Mercurial > repos > iuc > maker
changeset 4:5e96efe6e6c6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b"
| author | iuc |
|---|---|
| date | Thu, 10 Oct 2019 02:56:46 -0400 |
| parents | 96ac930d84fa |
| children | 5201ec38c01f |
| files | maker.xml |
| diffstat | 1 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/maker.xml Mon May 06 10:06:04 2019 -0400 +++ b/maker.xml Thu Oct 10 02:56:46 2019 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="maker" name="Maker" profile="16.04" version="@VERSION@"> +<tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy1"> <description>genome annotation pipeline</description> <macros> <import>macros.xml</import> @@ -125,7 +125,11 @@ #else if $repeat_masking.repeat_source.source_type == 'library' model_org= # select a model organism for RepBase masking in RepeatMasker -rmlib=${repeat_masking.repeat_source.repeatmasker.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker +#if $repeat_masking.repeat_source.rmlib +rmlib=${repeat_masking.repeat_source.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker +#else +rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker +#end if #if $repeat_masking.repeat_source.repeat_protein repeat_protein=${repeat_masking.repeat_source.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner @@ -432,8 +436,9 @@ <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/> </when> <when value="library"> + <param name="rmlib" type="data" format="fasta" label="Transposable element sequences for RepeatRunner" optional="True" /> <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" /> - <param name="rm_gff" type="data" format="fasta" label="Pre-identified repeat elements from an external GFF file" optional="True" /> + <param name="rm_gff" type="data" format="gff" label="Pre-identified repeat elements from an external GFF file" optional="True" /> <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/> </when> <when value="no"/>