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comparison ideas.xml @ 129:d064db60a06d draft

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author greg
date Wed, 22 Nov 2017 10:24:04 -0500
parents de93d8e8a096
children d088f25661d9
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128:de93d8e8a096 129:d064db60a06d
7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement> 7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement>
8 <requirement type="package" version="1.20">ideas</requirement> 8 <requirement type="package" version="1.20">ideas</requirement>
9 <requirement type="package" version="1.4.4">r-optparse</requirement> 9 <requirement type="package" version="1.4.4">r-optparse</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #set window_positions_by_chrom = "window.inv"
13 #set output_pdf_dir = "output_pdf_dir" 12 #set output_pdf_dir = "output_pdf_dir"
14 #set output_txt_dir = "output_txt_dir" 13 #set output_txt_dir = "output_txt_dir"
15 #set tmp_dir = "tmp" 14 #set tmp_dir = "tmp"
16 #set prep_input_config = "prep_input_config.txt" 15 #set prep_input_config = "prep_input_config.txt"
17 #set prep_output_config = "prep_output_config.txt" 16 #set prep_output_config = "prep_output_config.txt"
24 cp '$gen_prep_input_config' $prep_input_config && 23 cp '$gen_prep_input_config' $prep_input_config &&
25 prepMat 24 prepMat
26 $prep_input_config 25 $prep_input_config
27 #if str($specify_genomic_window) == "yes": 26 #if str($specify_genomic_window) == "yes":
28 -bed '$specify_genomic_window_cond.bed_input' 27 -bed '$specify_genomic_window_cond.bed_input'
29 #import collections
30 chroms = collections.OrderedDict()
31 #else: 28 #else:
32 -gsz '$chromInfo' 29 -gsz '$chromInfo'
33 -wsz $specify_genomic_window_cond.window_size 30 -wsz $specify_genomic_window_cond.window_size
34 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes 31 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes
35 #if str($restrict_chromosomes) == "yes": 32 #if str($restrict_chromosomes) == "yes":
58 ## If using a genomic window bed file, categorize 55 ## If using a genomic window bed file, categorize
59 ## the window positions by chromosome to enable 56 ## the window positions by chromosome to enable
60 ## the IDEAS -inv option. 57 ## the IDEAS -inv option.
61 ############################################## 58 ##############################################
62 #if str($specify_genomic_window) == "yes": 59 #if str($specify_genomic_window) == "yes":
63 $categorize_window_positions_by_chrom 60 #import collections
64 #for chrom, tup in $chroms.items(): 61 #set window_positions_by_chroms = collections.OrderedDict()
62 #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')):
63 #set $line = $line.strip()
64 #if not $line or $line.startswith('#'):
65 #continue
66 #end if
67 #set items = $line.split('\t')
68 #if $items[0] in $window_positions_by_chroms:
69 #set tup = $window_positions_by_chroms[$items[0]]
70 #set $tup[1] += 1
71 #set $window_positions_by_chroms[$items[0]] = $tup
72 #else:
73 #set $window_positions_by_chroms[$items[0]] = [$count, $count+1]
74 #end if
75 #end for
76 #for chrom, tup in $window_positions_by_chroms.items():
65 && ideas 77 && ideas
66 '$prep_output_config' 78 '$prep_output_config'
67 $ideas_options 79 '$specify_genomic_window_cond.bed_input'
80 $hp
81 -inv $tup[0] $tup[1]
82 #if str($log2) != "0.0":
83 -log2 $log2
84 #end if
85 #if str($max_states) != "0.0":
86 -G $max_states
87 #end if
88 #if str($initial_states) != "0":
89 -C $initial_states
90 #end if
91 #if str($max_position_classes) != "0":
92 -P $max_position_classes
93 #end if
94 #if str($max_cell_type_clusters) != "0":
95 -K $max_cell_type_clusters
96 #end if
97 #if str($prior_concentration) != "0.0":
98 -A $prior_concentration
99 #end if
100 -sample $burnin_num $mcmc_num
101 #if str($minerr) != "0.0":
102 -minerr $minerr
103 #end if
104 #if str($maxerr) != "0.0":
105 -maxerr $maxerr
106 #end if
107 -rseed $rseed
108 -thread \${GALAXY_SLOTS:-4}
109 -o '$project_name.$chrom'
110 #if str($save_ideas_log) == "yes":
111 >> $output_log
112 #else:
113 > /dev/null
114 #end if
68 #end for 115 #end for
69 #else: 116 #else:
70 && ideas 117 && ideas
71 '$prep_output_config' 118 '$prep_output_config'
72 $ideas_options 119 $tmp_dir/*.bed
73 && mv ./*.cluster '$output_txt_dir' 120 $hp
74 && mv ./*.para '$output_txt_dir' 121 #if str($log2) != "0.0":
75 && mv ./*.profile '$output_txt_dir' 122 -log2 $log2
