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comparison ideas.xml @ 59:9fbd77da3043 draft

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Uploaded
author greg
date Wed, 23 Aug 2017 14:58:43 -0400
parents c2642e6cb30e
children ec0e85a08def
comparison
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58:c2642e6cb30e 59:9fbd77da3043
21 #set input_type = $input_type_cond.input_type 21 #set input_type = $input_type_cond.input_type
22 #if str($input_type) == 'datasets': 22 #if str($input_type) == 'datasets':
23 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond 23 #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
24 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor 24 #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
25 #if str($cell_type_epigenetic_factor) == 'extract': 25 #if str($cell_type_epigenetic_factor) == 'extract':
26 '$extract_prep_input_config' &&
27 cp '$extract_prep_input_config' "prep_input_config.txt" && 26 cp '$extract_prep_input_config' "prep_input_config.txt" &&
28 #else: 27 #else:
29 '$manual_prep_input_config' &&
30 cp '$manual_prep_input_config' "prep_input_config.txt" && 28 cp '$manual_prep_input_config' "prep_input_config.txt" &&
31 #end if 29 #end if
32 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond 30 #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
33 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 31 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
34 prepMat 32 prepMat
33 "prep_input_config.txt"
35 #if str($specify_genomic_window) == 'yes': 34 #if str($specify_genomic_window) == 'yes':
36 -bed '$specify_genomic_window_cond.bed_input' 35 -bed '$specify_genomic_window_cond.bed_input'
37 #else: 36 #else:
38 -gsz '$chromInfo' 37 -gsz '$chromInfo'
39 -wsz $specify_genomic_window_cond.window_size 38 -wsz $specify_genomic_window_cond.window_size
118 && mv ./*.state $output_state 117 && mv ./*.state $output_state
119 ]]></command> 118 ]]></command>
120 <configfiles> 119 <configfiles>
121 <configfile name="manual_prep_input_config"><![CDATA[ 120 <configfile name="manual_prep_input_config"><![CDATA[
122 #if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "manual": 121 #if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "manual":
123 #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat: 122 #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat:
124 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 123 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
125 #end for 124 #end for
126 #end if]]></configfile> 125 #end if]]></configfile>
127 <configfile name="extract_prep_input_config"><![CDATA[ 126 <configfile name="extract_prep_input_config"><![CDATA[
128 #import os 127 #import os
129 #if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "extract": 128 #if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "extract":
130 #set $cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond 129 #set $cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
131 #set $input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 130 #set $input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
132 #for $i in $cell_type_epigenetic_factor_cond.input: 131 #for $i in $cell_type_epigenetic_factor_cond.input:
133 #set $file_name_with_ext = $os.path.basename($i) 132 #set $file_name_with_ext = $os.path.basename($i)
134 #set $file_name = $file_name_with_ext.split('.')[0] 133 #set $file_name = $file_name_with_ext.split('.')[0]
135 #if $input_name_positions == "cell_first": 134 #if $input_name_positions == "cell_first":
136 #set $cell_type_name = $file_name.split('-')[0] 135 #set $cell_type_name = $file_name.split('-')[0]
137 #set $epigenetic_factor_name = $file_name.split('-')[1] 136 #set $epigenetic_factor_name = $file_name.split('-')[1]
138 #else: 137 #else:
139 #set $cell_type_name = $file_name.split('-')[1] 138 #set $cell_type_name = $file_name.split('-')[1]
140 #set $epigenetic_factor_name = $file_name.split('-')[0] 139 #set $epigenetic_factor_name = $file_name.split('-')[0]
141 #end if 140 #end if
142 ${cell_type_name} ${epigenetic_factor_name} ${i} 141 ${cell_type_name} ${epigenetic_factor_name} ${i}
143 #end for 142 #end for
144 #end if]]></configfile> 143 #end if]]></configfile>
145 </configfiles> 144 </configfiles>
146 <inputs> 145 <inputs>
147 <conditional name="input_type_cond"> 146 <conditional name="input_type_cond">
148 <param name="input_type" type="select" label="Select input type"> 147 <param name="input_type" type="select" label="Select input type">