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planemo upload for repository https://github.com/ncbi/egapx commit bdbe05027c2c40e217a2ff0c9e0556450c443e54
author fubar
date Mon, 05 Aug 2024 03:56:41 +0000
parents d9c5c5b87fec
children
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d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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1 tasks:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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2 setup:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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3 convert_genome: force-local-ids
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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4 convert_proteins: force-local-ids
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5 bam_bin_and_sort:
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6 bam_bin: -avg-size-per-bin 200000000 -file-pattern 'bin#.bam' -exclude-organelle
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7 bam_strandedness:
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8 rnaseq_divide_by_strandedness: -min-aligned 1000000 -min-unambiguous 200 -min-unambiguous-pct
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9 2 -percentage-threshold 98
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10 chainer:
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11 chainer_wnode: -altfrac 80.0 -capgap 5 -cdsbonus 0.05 -composite 10000 -end-pair-support-cutoff
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12 0.1 -endprotfrac 0.05 -filters 'remove_single_exon_est_models remove_single_exon_noncoding_models'
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13 -high-identity 0.98 -hmaxlen 0.25 -hthresh 0.02 -i3p 14.0 -i5p 7.0 -lenpen 0.005
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14 -longenoughcds 900 -max-extension 20 -min-consensus-support 2 -min-edge-coverage
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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15 5 -min-non-consensussupport 10 -min-support-fraction 0.03 -minex 10 -mininframefrac
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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16 0.95 -minlen 225 -minpolya 6 -minprotfrac 0.9 -minscor 40.0 -minsupport 3 -minsupport_mrna
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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17 1 -minsupport_rnaseq 5 -mrnaCDS use_objmgr -oep 10 -protcdslen 450 -sharp-boundary
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18 0.2 -tolerance 3 -trim 6 -utrclipthreshold 0.01 -fillgenomicgaps -filterest
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19 -filtermrna -filterprots -opposite
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20 gpx_make_outputs: -default-output-name chains -slices-for affinity -sort-by affinity
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21 input_aligns_sort: merge_only
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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22 submit_chainer: -minimum-abut-margin 20 -separate-within-introns
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23 convert_from_bam:
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24 sam2asn: -filter 'pct_identity_gap >= 95' -ofmt seq-align-compressed -collapse-identical
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25 -no-scores
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26 getfasta:
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27 getfasta: -u full-assembly -bare-accession -use-reference-non-nuclear
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28 gnomon:
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29 annot_wnode: -margin 1000 -mincont 1000 -minlen 225 -mpp 10.0 -ncsp 25 -window
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30 200000 -nonconsens -open
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31 generic_action_node: -app annot_wnode
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32 gpx_qdump: -slices-for affinity -sort-by affinity -unzip '*'
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33 gpx_qsubmit: ''
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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34 prot_gnomon_prepare:
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35 prot_gnomon_prepare: ''
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36 rnaseq_collapse:
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37 gpx_make_outputs: -default-output-name align -slices-for affinity -sort-by job-id
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38 -unzip align
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39 gpx_qsubmit: -affinity subject
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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40 rnaseq_collapse: -backlog 1 -max-jobs 1 -support-non-sra
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41 # -rank-counts-precalculated
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42 rnaseq_collapse_create_jobs: -alignments-per-job 50000 -min-range 100000
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43 star_index:
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44 STAR: --runThreadN 8
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45 star_wnode:
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46 gpx_qdump: -unzip '*'
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47 gpx_qsubmit: -affinity subject
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48 star_wnode: -cpus-per-worker 16 -csi-threshold 512000000 -preserve-star-logs
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49 star-params: --alignSJoverhangMin 8 --outFilterMultimapNmax 200 --outFilterMismatchNmax
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50 50 --runThreadN 16 --genomeLoad NoSharedMemory --outSAMtype SAM --outSAMattributes
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51 'NH HI AS nM NM MD jM jI XS MC' --outSAMprimaryFlag AllBestScore --outFilterMultimapScoreRange
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52 50 --seedSearchStartLmax 15 --limitOutSAMoneReadBytes 1000000 --outSJtype None
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53 miniprot:
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54 split_proteins: -n 100000
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55 miniprot: -t 31 -p 0.4 --outs=0.4
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56 paf2asn:
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57 paf2asn: -prosplign-refinement
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58 best_aligned_prot:
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59 best_aligned_prot: -asm_alns_filter 'reciprocity = 3'
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60 chainer_sort_alignments:
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61 align_sort: -ifmt seq-align -k subject,subject_start,-subject_end,subject_strand,query,query_start,-query_end,query_strand,-num_ident,gap_count
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62 align_filter_sa:
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63 align_filter: -filter 'rank=1 OR (pct_identity_gapopen_only > 58 AND (pct_coverage > 50 OR align_length_ungap > 1000))' -ifmt seq-align
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64 gnomon_training:
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65 gnomon_training: -asn -b
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66 diamond:
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67 diamond: -query-fmt seq-ids -subject-fmt seq-ids -output-prefix hits -ofmt seq-align-set
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68 diamond_blastp: --sam-query-len --very-sensitive --unal 0 --comp-based-stats 0 --masking 0
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69 diamond_orthology:
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70 diamond_orhtology: -ofmt seq-align-set -query-fmt seq-ids -subject-fmt seq-ids -output-prefix hits
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71 diamond_orthology_blastp: --sam-query-len --very-sensitive --unal 0 --comp-based-stats 0 --masking 0