Mercurial > repos > devteam > cuffmerge
comparison cuffmerge_wrapper.xml @ 9:424d49834830
Fix issue reported by Nicola Soranzo: https://trello.com/c/GvypU9T7. Put quotes around filenames.
author | Daniel Blankenberg <dan@bx.psu.edu> |
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date | Mon, 20 Jan 2014 11:09:02 -0500 |
parents | 5543c3d33e26 |
children | b6e3849293b1 |
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8:5543c3d33e26 | 9:424d49834830 |
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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=""/> |