moving hifiasm tool to IUC (#6141)

galaxyproject · Jul 11, 2024 · 4763703 · 4763703
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diff --git a/tools/hifiasm/.shed.yml b/tools/hifiasm/.shed.yml
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+categories:
+- Assembly
+description: A fast haplotype-resolved de novo assembler
+homepage_url: https://github.com/chhylp123/hifiasm
+long_description: |
+  Hifiasm is a fast haplotype-resolved de novo assembler
+  for PacBio Hifi reads. It can assemble a human genome
+  in several hours and works with the California redwood
+  genome, one of the most complex genomes sequenced so
+  far. Hifiasm can produce primary/alternate assemblies
+  of quality competitive with the best assemblers. It
+  also introduces a new graph binning algorithm and
+  achieves the best haplotype-resolved assembly given
+  trio data.
+name: hifiasm
+owner: bgruening
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm
+type: unrestricted
diff --git a/tools/hifiasm/hifiasm.xml b/tools/hifiasm/hifiasm.xml
diff --git a/tools/hifiasm/test-data/child.fasta.gz b/tools/hifiasm/test-data/child.fasta.gz
diff --git a/tools/hifiasm/test-data/hic_1.fastq.gz b/tools/hifiasm/test-data/hic_1.fastq.gz
diff --git a/tools/hifiasm/test-data/hic_2.fastq.gz b/tools/hifiasm/test-data/hic_2.fastq.gz
diff --git a/tools/hifiasm/test-data/hifiasm-in1.fa.gz b/tools/hifiasm/test-data/hifiasm-in1.fa.gz
diff --git a/tools/hifiasm/test-data/hifiasm-in2-0.fa.gz b/tools/hifiasm/test-data/hifiasm-in2-0.fa.gz
diff --git a/tools/hifiasm/test-data/hifiasm-in2-1.fa.gz b/tools/hifiasm/test-data/hifiasm-in2-1.fa.gz
diff --git a/tools/hifiasm/test-data/hifiasm-in2-2.fa.gz b/tools/hifiasm/test-data/hifiasm-in2-2.fa.gz
diff --git a/tools/hifiasm/test-data/hifiasm-in2-3.fa.gz b/tools/hifiasm/test-data/hifiasm-in2-3.fa.gz
diff --git a/tools/hifiasm/test-data/hifiasm-in2-4.fa.gz b/tools/hifiasm/test-data/hifiasm-in2-4.fa.gz
diff --git a/tools/hifiasm/test-data/hifiasm-out-hifi-a.gfa b/tools/hifiasm/test-data/hifiasm-out-hifi-a.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out-hifi-p.gfa b/tools/hifiasm/test-data/hifiasm-out-hifi-p.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out-hifiul.bp.p_ctg.gfa b/tools/hifiasm/test-data/hifiasm-out-hifiul.bp.p_ctg.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out-hifiul.bp.r_utg.gfa b/tools/hifiasm/test-data/hifiasm-out-hifiul.bp.r_utg.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out1-primary.gfa b/tools/hifiasm/test-data/hifiasm-out1-primary.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out1-processed.gfa b/tools/hifiasm/test-data/hifiasm-out1-processed.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out1-raw.gfa b/tools/hifiasm/test-data/hifiasm-out1-raw.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out11-primary.gfa b/tools/hifiasm/test-data/hifiasm-out11-primary.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out11-raw.gfa b/tools/hifiasm/test-data/hifiasm-out11-raw.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out13.ovlp.source.bin b/tools/hifiasm/test-data/hifiasm-out13.ovlp.source.bin
diff --git a/tools/hifiasm/test-data/hifiasm-out2-primary.gfa b/tools/hifiasm/test-data/hifiasm-out2-primary.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out2-processed.gfa b/tools/hifiasm/test-data/hifiasm-out2-processed.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out2-raw.gfa b/tools/hifiasm/test-data/hifiasm-out2-raw.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out3-primary.gfa b/tools/hifiasm/test-data/hifiasm-out3-primary.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out3-processed.gfa b/tools/hifiasm/test-data/hifiasm-out3-processed.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out3-raw.gfa b/tools/hifiasm/test-data/hifiasm-out3-raw.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out4-primary.gfa b/tools/hifiasm/test-data/hifiasm-out4-primary.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out4-processed.gfa b/tools/hifiasm/test-data/hifiasm-out4-processed.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out4-raw.gfa b/tools/hifiasm/test-data/hifiasm-out4-raw.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out5-primary.gfa b/tools/hifiasm/test-data/hifiasm-out5-primary.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out5-processed.gfa b/tools/hifiasm/test-data/hifiasm-out5-processed.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out5-raw.gfa b/tools/hifiasm/test-data/hifiasm-out5-raw.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out6-primary.gfa b/tools/hifiasm/test-data/hifiasm-out6-primary.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out6-processed.gfa b/tools/hifiasm/test-data/hifiasm-out6-processed.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out6-raw.gfa b/tools/hifiasm/test-data/hifiasm-out6-raw.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out7-primary.gfa b/tools/hifiasm/test-data/hifiasm-out7-primary.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out7-processed.gfa b/tools/hifiasm/test-data/hifiasm-out7-processed.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out7-raw.gfa b/tools/hifiasm/test-data/hifiasm-out7-raw.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out8-primary.gfa b/tools/hifiasm/test-data/hifiasm-out8-primary.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out8-processed.gfa b/tools/hifiasm/test-data/hifiasm-out8-processed.gfa
diff --git a/tools/hifiasm/test-data/hifiasm-out8-raw.gfa b/tools/hifiasm/test-data/hifiasm-out8-raw.gfa
diff --git a/tools/hifiasm/test-data/maternal.fasta.gz b/tools/hifiasm/test-data/maternal.fasta.gz
diff --git a/tools/hifiasm/test-data/maternal.headers.txt b/tools/hifiasm/test-data/maternal.headers.txt
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diff --git a/tools/hifiasm/test-data/nanopore.fasta.gz b/tools/hifiasm/test-data/nanopore.fasta.gz
diff --git a/tools/hifiasm/test-data/paternal.fasta.gz b/tools/hifiasm/test-data/paternal.fasta.gz
diff --git a/tools/hifiasm/test-data/paternal.headers.txt b/tools/hifiasm/test-data/paternal.headers.txt
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