Mercurial > repos > devteam > cuffdiff
comparison cuffdiff_wrapper.xml @ 3:beab768feb92
Update to the new data table specification.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Wed, 04 Dec 2013 13:24:38 -0500 |
| parents | 2d6a90609943 |
| children | 604fa75232a2 |
comparison
equal
deleted
inserted
replaced
| 2:2d6a90609943 | 3:beab768feb92 |
|---|---|
| 1 <tool id="cuffdiff" name="Cuffdiff" version="0.0.6"> | 1 <tool id="cuffdiff" name="Cuffdiff" version="0.0.7"> |
| 2 <!-- Wrapper supports Cuffdiff versions 2.1.0-2.1.1 --> | 2 <!-- Wrapper supports Cuffdiff versions 2.1.0-2.1.1 --> |
| 3 <description>find significant changes in transcript expression, splicing, and promoter use</description> | 3 <description>find significant changes in transcript expression, splicing, and promoter use</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> |
| 31 #if $bias_correction.seq_source.index_source == "history": | 31 #if $bias_correction.seq_source.index_source == "history": |
| 32 ## Custom genome from history. | 32 ## Custom genome from history. |
| 33 $bias_correction.seq_source.ref_file | 33 $bias_correction.seq_source.ref_file |
| 34 #else: | 34 #else: |
| 35 ## Built-in genome. | 35 ## Built-in genome. |
| 36 ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')} | 36 ${__get_data_table_entry__('fasta_indexes', 'value', $gtf_input.dbkey, 'path')} |
| 37 #end if | 37 #end if |
| 38 #end if | 38 #end if |
| 39 | 39 |
| 40 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $conditions ] ) + '\'' | 40 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $conditions ] ) + '\'' |
| 41 --labels $labels | 41 --labels $labels |
| 87 <conditional name="seq_source"> | 87 <conditional name="seq_source"> |
| 88 <param name="index_source" type="select" label="Reference sequence data"> | 88 <param name="index_source" type="select" label="Reference sequence data"> |
| 89 <option value="cached">Locally cached</option> | 89 <option value="cached">Locally cached</option> |
| 90 <option value="history">History</option> | 90 <option value="history">History</option> |
| 91 </param> | 91 </param> |
| 92 <when value="cached"></when> | 92 <when value="cached"> |
| 93 <param name="index" type="select" label="Using reference genome"> | |
| 94 <options from_data_table="fasta_indexes"> | |
| 95 <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" /> | |
| 96 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> | |
| 97 </options> | |
| 98 </param> | |
| 99 </when> | |
| 93 <when value="history"> | 100 <when value="history"> |
| 94 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | 101 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> |
| 95 </when> | 102 </when> |
| 96 </conditional> | 103 </conditional> |
| 97 </when> | 104 </when> |