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comparison ragtag.xml @ 1:c877619c2de2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071
author iuc
date Thu, 23 Jun 2022 17:27:58 +0000
parents 7ec824b37dec
children 7ac8eea4245c
comparison
equal deleted inserted replaced
0:7ec824b37dec 1:c877619c2de2
21 ln -s '${j}' $out_file && 21 ln -s '${j}' $out_file &&
22 $input_files.append($out_file) 22 $input_files.append($out_file)
23 #end for 23 #end for
24 #set $merge_files = " ".join($input_files) 24 #set $merge_files = " ".join($input_files)
25 #end if 25 #end if
26
27 ## symlink reference because a .fai file is created
28 #if $mode_conditional.mode_option in ['correct', 'scaffold', 'patch']
29 ln -s '$mode_conditional.reference' reference.fa &&
30 ln -s '$mode_conditional.query' query.fa &&
31 #else
32 ln -s '$assembly_fasta' assembly.fa &&
33 #end if
34
26 ragtag.py $mode_conditional.mode_option -u 35 ragtag.py $mode_conditional.mode_option -u
27 #if $mode_conditional.mode_option == 'correct' 36 #if $mode_conditional.mode_option == 'correct'
28 @INPUTS@ 37 @INPUTS@
29 @COMMON_PARAMETERS@ 38 @COMMON_PARAMETERS@
30 #if $mode_conditional.validation_conditional.validation_option == 'true' 39 #if $mode_conditional.validation_conditional.validation_option == 'true'
70 -i $mode_conditional.advanced_options.i 79 -i $mode_conditional.advanced_options.i
71 #if $mode_conditional.advanced_options.patching_mode 80 #if $mode_conditional.advanced_options.patching_mode
72 $mode_conditional.advanced_options.patching_mode 81 $mode_conditional.advanced_options.patching_mode
73 #end if 82 #end if
74 #else 83 #else
75 $assembly_fasta 84 assembly.fa
76 #if $mode_conditional.scaffold_files 85 #if $mode_conditional.scaffold_files
77 $merge_files 86 $merge_files
78 #end if 87 #end if
79 #if $mode_conditional.merging_options.j 88 #if $mode_conditional.merging_options.j
80 -j $mode_conditional.merging_options.j 89 -j $mode_conditional.merging_options.j