Mercurial > repos > yating-l > jbrowsearchivecreator

comparison jbrowseArchiveCreator.xml @ 19:62dee5369e80 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit afd782e8741a859506794bea92475f620265c50e
author sargentl
date Thu, 13 Sep 2018 17:43:23 -0400
parents 79b23a8afb15
children 85971ec2a527
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18:79b23a8afb15 19:62dee5369e80
18 <stdio> 18 <stdio>
19 </stdio> 19 </stdio>
20 20
21 <command detect_errors="exit_code"><![CDATA[ 21 <command detect_errors="exit_code"><![CDATA[
22 mkdir -p $output.extra_files_path; 22 mkdir -p $output.extra_files_path;
23 23
24 ## Dump the tool parameters into a JSON file 24 ## Dump the tool parameters into a JSON file
25 python $json_file parameters.json; 25 python2 $json_file parameters.json;
26 26
27 python $__tool_directory__/jbrowseArchiveCreator.py --data_json parameters.json -o $output 27 python2 $__tool_directory__/jbrowseArchiveCreator.py --data_json parameters.json -o $output
28 ]]></command> 28 ]]></command>
29 <configfiles> 29 <configfiles>
30 <configfile name="json_file"> 30 <configfile name="json_file">
31 import json 31 import json
32 import sys 32 import sys
52 #silent $data_parameter_dict[$datatype].append($data_dict) 52 #silent $data_parameter_dict[$datatype].append($data_dict)
53 #else 53 #else
54 #set array_inputs = [] 54 #set array_inputs = []
55 #silent $array_inputs.append($data_dict) 55 #silent $array_inputs.append($data_dict)
56 #silent $data_parameter_dict.update({$datatype: $array_inputs}) 56 #silent $data_parameter_dict.update({$datatype: $array_inputs})
57 #end if 57 #end if
58 #end def 58 #end def
59 59
60 ## Get the number of digits from tracks, to have a unique integer from group index and track index 60 ## Get the number of digits from tracks, to have a unique integer from group index and track index
61 61
62 #set temp_max_digit = 0 62 #set temp_max_digit = 0
206 <valid initial="string.letters,string.digits"> 206 <valid initial="string.letters,string.digits">
207 <add value="#"/> 207 <add value="#"/>
208 </valid> 208 </valid>
209 </sanitizer> 209 </sanitizer>
210 </param> 210 </param>
211 </when> 211 </when>
212 <when value="bed"> 212 <when value="bed">
213 <conditional name="bedChoice"> 213 <conditional name="bedChoice">
214 <param name="bed_select" type="select" label="Bed Choice"> 214 <param name="bed_select" type="select" label="Bed Choice">
215 <option value="bed_generic">BED Generic</option> 215 <option value="bed_generic">BED Generic</option>
216 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> 216 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>