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comparison cuffmerge_wrapper.xml @ 9:424d49834830

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Fix issue reported by Nicola Soranzo: https://trello.com/c/GvypU9T7. Put quotes around filenames.
author Daniel Blankenberg <dan@bx.psu.edu>
date Mon, 20 Jan 2014 11:09:02 -0500
parents 5543c3d33e26
children b6e3849293b1
comparison
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8:5543c3d33e26 9:424d49834830
9 9
10 --num-threads="\${GALAXY_SLOTS:-4}" 10 --num-threads="\${GALAXY_SLOTS:-4}"
11 11
12 ## Use annotation reference? 12 ## Use annotation reference?
13 #if $annotation.use_ref_annotation == "Yes": 13 #if $annotation.use_ref_annotation == "Yes":
14 -g $annotation.reference_annotation 14 -g "${annotation.reference_annotation}"
15 #end if 15 #end if
16 16
17 ## Use sequence data? 17 ## Use sequence data?
18 #if $seq_data.use_seq_data == "Yes": 18 #if $seq_data.use_seq_data == "Yes":
19 -s 19 -s
20 #if $seq_data.seq_source.index_source == "history": 20 #if $seq_data.seq_source.index_source == "history":
21 --ref_file=$seq_data.seq_source.ref_file 21 --ref_file="${seq_data.seq_source.ref_file}"
22 #else: 22 #else:
23 --index=${bias_correction.seq_source.index.fields.path} 23 --index="${seq_data.seq_source.index.fields.path}"
24 #end if 24 #end if
25 #end if 25 #end if
26 26
27 ## Outputs. 27 ## Outputs.
28 --merged-transcripts=${merged_transcripts} 28 --merged-transcripts="${merged_transcripts}"
29 29
30 ## Inputs. 30 ## Inputs.
31 ${first_input} 31 "${first_input}"
32 #for $input_file in $input_files: 32 #for $input_file in $input_files:
33 ${input_file.additional_input} 33 "${input_file.additional_input}"
34 #end for 34 #end for
35 35
36 </command> 36 </command>
37 <inputs> 37 <inputs>
38 <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/> 38 <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/>