Mercurial > repos > devteam > cuffmerge
comparison cuffmerge_wrapper.xml @ 4:9cfc0b970015
Merge heads.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Wed, 08 Jan 2014 09:16:08 -0500 |
| parents | 5b285b6e4ee3 |
| children | 68eaaae05c51 |
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| 3:aa209d311ece | 4:9cfc0b970015 |
|---|---|
| 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> |