76 && mv ./*.state '$output_txt_dir' 123 #end if
124 #if str($max_states) != "0.0":
125 -G $max_states
126 #end if
127 #if str($initial_states) != "0":
128 -C $initial_states
129 #end if
130 #if str($max_position_classes) != "0":
131 -P $max_position_classes
132 #end if
133 #if str($max_cell_type_clusters) != "0":
134 -K $max_cell_type_clusters
135 #end if
136 #if str($prior_concentration) != "0.0":
137 -A $prior_concentration
138 #end if
139 -sample $burnin_num $mcmc_num
140 #if str($minerr) != "0.0":
141 -minerr $minerr
142 #end if
143 #if str($maxerr) != "0.0":
144 -maxerr $maxerr
145 #end if
146 -rseed $rseed
147 -thread \${GALAXY_SLOTS:-4}
77 -o '$project_name' 148 -o '$project_name'
78 #if str($save_ideas_log) == "yes": 149 #if str($save_ideas_log) == "yes":
79 > $output_log 150 > $output_log
80 #else: 151 #else:
81 > /dev/null 152 > /dev/null
82 #end if 153 #end if
83 && Rscript '$__tool_directory__/create_heatmap.R'
84 -i '$output_txt_dir'
85 -o '$output_pdf_dir'
86 #end if 154 #end if
155 && mv ./*.cluster '$output_txt_dir'
156 && mv ./*.para '$output_txt_dir'
157 && mv ./*.profile '$output_txt_dir'
158 && mv ./*.state '$output_txt_dir'
159 && Rscript '$__tool_directory__/create_heatmap.R'
160 -i '$output_txt_dir'
161 -o '$output_pdf_dir'
87 ]]></command> 162 ]]></command>
88 <configfiles> 163 <configfiles>
89 <configfile name="categorize_window_positions_by_chrom"><![CDATA[#with #open($specify_genomic_window_cond.bed_input, 'r') as fh:
90 #for count, line in enumerate($fh):
91 $line = $line.strip()
92 #if not $line or $line.startswith('#'):
93 #continue
94 items = $line.split('\t')
95 chrom = $items[0]
96 #if $chrom in $chroms:
97 tup = $chroms[$chrom]
98 $tup[1] += 1
99 $chroms[$chrom] = $tup
100 else:
101 $chroms[$chrom] = [$count, $count+1]]]></configfile>
102 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 164 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
103 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 165 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
104 #for $i in $cell_type_epigenetic_factor_cond.input: 166 #for $i in $cell_type_epigenetic_factor_cond.input:
105 #set file_name_with_ext = $i.name 167 #set file_name_with_ext = $i.name
106 #assert str($file_name_with_ext).find("-") >= 0, "The selected input '%s' is invalid because it does not include the '-' character which is required when setting cell type and epigenetic factor names by extracting them from the input file names." % $file_name_with_ext 168 #assert str($file_name_with_ext).find("-") >= 0, "The selected input '%s' is invalid because it does not include the '-' character which is required when setting cell type and epigenetic factor names by extracting them from the input file names." % $file_name_with_ext
117 #else: 179 #else:
118 #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat: 180 #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat:
119 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 181 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
120 #end for 182 #end for
121 #end if]]></configfile> 183 #end if]]></configfile>
122 <configfile name="ideas_options"><![CDATA[#if str($specify_genomic_window) == "yes":
123 '$specify_genomic_window_cond.bed_input'
124 #else:
125 $tmp_dir/*.bed
126 #end if
127 $hp
128 #if str($log2) != "0.0":
129 -log2 $log2
130 #end if
131 #if str($max_states) != "0.0":
132 -G $max_states
133 #end if
134 #if str($initial_states) != "0":
135 -C $initial_states
136 #end if
137 #if str($max_position_classes) != "0":
138 -P $max_position_classes
139 #end if
140 #if str($max_cell_type_clusters) != "0":
141 -K $max_cell_type_clusters
142 #end if
143 #if str($prior_concentration) != "0.0":
144 -A $prior_concentration
145 #end if
146 -sample $burnin_num $mcmc_num
147 #if str($minerr) != "0.0":
148 -minerr $minerr
149 #end if
150 #if str($maxerr) != "0.0":
151 -maxerr $maxerr
152 #end if
153 -rseed $rseed
154 -thread \${GALAXY_SLOTS:-4}]]></configfile>
155 </configfiles> 184 </configfiles>
156 <inputs> 185 <inputs>
157 <conditional name="cell_type_epigenetic_factor_cond"> 186 <conditional name="cell_type_epigenetic_factor_cond">
158 <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by"> 187 <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by">
159 <option value="extract" selected="true">extracting them from the selected input file names</option> 188 <option value="extract" selected="true">extracting them from the selected input file names</option>