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comparison ideas.xml @ 128:de93d8e8a096 draft

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Uploaded
author greg
date Wed, 22 Nov 2017 08:37:10 -0500
parents dcc642e255ec
children d064db60a06d
comparison
equal deleted inserted replaced
127:1c49e78e4ee7 128:de93d8e8a096
24 cp '$gen_prep_input_config' $prep_input_config && 24 cp '$gen_prep_input_config' $prep_input_config &&
25 prepMat 25 prepMat
26 $prep_input_config 26 $prep_input_config
27 #if str($specify_genomic_window) == "yes": 27 #if str($specify_genomic_window) == "yes":
28 -bed '$specify_genomic_window_cond.bed_input' 28 -bed '$specify_genomic_window_cond.bed_input'
29 #import collections
30 chroms = collections.OrderedDict()
29 #else: 31 #else:
30 -gsz '$chromInfo' 32 -gsz '$chromInfo'
31 -wsz $specify_genomic_window_cond.window_size 33 -wsz $specify_genomic_window_cond.window_size
32 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes 34 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes
33 #if str($restrict_chromosomes) == "yes": 35 #if str($restrict_chromosomes) == "yes":
51 ############################################## 53 ##############################################
52 && cut -d' ' $prep_input_config -f1,2 > file1.txt 54 && cut -d' ' $prep_input_config -f1,2 > file1.txt
53 && ls tmp/*.bed.gz > file2.txt 55 && ls tmp/*.bed.gz > file2.txt
54 && paste <(cat file1.txt) <(cat file2.txt) -d' ' > $prep_output_config 56 && paste <(cat file1.txt) <(cat file2.txt) -d' ' > $prep_output_config
55 ############################################## 57 ##############################################
56 ## If using a genomic window bed file, then 58 ## If using a genomic window bed file, categorize
57 ## generate a text file that categorizes the 59 ## the window positions by chromosome to enable
58 ## window positions by chromosome to enable
59 ## the IDEAS -inv option. 60 ## the IDEAS -inv option.
60 ############################################## 61 ##############################################
61 #if str($specify_genomic_window) == "yes": 62 #if str($specify_genomic_window) == "yes":
62 && python '$__tool_directory__/create_window_positions_by_chrom.py' 63 $categorize_window_positions_by_chrom
63 --input '$specify_genomic_window_cond.bed_input' 64 #for chrom, tup in $chroms.items():
64 --output $window_positions_by_chrom 65 && ideas
65 #end if 66 '$prep_output_config'
66 ############################################## 67 $ideas_options
67 ## Run IDEAS 68 #end for
68 ##############################################
69 && ideas
70 '$prep_output_config'
71 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
72 #if str($specify_genomic_window) == "yes":
73 '$specify_genomic_window_cond.bed_input'
74 -inv $window_positions_by_chrom
75 #else: 69 #else:
76 $tmp_dir/*.bed 70 && ideas
77 #end if 71 '$prep_output_config'
78 $hp 72 $ideas_options
79 #if str($log2) != "0.0": 73 && mv ./*.cluster '$output_txt_dir'
80 -log2 $log2 74 && mv ./*.para '$output_txt_dir'
81 #end if 75 && mv ./*.profile '$output_txt_dir'
82 #if str($max_states) != "0.0": 76 && mv ./*.state '$output_txt_dir'
83 -G $max_states 77 -o '$project_name'
84 #end if 78 #if str($save_ideas_log) == "yes":
85 #if str($initial_states) != "0": 79 > $output_log
86 -C $initial_states 80 #else:
87 #end if 81 > /dev/null
88 #if str($max_position_classes) != "0": 82 #end if
89 -P $max_position_classes 83 && Rscript '$__tool_directory__/create_heatmap.R'
90 #end if 84 -i '$output_txt_dir'
91 #if str($max_cell_type_clusters) != "0": 85 -o '$output_pdf_dir'
92 -K $max_cell_type_clusters 86 #end if
93 #end if
94 #if str($prior_concentration) != "0.0":
95 -A $prior_concentration
96 #end if
97 -sample $burnin_num $mcmc_num
98 #if str($minerr) != "0.0":
99 -minerr $minerr
100 #end if
101 #if str($maxerr) != "0.0":
102 -maxerr $maxerr
103 #end if
104 -rseed $rseed
105 -thread \${GALAXY_SLOTS:-4}
106 -o '$project_name'
107 #if str($save_ideas_log) == "yes":
108 > $output_log
109 #else:
110 > /dev/null
111 #end if
112 && mv ./*.cluster '$output_txt_dir'
113 && mv ./*.para '$output_txt_dir'
114 && mv ./*.profile '$output_txt_dir'
115 && mv ./*.state '$output_txt_dir'
116 && Rscript '$__tool_directory__/create_heatmap.R'
117 -i '$output_txt_dir'
118 -o '$output_pdf_dir'
119 ]]></command> 87 ]]></command>
120 <configfiles> 88 <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, $count+1]]]></configfile>
121 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract": 102 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
122 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 103 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
123 #for $i in $cell_type_epigenetic_factor_cond.input: 104 #for $i in $cell_type_epigenetic_factor_cond.input:
124 #set file_name_with_ext = $i.name 105 #set file_name_with_ext = $i.name
125 #assert str($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." % $file_name_with_ext 106 #assert str($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
136 #else: 117 #else:
137 #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat: 118 #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat:
138 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 119 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
139 #end for 120 #end for
140 #end if]]></configfile> 121 #end if]]></configfile>
122 <configfile name="ideas_options"><![CDATA[#if str($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>
141 </configfiles> 155 </configfiles>
142 <inputs> 156 <inputs>
143 <conditional name="cell_type_epigenetic_factor_cond"> 157 <conditional name="cell_type_epigenetic_factor_cond">
144 <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by"> 158 <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by">
145 <option value="extract" selected="true">extracting them from the selected input file names</option> 159 <option value="extract" selected="true">extracting them from the selected input file names</option>