Mercurial > repos > cpt > cpt_shinefind
changeset 1:27a72d39b21c draft
Uploaded
| author | cpt |
|---|---|
| date | Thu, 19 May 2022 23:58:34 +0000 |
| parents | 88410a18199f |
| children | 0a1f3ac467ee |
| files | cpt_shinefind/macros.xml |
| diffstat | 1 files changed, 2 insertions(+), 25 deletions(-) [+] |
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--- a/cpt_shinefind/macros.xml Fri May 13 18:02:20 2022 +0000 +++ b/cpt_shinefind/macros.xml Thu May 19 23:58:34 2022 +0000 @@ -9,20 +9,7 @@ </requirements> </xml> <xml name="genome_selector"> - <conditional name="reference_genome"> - <param name="reference_genome_source" type="select" label="Reference Genome"> - <option value="history" selected="True">From History</option> - <option value="cached">Locally Cached</option> - </param> - <when value="cached"> - <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> - <options from_data_table="all_fasta"/> - </param> - </when> - <when value="history"> - <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> - </when> - </conditional> + <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> </xml> <xml name="gff3_input"> <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> @@ -35,23 +22,13 @@ "$gff3_data" </token> <token name="@INPUT_FASTA@"> -#if str($reference_genome.reference_genome_source) == 'cached': - "${reference_genome.fasta_indexes.fields.path}" -#else if str($reference_genome.reference_genome_source) == 'history': genomeref.fa -#end if </token> <token name="@GENOME_SELECTOR_PRE@"> -#if $reference_genome.reference_genome_source == 'history': - ln -s $reference_genome.genome_fasta genomeref.fa; -#end if + ln -s $genome_fasta genomeref.fa; </token> <token name="@GENOME_SELECTOR@"> -#if str($reference_genome.reference_genome_source) == 'cached': - "${reference_genome.fasta_indexes.fields.path}" -#else if str($reference_genome.reference_genome_source) == 'history': genomeref.fa -#end if </token> <xml name="input/fasta"> <param label="Fasta file" name="sequences" type="data" format="fasta"/>