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comparison ideas.xml @ 78:949de45a7269 draft

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Uploaded
author greg
date Thu, 24 Aug 2017 09:10:01 -0400
parents 670d811d3244
children 20d4dc694105
comparison
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77:670d811d3244 78:949de45a7269
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 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 22 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
23 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 23 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
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 '$specify_genomic_window_cond.bed_input'
29 #else: 29 #else:
30 -gsz '$chromInfo' 30 -gsz '$chromInfo'
31 -wsz $specify_genomic_window_cond.window_size 31 -wsz $specify_genomic_window_cond.window_size
32 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes 32 #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes
33 #if str($restrict_chromosomes) == 'yes': 33 #if str($restrict_chromosomes) == "yes":
34 #set chroms = [] 34 #set chroms = []
35 #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat 35 #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat
36 #for $i in $chrom_repeat.chrom 36 #for $i in $chrom_repeat.chrom
37 $chroms.append($i) 37 $chroms.append($i)
38 #end for 38 #end for
40 #end if 40 #end if
41 #end if 41 #end if
42 #end if 42 #end if
43 $bychr 43 $bychr
44 -c $reads_per_bp 44 -c $reads_per_bp
45 #if str($blacklist_input) not in ['None', '']: 45 #if str($blacklist_input) not in ["None", ""]:
46 -exclude '$blacklist_input' 46 -exclude '$blacklist_input'
47 #end if 47 #end if
48 $norm 48 $norm
49 ############################################## 49 ##############################################
50 ## Coerce the prepMat config output to the 50 ## Coerce the prepMat config output to the
63 ############################################## 63 ##############################################
64 ## Run IDEAS 64 ## Run IDEAS
65 ############################################## 65 ##############################################
66 && ideas 66 && ideas
67 '$prep_output_config' 67 '$prep_output_config'
68 #if str($input_type) == 'datasets': 68 #if str($input_type) == "datasets":
69 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 69 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
70 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 70 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
71 #if str($specify_genomic_window) == 'yes': 71 #if str($specify_genomic_window) == "yes":
72 '$specify_genomic_window_cond.bed_input' 72 '$specify_genomic_window_cond.bed_input'
73 #else: 73 #else:
74 $tmp_dir/*.bed 74 $tmp_dir/*.bed
75 #end if 75 #end if
76 #else: 76 #else:
77 $tmp_dir/*.bed 77 $tmp_dir/*.bed
78 #end if 78 #end if
79 $hp 79 $hp
80 #if str($log2) != '0.0': 80 #if str($log2) != "0.0":
81 -log2 $log2 81 -log2 $log2
82 #end if 82 #end if
83 #if str($max_states) != '0.0': 83 #if str($max_states) != "0.0":
84 -G $max_states 84 -G $max_states
85 #end if 85 #end if
86 #if str($initial_states) != '0': 86 #if str($initial_states) != "0":
87 -C $initial_states 87 -C $initial_states
88 #end if 88 #end if
89 #if str($max_position_classes) != '0': 89 #if str($max_position_classes) != "0":
90 -P $max_position_classes 90 -P $max_position_classes
91 #end if 91 #end if
92 #if str($max_cell_type_clusters) != '0': 92 #if str($max_cell_type_clusters) != "0":
93 -K $max_cell_type_clusters 93 -K $max_cell_type_clusters
94 #end if 94 #end if
95 #if str($prior_concentration) != '0.0': 95 #if str($prior_concentration) != "0.0":
96 -A $prior_concentration 96 -A $prior_concentration
97 #end if 97 #end if
98 -sample $burnin_num $mcmc_num 98 -sample $burnin_num $mcmc_num
99 #if str($minerr) != '0.0': 99 #if str($minerr) != "0.0":
100 -minerr $minerr 100 -minerr $minerr
101 #end if 101 #end if
102 #if str($maxerr) != '0.0': 102 #if str($maxerr) != "0.0":
103 -maxerr $maxerr 103 -maxerr $maxerr
104 #end if 104 #end if
105 -thread \${GALAXY_SLOTS:-4} 105 -thread \${GALAXY_SLOTS:-4}
106 > $output_log 106 > $output_log
107 && mv ./*.cluster $output_cluster 107 && mv ./*.cluster $output_cluster
108 && mv ./*.para $output_para 108 && mv ./*.para $output_para
109 && mv ./*.profile $output_profile 109 && mv ./*.profile $output_profile
110 && mv ./*.state $output_state 110 && mv ./*.state $output_state
111 ]]></command> 111 ]]></command>
112 <configfiles> 112 <configfiles>
113 <configfile name="gen_prep_input_config"><![CDATA[#if str($input_type_cond.input_type) == "datasets" and str($input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "manual": 113 <configfile name="gen_prep_input_config"><![CDATA[#if str($input_type_cond.input_type) == "datasets":
114 #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat: 114 #if str($input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "manual":
115 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 115 #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat:
116 #end for 116 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
117 #end for
118 #else if str($input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
119 #set $cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
120 #set $input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
121 #for $i in $cell_type_epigenetic_factor_cond.input:
122 #set $file_name_with_ext = $os.path.basename($i)
123 #set $file_name = $file_name_with_ext.split(".")[0]
124 #if $input_name_positions == "cell_first":
125 #set $cell_type_name = $file_name.split("-")[0]
126 #set $epigenetic_factor_name = $file_name.split("-")[1]
127 #else:
128 #set $cell_type_name = $file_name.split("-")[1]
129 #set $epigenetic_factor_name = $file_name.split("-")[0]
130 #end if
131 ${cell_type_name} ${epigenetic_factor_name} ${i}
132 #end for
133 #end if
117 #end if]]></configfile> 134 #end if]]></configfile>
118 </configfiles> 135 </configfiles>
119 <inputs> 136 <inputs>
120 <conditional name="input_type_cond"> 137 <conditional name="input_type_cond">
121 <param name="input_type" type="select" label="Select input type"> 138 <param name="input_type" type="select" label="Select input type">