Mercurial > repos > cpt > cpt_gff_extract_seq
changeset 1:adc5dd1ff7bd draft
Uploaded
| author | cpt |
|---|---|
| date | Fri, 20 May 2022 00:05:15 +0000 |
| parents | 706787ae2767 |
| children | 82f3ab3c3443 |
| files | cpt_gff_extract_seq/macros.xml |
| diffstat | 1 files changed, 2 insertions(+), 25 deletions(-) [+] |
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--- a/cpt_gff_extract_seq/macros.xml Fri May 13 04:58:28 2022 +0000 +++ b/cpt_gff_extract_seq/macros.xml Fri May 20 00:05:15 2022 +0000 @@ -28,20 +28,7 @@ <param label="Genome Annotations" name="gff3" type="data" format="gff3" /> </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"/> @@ -54,23 +41,13 @@ "$gff3_data" </token> <token name="@INPUT_FASTA@"> -#if str($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"/>