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comparison ideas.xml @ 173:843bfa2dff2c draft

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Uploaded
author greg
date Thu, 25 Jan 2018 11:53:07 -0500
parents 473a089c5fb6
children e0d5669fee03
comparison
equal deleted inserted replaced
172:473a089c5fb6 173:843bfa2dff2c
8 <requirement type="package" version="1.20">ideas</requirement> 8 <requirement type="package" version="1.20">ideas</requirement>
9 <requirement type="package" version="1.10.4">r-data.table</requirement> 9 <requirement type="package" version="1.10.4">r-data.table</requirement>
10 <requirement type="package" version="1.4.4">r-optparse</requirement> 10 <requirement type="package" version="1.4.4">r-optparse</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 ## Sylink all files from input.metadata.tmp
14 ## to the current working directory.
15 #import os
16 #set tmp_dir = "tmp"
17 #set from_tmp_path = $os.path.join($input.extra_files_path, "tmp")
18 mkdir $tmp_dir &&
19 #for f in $os.listdir($from_tmp_path):
20 ln -s $os.path.join($from_tmp_path, $f) $tmp_dir &&
21 #end for
13 #set output_pdf_dir = "output_pdf_dir" 22 #set output_pdf_dir = "output_pdf_dir"
14 #set output_txt_dir = "output_txt_dir" 23 #set output_txt_dir = "output_txt_dir"
15 #set output_training_dir = "output_training_dir" 24 #set output_training_dir = "output_training_dir"
16 #set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt" 25 #set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt"
17 #set perform_training = $perform_training_cond.perform_training 26 #set perform_training = $perform_training_cond.perform_training
23 mkdir '$output_training_dir' && 32 mkdir '$output_training_dir' &&
24 #else: 33 #else:
25 #set output_dir = $output_txt_dir 34 #set output_dir = $output_txt_dir
26 mkdir '$output_txt_dir' && 35 mkdir '$output_txt_dir' &&
27 #end if 36 #end if
28 && Rscript '$__tool_directory__/ideas.R' 37 Rscript '$__tool_directory__/ideas.R'
29 --burnin_num $burnin_num 38 --burnin_num $burnin_num
30 #if str($bychr) == "true": 39 #if str($bychr) == "true":
31 --bychr true 40 --bychr true
32 #end if 41 #end if
33 --chrom_bed_input $input.metadata.chrom_bed_input 42 --chrom_bed_input $input.metadata.chrom_bed
34 --chromosome_windows $input.metadata.chromosome_windows 43 --chromosome_windows $input.metadata.chrom_windows
35 #if str($hp) == "true": 44 #if str($hp) == "true":
36 --hp true 45 --hp true
37 #end if 46 #end if
38 #if str($initial_states) != "0": 47 #if str($initial_states) != "0":
39 --initial_states $initial_states 48 --initial_states $initial_states
40 #end if 49 #end if
41 --input $input 50 --input $input
42 --input_files_path $input.extra_files_path 51 --input_files_path $input.extra_files_path
43 --ideas_input_config $input.metadata.ideas_input_config 52 --ideas_input_config $input.metadata.input_config
44 #if str($log2) != "0.0": 53 #if str($log2) != "0.0":
45 --log2 $log2 54 --log2 $log2
46 #end if 55 #end if
47 #if str($maxerr) != "0.0": 56 #if str($maxerr) != "0.0":
48 --maxerr $maxerr 57 --maxerr $maxerr
58 #end if 67 #end if
59 --mcmc_num $mcmc_num 68 --mcmc_num $mcmc_num
60 #if str($minerr) != "0.0": 69 #if str($minerr) != "0.0":
61 --minerr $minerr 70 --minerr $minerr
62 #end if 71 #end if
72 --output_dir $output_dir
63 #if str($prior_concentration) != "0.0": 73 #if str($prior_concentration) != "0.0":
64 --prior_concentration $prior_concentration 74 --prior_concentration $prior_concentration
65 #end if 75 #end if
66 --project_name '$project_name' 76 --project_name '$project_name'
67 #if str($save_ideas_log) == "yes": 77 #if str($save_ideas_log) == "yes":
162 <param name="input" value="input.ideaspre" ftype="ideaspre" dbkey="hg19"/> 172 <param name="input" value="input.ideaspre" ftype="ideaspre" dbkey="hg19"/>
163 <param name="project_name" value="IDEAS_out"/> 173 <param name="project_name" value="IDEAS_out"/>
164 <param name="initial_states" value="2"/> 174 <param name="initial_states" value="2"/>
165 <param name="maxerr" value="1000"/> 175 <param name="maxerr" value="1000"/>
166 <param name="output_heatmaps" value="no"/> 176 <param name="output_heatmaps" value="no"/>
177 <param name="save_ideas_log" value="yes"/>
167 <output_collection name="output_txt_collection" type="list"> 178 <output_collection name="output_txt_collection" type="list">
168 <element name="IDEAS_out.chr1.cluster" file="IDEAS_out.cluster" ftype="txt"/> 179 <element name="IDEAS_out.chr1.cluster" file="IDEAS_out.cluster" ftype="txt"/>
169 <element name="IDEAS_out.chr1.para" file="IDEAS_out.para" ftype="txt"/> 180 <element name="IDEAS_out.chr1.para" file="IDEAS_out.para" ftype="txt"/>
170 <element name="IDEAS_out.chr1.profile" file="IDEAS_out.profile" ftype="txt"/> 181 <element name="IDEAS_out.chr1.profile" file="IDEAS_out.profile" ftype="txt"/>
171 <element name="IDEAS_out.chr1.state" file="IDEAS_out.state" ftype="txt"/> 182 <element name="IDEAS_out.chr1.state" file="IDEAS_out.state" ftype="txt"/>