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comparison ideas.xml @ 61:d89f1a065d5c draft

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author greg
date Wed, 23 Aug 2017 15:11:44 -0400
parents ec0e85a08def
children cf0fbd58feb4
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60:ec0e85a08def 61:d89f1a065d5c
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 #set tmp_dir = 'tmp' 12 #set tmp_dir = "tmp"
13 #set prep_input_config = "prep_input_config.txt" 13 #set prep_input_config = "prep_input_config.txt"
14 #set prep_output_config = 'prep_output_config.txt' 14 #set prep_output_config = "prep_output_config.txt"
15 ############################################## 15 ##############################################
16 ## Create the config file and prepare the data 16 ## Create the config file and prepare the data
17 ############################################## 17 ##############################################
18 #set input_type = $input_type_cond.input_type 18 #set input_type = $input_type_cond.input_type
19 #if str($input_type) == 'datasets': 19 #if str($input_type) == "datasets":
20 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond 20 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
21 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor 21 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
22 #if str($cell_type_epigenetic_factor) == 'extract': 22 #if str($cell_type_epigenetic_factor) == "extract":
23 cp '$extract_prep_input_config' $prep_input_config && 23 cp '$extract_prep_input_config' $prep_input_config &&
24 #else: 24 #else:
25 cp '$manual_prep_input_config' $prep_input_config && 25 cp '$manual_prep_input_config' $prep_input_config &&
26 #end if 26 #end if
27 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 27 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
28 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 28 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
29 prepMat 29 prepMat
30 $prep_input_config 30 $prep_input_config
31 #if str($specify_genomic_window) == 'yes': 31 #if str($specify_genomic_window) == "yes":
32 -bed '$specify_genomic_window_cond.bed_input' 32 -bed '$specify_genomic_window_cond.bed_input'
33 #else: 33 #else:
34 -gsz '$chromInfo' 34 -gsz '$chromInfo'
35 -wsz $specify_genomic_window_cond.window_size 35 -wsz $specify_genomic_window_cond.window_size
36 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes 36 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes
37 #if str($restrict_chromosomes) == 'yes': 37 #if str($restrict_chromosomes) == "yes":
38 #set chroms = [] 38 #set chroms = []
39 #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat 39 #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat
40 #for $i in $chrom_repeat.chrom 40 #for $i in $chrom_repeat.chrom
41 $chroms.append($i) 41 $chroms.append($i)
42 #end for 42 #end for
44 #end if 44 #end if
45 #end if 45 #end if
46 #end if 46 #end if
47 $bychr 47 $bychr
48 -c $reads_per_bp 48 -c $reads_per_bp
49 #if str($blacklist_input) not in ['None', '']: 49 #if str($blacklist_input) not in ["None", ""]:
50 -exclude '$blacklist_input' 50 -exclude '$blacklist_input'
51 #end if 51 #end if
52 $norm 52 $norm
53 ############################################## 53 ##############################################
54 ## Coerce the prepMat config output to the 54 ## Coerce the prepMat config output to the
67 ############################################## 67 ##############################################
68 ## Run IDEAS 68 ## Run IDEAS
69 ############################################## 69 ##############################################
70 && ideas 70 && ideas
71 '$prep_output_config' 71 '$prep_output_config'
72 #if str($input_type) == 'datasets': 72 #if str($input_type) == "datasets":
73 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 73 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
74 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 74 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
75 #if str($specify_genomic_window) == 'yes': 75 #if str($specify_genomic_window) == "yes":
76 '$specify_genomic_window_cond.bed_input' 76 '$specify_genomic_window_cond.bed_input'
77 #else: 77 #else:
78 $tmp_dir/*.bed 78 $tmp_dir/*.bed
79 #end if 79 #end if
80 #else: 80 #else:
81 $tmp_dir/*.bed 81 $tmp_dir/*.bed
82 #end if 82 #end if
83 $hp 83 $hp
84 #if str($log2) != '0.0': 84 #if str($log2) != "0.0":
85 -log2 $log2 85 -log2 $log2
86 #end if 86 #end if
87 #if str($max_states) != '0.0': 87 #if str($max_states) != "0.0":
88 -G $max_states 88 -G $max_states
89 #end if 89 #end if
90 #if str($initial_states) != '0': 90 #if str($initial_states) != "0":
91 -C $initial_states 91 -C $initial_states
92 #end if 92 #end if
93 #if str($max_position_classes) != '0': 93 #if str($max_position_classes) != "0":
94 -P $max_position_classes 94 -P $max_position_classes
95 #end if 95 #end if
96 #if str($max_cell_type_clusters) != '0': 96 #if str($max_cell_type_clusters) != "0":
97 -K $max_cell_type_clusters 97 -K $max_cell_type_clusters
98 #end if 98 #end if
99 #if str($prior_concentration) != '0.0': 99 #if str($prior_concentration) != "0.0":
100 -A $prior_concentration 100 -A $prior_concentration
101 #end if 101 #end if
102 -sample $burnin_num $mcmc_num 102 -sample $burnin_num $mcmc_num
103 #if str($minerr) != '0.0': 103 #if str($minerr) != "0.0":
104 -minerr $minerr 104 -minerr $minerr
105 #end if 105 #end if
106 #if str($maxerr) != '0.0': 106 #if str($maxerr) != "0.0":
107 -maxerr $maxerr 107 -maxerr $maxerr
108 #end if 108 #end if
109 -thread \${GALAXY_SLOTS:-4} 109 -thread \${GALAXY_SLOTS:-4}
110 > $output_log 110 > $output_log
111 && mv ./*.cluster $output_cluster 111 && mv ./*.cluster $output_cluster
125 #if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "extract": 125 #if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "extract":
126 #set $cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond 126 #set $cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
127 #set $input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 127 #set $input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
128 #for $i in $cell_type_epigenetic_factor_cond.input: 128 #for $i in $cell_type_epigenetic_factor_cond.input:
129 #set $file_name_with_ext = $os.path.basename($i) 129 #set $file_name_with_ext = $os.path.basename($i)
130 #set $file_name = $file_name_with_ext.split('.')[0] 130 #set $file_name = $file_name_with_ext.split(".")[0]
131 #if $input_name_positions == "cell_first": 131 #if $input_name_positions == "cell_first":
132 #set $cell_type_name = $file_name.split('-')[0] 132 #set $cell_type_name = $file_name.split("-")[0]
133 #set $epigenetic_factor_name = $file_name.split('-')[1] 133 #set $epigenetic_factor_name = $file_name.split("-")[1]
134 #else: 134 #else:
135 #set $cell_type_name = $file_name.split('-')[1] 135 #set $cell_type_name = $file_name.split("-")[1]
136 #set $epigenetic_factor_name = $file_name.split('-')[0] 136 #set $epigenetic_factor_name = $file_name.split("-")[0]
137 #end if 137 #end if
138 ${cell_type_name} ${epigenetic_factor_name} ${i} 138 ${cell_type_name} ${epigenetic_factor_name} ${i}
139 #end for 139 #end for
140 #end if]]></configfile> 140 #end if]]></configfile>
141 </configfiles> 141 </configfiles>