Mercurial > repos > cpt > cpt_psm_recombine
view cpt_psm_recombine/macros.xml @ 0:b18e8268bf4e draft
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author | cpt |
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date | Tue, 05 Jul 2022 05:05:13 +0000 |
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<?xml version="1.0"?> <macros> <xml name="requirements"> <requirements> <requirement type="package" version="5.26.2">perl</requirement> <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> <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>