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comparison ideas_preprocessor.xml @ 4:f577a83e86c4 draft

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author greg
date Wed, 24 Jan 2018 08:29:58 -0500
parents 248b5f72fc02
children 6fe65d1379a8
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3:e97851e8951b 4:f577a83e86c4
7 <requirement type="package" version="1.6">samtools</requirement> 7 <requirement type="package" version="1.6">samtools</requirement>
8 <requirement type="package" version="357">ucsc-bigwigaverageoverbed</requirement> 8 <requirement type="package" version="357">ucsc-bigwigaverageoverbed</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #set tmp_dir = "tmp" 11 #set tmp_dir = "tmp"
12 #set prep_input_config = "prep_input_config.txt" 12 #set ideaspre_input_config = "ideaspre_input_config.txt"
13 #set prep_output_config = "prep_output_config.txt" 13 #set ideas_input_config = "IDEAS_input_config.txt"
14 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 14 #set specify_chrom_window = $specify_chrom_window_cond.specify_chrom_window
15 mkdir $tmp_dir && 15 mkdir $tmp_dir &&
16 mkdir $output.files_path && 16 mkdir $output.files_path &&
17 #if str($specify_genomic_window) == "yes": 17 #if str($specify_chrom_window) == "yes":
18 ############################################## 18 ##############################################
19 ## Using a genomic window bed file, so categorize 19 ## Using a genomic window bed file, so categorize
20 ## the window positions by chromosome to enable 20 ## the window positions by chromosome to enable
21 ## the IDEAS -inv option. 21 ## the IDEAS -inv option.
22 ############################################## 22 ##############################################
23 #set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt" 23 #set chromosome_windows = "chromosome_windows.txt"
24 cp '$gen_windows_positions_by_chroms_config' $windows_positions_by_chroms_config && 24 cp '$gen_chromosome_windows' $chromosome_windows &&
25 #end if 25 #end if
26 ############################################## 26 ##############################################
27 ## Create the config file and prepare the data 27 ## Create the config file and prepare the data
28 ############################################## 28 ##############################################
29 cp '$gen_prep_input_config' $prep_input_config && 29 cp '$gen_ideaspre_input_config' $ideaspre_input_config &&
30 sort $prep_input_config -o $prep_input_config && 30 sort $ideaspre_input_config -o $ideaspre_input_config &&
31 Rscript '$__tool_directory__/ideas_preprocessor.R' 31 Rscript '$__tool_directory__/ideas_preprocessor.R'
32 --prep_input_config '$prep_input_config' 32 --ideaspre_input_config '$ideaspre_input_config'
33 #if str($specify_genomic_window) == "yes": 33 #if str($specify_chrom_window) == "yes":
34 --prep_output_config '$prep_output_config' 34 --ideas_input_config '$ideas_input_config'
35 --windows_positions_by_chroms_config '$windows_positions_by_chroms_config' 35 --chromosome_windows '$chromosome_windows'
36 #end if 36 #end if
37 #if str($specify_genomic_window) == "yes": 37 #if str($specify_chrom_window) == "yes":
38 --bed_input '$specify_genomic_window_cond.bed_input' 38 --chrom_bed_input '$specify_chrom_window_cond.chrom_bed_input'
39 #else: 39 #else:
40 --chrom_len_file '$chromInfo' 40 --chrom_len_file '$chromInfo'
41 --window_size $specify_genomic_window_cond.window_size 41 --window_size $specify_chrom_window_cond.window_size
42 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes 42 #set restrict_chromosomes = $specify_chrom_window_cond.restrict_chromosomes_cond.restrict_chromosomes
43 #if str($restrict_chromosomes) == "yes": 43 #if str($restrict_chromosomes) == "yes":
44 #set chroms = [] 44 #set chroms = []
45 #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat 45 #set chrom_repeat = $specify_chrom_window_cond.restrict_chromosomes_cond.chrom_repeat
46 #for $i in $chrom_repeat.chrom 46 #for $i in $chrom_repeat.chrom
47 $chroms.append($i) 47 $chroms.append($i)
48 #end for 48 #end for
49 --restrict_to_chroms ",".join(chroms) 49 --restrict_to_chroms ",".join(chroms)
50 #end if 50 #end if
52 --reads_per_bp $reads_per_bp 52 --reads_per_bp $reads_per_bp
53 #if str($exclude_input) not in ["None", ""]: 53 #if str($exclude_input) not in ["None", ""]:
54 --exclude_input '$exclude_input' 54 --exclude_input '$exclude_input'
55 #end if 55 #end if
56 --output '$output' 56 --output '$output'
57 --output_hid $output.hid
57 --output_files_path '$output.files_path' 58 --output_files_path '$output.files_path'
58 &> ideas_preprocessor_log.txt; 59 &> ideas_preprocessor_log.txt;
59 if [[ $? -ne 0 ]]; then 60 if [[ $? -ne 0 ]]; then
