Mercurial > repos > iuc > crossmap_vcf
changeset 3:b878e87edb81 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
author | iuc |
---|---|
date | Fri, 20 Oct 2017 11:32:26 -0400 |
parents | 37c8b1afc814 |
children | 69349b98b727 |
files | crossmap_vcf.xml macros.xml test-data/cached_locally/liftOver.loc |
diffstat | 3 files changed, 7 insertions(+), 6 deletions(-) [+] |
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--- a/crossmap_vcf.xml Thu Oct 19 12:40:03 2017 -0400 +++ b/crossmap_vcf.xml Fri Oct 20 11:32:26 2017 -0400 @@ -14,9 +14,9 @@ #if $seq_source.index_source_s == "cached" ## This is the 2nd dbkey, and the corresponding value has to be looked up - "${filter(lambda x: str( x[1] ) == str($chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" + "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" #else - '${chain_source.input_chain}' + '${seq_source.chain_source.input_chain}' #end if '${input_file}' @@ -45,14 +45,17 @@ <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"> <options from_data_table="all_fasta"/> </param> + + <expand macro="chain" /> </when> <when value="history"> <param name="input" type="data" format="vcf" label="VCF file"/> <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/> + + <expand macro="chain" /> </when> </conditional> - <expand macro="chain" /> </inputs> <outputs>
--- a/macros.xml Thu Oct 19 12:40:03 2017 -0400 +++ b/macros.xml Fri Oct 20 11:32:26 2017 -0400 @@ -28,9 +28,7 @@ <when value="cached"> <param name="input_chain" type="select" label="Lift Over To"> <options from_data_table="liftOver"> - <!-- <filter type="data_meta" ref="input" key="dbkey" column="0"/> - --> </options> </param> </when>
--- a/test-data/cached_locally/liftOver.loc Thu Oct 19 12:40:03 2017 -0400 +++ b/test-data/cached_locally/liftOver.loc Fri Oct 20 11:32:26 2017 -0400 @@ -29,4 +29,4 @@ #anoCar1 hg18 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain #...etc... -A B ${__HERE__}/aToB.over.chain +hg18 hg19 ${__HERE__}/aToB.over.chain