Mercurial > repos > devteam > cuffcompare

comparison cuffcompare_wrapper.xml @ 2:8b22e9adae34

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to the new data table specification.
author Dave Bouvier <dave@bx.psu.edu>
date Wed, 04 Dec 2013 13:24:29 -0500
parents 9d35cf35634e
children 8e534225baa9
comparison
equal deleted inserted replaced
1:9a3f7a890da6 2:8b22e9adae34
1 <tool id="cuffcompare" name="Cuffcompare" version="0.0.5"> 1 <tool id="cuffcompare" name="Cuffcompare" version="0.0.6">
2 <!-- Wrapper supports Cuffcompare versions v1.3.0 and newer --> 2 <!-- Wrapper supports Cuffcompare versions v1.3.0 and newer -->
3 <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description> 3 <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</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>
16 #end if 16 #end if
17 #end if 17 #end if
18 18
19 ## Use sequence data? 19 ## Use sequence data?
20 #if $seq_data.use_seq_data == "Yes": 20 #if $seq_data.use_seq_data == "Yes":
21 -s 21 -s
22 #if $seq_data.seq_source.index_source == "history": 22 #if $seq_data.seq_source.index_source == "history":
23 --ref_file=$seq_data.seq_source.ref_file 23 --ref_file=$seq_data.seq_source.ref_file
24 #else: 24 #else:
25 --ref_file="None" 25 --index=${seq_data.seq_source.index.fields.path}
26 #end if 26 #end if
27 --dbkey=${first_input.metadata.dbkey}
28 --index_dir=${GALAXY_DATA_INDEX_DIR}
29 #end if 27 #end if
30 28
31 ## Outputs. 29 ## Outputs.
32 --combined-transcripts=${transcripts_combined} 30 --combined-transcripts=${transcripts_combined}
33 31
65 <conditional name="seq_source"> 63 <conditional name="seq_source">
66 <param name="index_source" type="select" label="Choose the source for the reference list"> 64 <param name="index_source" type="select" label="Choose the source for the reference list">
67 <option value="cached">Locally cached</option> 65 <option value="cached">Locally cached</option>
68 <option value="history">History</option> 66 <option value="history">History</option>
69 </param> 67 </param>
70 <when value="cached"></when> 68 <when value="cached">
69 <param name="index" type="select" label="Using reference genome">
70 <options from_data_table="fasta_indexes">
71 <filter type="data_meta" ref="first_input" key="dbkey" column="1" />
72 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
73 </options>
74 </param>
75 </when>
71 <when value="history"> 76 <when value="history">
72 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> 77 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
73 </when> 78 </when>
74 </conditional> 79 </conditional>
75 </when> 80 </when>