60 cp ideas_preprocessor_log.txt '$output'; 61 cp ideas_preprocessor_log.txt '$output';
61 exit 1; 62 exit 1;
62 fi 63 fi
63 ]]></command> 64 ]]></command>
64 <configfiles> 65 <configfiles>
65 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 66 <configfile name="gen_ideaspre_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
66 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 67 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
67 #for $i in $cell_type_epigenetic_factor_cond.input: 68 #for $i in $cell_type_epigenetic_factor_cond.input:
68 #set file_name_with_ext = $i.name 69 #set file_name_with_ext = $i.name
69 #if str($file_name_with_ext).find("http") >= 0 or str($file_name_with_ext).find("ftp") >= 0: 70 #if str($file_name_with_ext).find("http") >= 0 or str($file_name_with_ext).find("ftp") >= 0:
70 #set file_name_with_ext = $file_name_with_ext.split('/')[-1] 71 #set file_name_with_ext = $file_name_with_ext.split('/')[-1]
83 #else: 84 #else:
84 #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat: 85 #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat:
85 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} ${file_name} ${input_items.input.ext} 86 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} ${file_name} ${input_items.input.ext}
86 #end for 87 #end for
87 #end if]]></configfile> 88 #end if]]></configfile>
88 <configfile name="gen_windows_positions_by_chroms_config"><![CDATA[#if str($specify_genomic_window_cond.specify_genomic_window) == "yes": 89 <configfile name="gen_chromosome_windows"><![CDATA[#if str($specify_chrom_window_cond.specify_chrom_window) == "yes":
89 #import collections 90 #import collections
90 #set window_positions_by_chroms_odict = $collections.OrderedDict() 91 #set window_positions_by_chroms_odict = $collections.OrderedDict()
91 #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')): 92 #for count, line in enumerate(open($specify_chrom_window_cond.chrom_bed_input.file_name, 'r')):
92 #set $line = $line.strip() 93 #set $line = $line.strip()
93 #if not $line or $line.startswith('#'): 94 #if not $line or $line.startswith('#'):
94 #continue 95 #continue
95 #end if 96 #end if
96 #set items = $line.split('\t') 97 #set items = $line.split('\t')
136 <validator type="unspecified_build"/> 137 <validator type="unspecified_build"/>
137 </param> 138 </param>
138 </repeat> 139 </repeat>
139 </when> 140 </when>
140 </conditional> 141 </conditional>
141 <conditional name="specify_genomic_window_cond"> 142 <conditional name="specify_chrom_window_cond">
142 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data"> 143 <param name="specify_chrom_window" type="select" label="Specify window positions using a bed file?">
143 <option value="no" selected="true">No</option> 144 <option value="no" selected="true">No</option>
144 <option value="yes">Yes</option> 145 <option value="yes">Yes</option>
145 </param> 146 </param>
146 <when value="no"> 147 <when value="no">
147 <param name="window_size" type="integer" value="200" label="Window size in base pairs"/> 148 <param name="window_size" type="integer" value="200" label="Window size in base pairs"/>
157 </repeat> 158 </repeat>
158 </when> 159 </when>
159 </conditional> 160 </conditional>
160 </when> 161 </when>
161 <when value="yes"> 162 <when value="yes">
162 <param name="bed_input" type="data" format="bed" label="Bed file specifying the genomic windows"/> 163 <param name="chrom_bed_input" type="data" format="bed" label="Bed file specifying the window positions"/>
163 </when> 164 </when>
164 </conditional> 165 </conditional>
165 <param argument="--bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/> 166 <param argument="--bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/>
166 <param name="reads_per_bp" type="select" display="radio" label="Calculate the signal in each genomic window using"> 167 <param name="reads_per_bp" type="select" display="radio" label="Calculate the signal in each genomic window using">
167 <option value="6" selected="true">mean</option> 168 <option value="6" selected="true">mean</option>
169 </param> 170 </param>
170 <param name="exclude_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/> 171 <param name="exclude_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/>
171 <param argument="--standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/> 172 <param argument="--standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/>
172 </inputs> 173 </inputs>
173 <outputs> 174 <outputs>
174 <data name="output" format="html"/> 175 <data name="output" format="ideaspre"/>
175 </outputs> 176 </outputs>
176 <tests> 177 <tests>
177 <test> 178 <test>
178 </test> 179 </test>
179 </tests> 180 </tests>