Mercurial > repos > cpt > cpt_blasttab_dice_filter
comparison cpt_blasttab_dice_filter/macros.xml @ 0:f430415c668f draft
Uploaded
| author | cpt |
|---|---|
| date | Fri, 13 May 2022 04:46:32 +0000 |
| parents | |
| children | 58458eb7ef95 |
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| -1:000000000000 | 0:f430415c668f |
|---|---|
| 1 <?xml version="1.0"?> | |
| 2 <macros> | |
| 3 <xml name="requirements"> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="3.6">python</requirement> | |
| 6 <requirement type="package" version="1.77">biopython</requirement> | |
| 7 <requirement type="package" version="1.1.3">cpt_gffparser</requirement> | |
| 8 <yield/> | |
| 9 </requirements> | |
| 10 </xml> | |
| 11 <token name="@BLAST_TSV@"> | |
| 12 "$blast_tsv" | |
| 13 </token> | |
| 14 <xml name="blast_tsv"> | |
| 15 <param label="Blast Results" help="TSV/tabular (25 Column)" | |
| 16 name="blast_tsv" type="data" format="tabular" /> | |
| 17 </xml> | |
| 18 | |
| 19 <token name="@BLAST_XML@"> | |
| 20 "$blast_xml" | |
| 21 </token> | |
| 22 <xml name="blast_xml"> | |
| 23 <param label="Blast Results" help="XML format" | |
| 24 name="blast_xml" type="data" format="blastxml" /> | |
| 25 </xml> | |
| 26 <xml name="gff3_with_fasta"> | |
| 27 <param label="Genome Sequences" name="fasta" type="data" format="fasta" /> | |
| 28 <param label="Genome Annotations" name="gff3" type="data" format="gff3" /> | |
| 29 </xml> | |
| 30 <xml name="genome_selector"> | |
| 31 <conditional name="reference_genome"> | |
| 32 <param name="reference_genome_source" type="select" label="Reference Genome"> | |
| 33 <option value="history" selected="True">From History</option> | |
| 34 <option value="cached">Locally Cached</option> | |
| 35 </param> | |
| 36 <when value="cached"> | |
| 37 <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> | |
| 38 <options from_data_table="all_fasta"/> | |
| 39 </param> | |
| 40 </when> | |
| 41 <when value="history"> | |
| 42 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> | |
| 43 </when> | |
| 44 </conditional> | |
| 45 </xml> | |
| 46 <xml name="gff3_input"> | |
| 47 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> | |
| 48 </xml> | |
| 49 <xml name="input/gff3+fasta"> | |
| 50 <expand macro="gff3_input" /> | |
| 51 <expand macro="genome_selector" /> | |
| 52 </xml> | |
| 53 <token name="@INPUT_GFF@"> | |
| 54 "$gff3_data" | |
| 55 </token> | |
| 56 <token name="@INPUT_FASTA@"> | |
| 57 #if str($reference_genome.reference_genome_source) == 'cached': | |
| 58 "${reference_genome.fasta_indexes.fields.path}" | |
| 59 #else if str($reference_genome.reference_genome_source) == 'history': | |
| 60 genomeref.fa | |
| 61 #end if | |
| 62 </token> | |
| 63 <token name="@GENOME_SELECTOR_PRE@"> | |
| 64 #if $reference_genome.reference_genome_source == 'history': | |
| 65 ln -s $reference_genome.genome_fasta genomeref.fa; | |
| 66 #end if | |
| 67 </token> | |
| 68 <token name="@GENOME_SELECTOR@"> | |
| 69 #if str($reference_genome.reference_genome_source) == 'cached': | |
| 70 "${reference_genome.fasta_indexes.fields.path}" | |
| 71 #else if str($reference_genome.reference_genome_source) == 'history': | |
| 72 genomeref.fa | |
| 73 #end if | |
| 74 </token> | |
| 75 <xml name="input/fasta"> | |
| 76 <param label="Fasta file" name="sequences" type="data" format="fasta"/> | |
| 77 </xml> | |
| 78 | |
| 79 <token name="@SEQUENCE@"> | |
| 80 "$sequences" | |
| 81 </token> | |
| 82 <xml name="input/fasta/protein"> | |
| 83 <param label="Protein fasta file" name="sequences" type="data" format="fasta"/> | |
| 84 </xml> | |
| 85 </macros> |