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comparison ideas.xml @ 62:cf0fbd58feb4 draft

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Uploaded
author greg
date Thu, 24 Aug 2017 07:41:00 -0400
parents d89f1a065d5c
children 2321d1e6237d
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61:d89f1a065d5c 62:cf0fbd58feb4
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":
23 cp '$extract_prep_input_config' $prep_input_config &&
24 #else:
25 cp '$manual_prep_input_config' $prep_input_config &&
26 #end if
27 #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
28 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 23 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
24 cp '$prep_input_config' $prep_input_config &&
29 prepMat 25 prepMat
30 $prep_input_config 26 $prep_input_config
31 #if str($specify_genomic_window) == "yes": 27 #if str($specify_genomic_window) == "yes":
32 -bed '$specify_genomic_window_cond.bed_input' 28 -bed '$specify_genomic_window_cond.bed_input'
33 #else: 29 #else:
112 && mv ./*.para $output_para 108 && mv ./*.para $output_para
113 && mv ./*.profile $output_profile 109 && mv ./*.profile $output_profile
114 && mv ./*.state $output_state 110 && mv ./*.state $output_state
115 ]]></command> 111 ]]></command>
116 <configfiles> 112 <configfiles>
117 <configfile name="manual_prep_input_config"><![CDATA[ 113 <configfile name="prep_input_config"><![CDATA[
114 #import os
118 #if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "manual": 115 #if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "manual":
119 #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat: 116 #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat:
120 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 117 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
121 #end for 118 #end for
122 #end if]]></configfile> 119 #else if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "extract":
123 <configfile name="extract_prep_input_config"><![CDATA[
124 #import os
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 120 #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 121 #set $input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
128 #for $i in $cell_type_epigenetic_factor_cond.input: 122 #for $i in $cell_type_epigenetic_factor_cond.input:
129 #set $file_name_with_ext = $os.path.basename($i) 123 #set $file_name_with_ext = $os.path.basename($i)
130 #set $file_name = $file_name_with_ext.split(".")[0] 124 #set $file_name = $file_name_with_ext.split(".")[0]