &&
18 mkdir -p $ideas_input_dir &&
14 ############################################## 19 ##############################################
15 ## Create the config file and prepare the data 20 ## Create the config file and prepare the data
16 ############################################## 21 ##############################################
17 #set input_type = $input_type_cond.input_type 22 #set input_type = $input_type_cond.input_type
18 cp '$build_config_file' 'config_file.txt' && 23 cp '$build_config_file' 'config_file.txt' &&
51 -norm 56 -norm
52 #end if 57 #end if
53 ############################################## 58 ##############################################
54 ## Build the R matrix from the prepMat output 59 ## Build the R matrix from the prepMat output
55 ############################################## 60 ##############################################
56 #set r_matrix_input = None
57 #for f in $os.listdir('tmp'):
58 #if f.endswith('.bed.gz'):
59 #set r_matrix_input = $os.path.join('tmp', $f)
60 #end if
61 #end for
62 #assert $r_matrix_input is not None and $os.path.getsize($r_matrix_input) > 0, "Output file from prepMat is missing or empty."
63 && Rscript '$__tool_directory__/build_matrix.R' 61 && Rscript '$__tool_directory__/build_matrix.R'
64 -i $r_matrix_input 62 -i $tmp_dir/*.bed.gz
65 -o '%s.input' % $f 63 -o $ideas_matrix_input_file
66 -w 'tmp' 64 -w $ideas_input_dir
67 ############################################## 65 ##############################################
68 ## Run IDEAS on the R matrix 66 ## Run IDEAS on the R matrix
69 ############################################## 67 ##############################################
70 && ideas 68 && ideas
71 '$build_config_file' 69 '$build_config_file'
117 #set set_max_standard_dev = $set_max_standard_dev_cond.set_max_standard_dev 115 #set set_max_standard_dev = $set_max_standard_dev_cond.set_max_standard_dev
118 #if str($set_max_standard_dev) == 'yes': 116 #if str($set_max_standard_dev) == 'yes':
119 -maxerr $set_max_standard_dev_cond.max_standard_dev 117 -maxerr $set_max_standard_dev_cond.max_standard_dev
120 #end if 118 #end if
121 -thread \${GALAXY_SLOTS:-4} 119 -thread \${GALAXY_SLOTS:-4}
122 -o 'prep_output' 120 -o $prep_output_dir
123 && mv prep_output/*.state $output_state 121 && mv $prep_output_dir/*.state $output_state
124 && mv prep_output/*.para $output_para 122 && mv $prep_output_dir/*.para $output_para
125 && mv prep_output/*cluster $output_cluster 123 && mv $prep_output_dir/*cluster $output_cluster
126 ]]></command> 124 ]]></command>
127 <configfiles> 125 <configfiles>
128 <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat: 126 <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat:
129 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 127 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
130 #end for ]]></configfile> 128 #end for ]]></configfile>