| Previous changeset 1:11665e761b33 (2022-06-17) Next changeset 3:134bb2d7cdfd (2023-06-05) |
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added:
cpt_genome_editor/macros.xml |
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| diff -r 11665e761b33 -r 787ce84e8d16 cpt_genome_editor/macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_genome_editor/macros.xml Fri Jun 17 12:52:23 2022 +0000 |
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| @@ -0,0 +1,62 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.8.13">python</requirement> + <requirement type="package" version="1.79">biopython</requirement> + <requirement type="package" version="1.2.2">cpt_gffparser</requirement> + <yield/> + </requirements> + </xml> + <token name="@BLAST_TSV@"> + "$blast_tsv" + </token> + <xml name="blast_tsv"> + <param label="Blast Results" help="TSV/tabular (25 Column)" + name="blast_tsv" type="data" format="tabular" /> + </xml> + + <token name="@BLAST_XML@"> + "$blast_xml" + </token> + <xml name="blast_xml"> + <param label="Blast Results" help="XML format" + name="blast_xml" type="data" format="blastxml" /> + </xml> + <xml name="gff3_with_fasta"> + <param label="Genome Sequences" name="fasta" type="data" format="fasta" /> + <param label="Genome Annotations" name="gff3" type="data" format="gff3" /> + </xml> + <xml name="genome_selector"> + <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"/> + </xml> + <xml name="input/gff3+fasta"> + <expand macro="gff3_input" /> + <expand macro="genome_selector" /> + </xml> + <token name="@INPUT_GFF@"> + "$gff3_data" + </token> + <token name="@INPUT_FASTA@"> + genomeref.fa + </token> + <token name="@GENOME_SELECTOR_PRE@"> + ln -s $genome_fasta genomeref.fa; + </token> + <token name="@GENOME_SELECTOR@"> + genomeref.fa + </token> + <xml name="input/fasta"> + <param label="Fasta file" name="sequences" type="data" format="fasta"/> + </xml> + + <token name="@SEQUENCE@"> + "$sequences" + </token> + <xml name="input/fasta/protein"> + <param label="Protein fasta file" name="sequences" type="data" format="fasta"/> + </xml> +</macros> |