Mercurial > repos > devteam > cuffmerge
comparison cuffmerge_wrapper.xml @ 4:9cfc0b970015
Merge heads.
author | Dave Bouvier <dave@bx.psu.edu> |
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date | Wed, 08 Jan 2014 09:16:08 -0500 |
parents | 5b285b6e4ee3 |
children | 68eaaae05c51 |
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3:aa209d311ece | 4:9cfc0b970015 |
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1 <tool id="cuffmerge" name="Cuffmerge" version="0.0.5"> | 1 <tool id="cuffmerge" name="Cuffmerge" version="0.0.6"> |
2 <!-- Wrapper supports Cuffmerge versions 1.3 and newer --> | 2 <!-- Wrapper supports Cuffmerge versions 1.3 and newer --> |
3 <description>merge together several Cufflinks assemblies</description> | 3 <description>merge together several Cufflinks assemblies</description> |
4 <requirements> | 4 <requirements> |
5 <requirement type="package" version="2.1.1">cufflinks</requirement> | 5 <requirement type="package" version="2.1.1">cufflinks</requirement> |
6 </requirements> | 6 </requirements> |
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=$seq_data.seq_source.ref_file |
22 #else: | 22 #else: |
23 --ref_file="None" | 23 --index=${bias_correction.seq_source.index.fields.path} |
24 #end if | 24 #end if |
25 --dbkey=${first_input.metadata.dbkey} | |
26 --index_dir=${GALAXY_DATA_INDEX_DIR} | |
27 #end if | 25 #end if |
28 | 26 |
29 ## Outputs. | 27 ## Outputs. |
30 --merged-transcripts=${merged_transcripts} | 28 --merged-transcripts=${merged_transcripts} |
31 | 29 |
62 <conditional name="seq_source"> | 60 <conditional name="seq_source"> |
63 <param name="index_source" type="select" label="Choose the source for the reference list"> | 61 <param name="index_source" type="select" label="Choose the source for the reference list"> |
64 <option value="cached">Locally cached</option> | 62 <option value="cached">Locally cached</option> |
65 <option value="history">History</option> | 63 <option value="history">History</option> |
66 </param> | 64 </param> |
67 <when value="cached"></when> | 65 <when value="cached"> |
66 <param name="index" type="select" label="Using reference genome"> | |
67 <options from_data_table="fasta_indexes"> | |
68 <filter type="data_meta" ref="input" key="dbkey" column="1" /> | |
69 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> | |
70 </options> | |
71 </param> | |
72 </when> | |
68 <when value="history"> | 73 <when value="history"> |
69 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | 74 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> |
70 </when> | 75 </when> |
71 </conditional> | 76 </conditional> |
72 </when> | 77 </when> |