Mercurial > repos > iuc > crossmap_vcf
comparison crossmap_vcf.xml @ 2:7a3c34157901 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
| author | iuc |
|---|---|
| date | Fri, 20 Oct 2017 11:34:06 -0400 |
| parents | a40d9af7d058 |
| children | 9db73ff23c9f |
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| 1:a40d9af7d058 | 2:7a3c34157901 |
|---|---|
| 12 | 12 |
| 13 CrossMap.py vcf | 13 CrossMap.py vcf |
| 14 | 14 |
| 15 #if $seq_source.index_source_s == "cached" | 15 #if $seq_source.index_source_s == "cached" |
| 16 ## This is the 2nd dbkey, and the corresponding value has to be looked up | 16 ## This is the 2nd dbkey, and the corresponding value has to be looked up |
| 17 "${filter(lambda x: str( x[1] ) == str($chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" | 17 "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" |
| 18 #else | 18 #else |
| 19 '${chain_source.input_chain}' | 19 '${seq_source.chain_source.input_chain}' |
| 20 #end if | 20 #end if |
| 21 | 21 |
| 22 '${input_file}' | 22 '${input_file}' |
| 23 '${seq_source.input_fasta}' | 23 '${seq_source.input_fasta}' |
| 24 | 24 |
| 43 --> | 43 --> |
| 44 </param> | 44 </param> |
| 45 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file"> | 45 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file"> |
| 46 <options from_data_table="all_fasta"/> | 46 <options from_data_table="all_fasta"/> |
| 47 </param> | 47 </param> |
| 48 | |
| 49 <expand macro="chain" /> | |
| 48 </when> | 50 </when> |
| 49 | 51 |
| 50 <when value="history"> | 52 <when value="history"> |
| 51 <param name="input" type="data" format="vcf" label="VCF file"/> | 53 <param name="input" type="data" format="vcf" label="VCF file"/> |
| 52 <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/> | 54 <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/> |
| 55 | |
| 56 <expand macro="chain" /> | |
| 53 </when> | 57 </when> |
| 54 </conditional> | 58 </conditional> |
| 55 <expand macro="chain" /> | |
| 56 </inputs> | 59 </inputs> |
| 57 | 60 |
| 58 <outputs> | 61 <outputs> |
| 59 <data name="output" format="vcf" label="${tool.name} on ${on_string}" /> | 62 <data name="output" format="vcf" label="${tool.name} on ${on_string}" /> |
| 60 <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" /> | 63 <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" /> |