annotate minimap2.xml @ 20:92678fcb1a5f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
author iuc
date Mon, 18 Mar 2024 16:43:36 +0000
parents c0c2d0941de8
children
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2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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1 <?xml version="1.0"?>
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2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="edam_ontology"/>
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8 <xrefs>
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9 <xref type="bio.tools">minimap2</xref>
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10 </xrefs>
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11 <expand macro="requirements"/>
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12 <stdio>
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13 <exit_code range="1:" level="fatal" />
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14 <regex match="\[ERROR\]" source="stderr" level="fatal" />
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15 </stdio>
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16 <version_command>minimap2 --version</version_command>
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17 <command>
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18 <![CDATA[
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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19 #if $reference_source.reference_source_selector == 'history':
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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20 ln -f -s '$reference_source.ref_file' reference.fa &&
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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21 #else:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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22 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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23 #end if
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24 minimap2
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25 #if str($fastq_input.analysis_type_selector) == 'self-homology':
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26 -DP -k19 -w19 -m200
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27 #elif $fastq_input.analysis_type_selector:
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28 -x ${fastq_input.analysis_type_selector}
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29 #end if
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30
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31 ## indexing options
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32 $indexing_options.H
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33 #if str($indexing_options.k):
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34 -k $indexing_options.k
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35 #end if
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36 #if str($indexing_options.w):
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37 -w $indexing_options.w
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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38 #end if
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39 #if str($indexing_options.I):
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2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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40 -I $indexing_options.I
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41 #end if
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42
0
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43 ## Mapping options
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44 #if str($mapping_options.f):
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45 -f $mapping_options.f
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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46 #end if
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47 #if str($mapping_options.min_occ_floor):
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48 --min-occ-floor $mapping_options.min_occ_floor
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49 #end if
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50 --q-occ-frac $mapping_options.q_occ_frac
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51 #if str($mapping_options.g):
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52 -g $mapping_options.g
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53 #end if
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54 #if str($mapping_options.r):
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55 -r $mapping_options.r
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56 #end if
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57 #if str($mapping_options.n):
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58 -n $mapping_options.n
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59 #end if
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60 #if str($mapping_options.m):
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61 -m $mapping_options.m
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62 #end if
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63 #if str($mapping_options.max_chain_skip):
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64 --max-chain-skip $mapping_options.max_chain_skip
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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65 #end if
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66 #if str($mapping_options.max_chain_iter):
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67 --max-chain-iter $mapping_options.max_chain_iter
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68 #end if
0
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69 $mapping_options.X
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70 #if str($mapping_options.p):
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71 -p $mapping_options.p
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72 #end if
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73 #if str($mapping_options.N):
0
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74 -N $mapping_options.N
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75 #end if
12
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76 #if str($mapping_options.mask_len):
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77 --mask-len $mapping_options.mask_len
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78 #end if
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79 #if str($mapping_options.kmer_ocurrence_interval.interval):
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80 -U $mapping_options.kmer_ocurrence_interval.lower_limit,$mapping_options.kmer_ocurrence_interval.upper_limit
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81 #end if
0
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82 ## Alignment options
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83 #if str($alignment_options.splicing.splice_mode) == '--splice':
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84 --frag=no --splice
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85 #if str($alignment_options.splicing.G):
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86 -G $alignment_options.splicing.G
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87 #end if
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iuc
parents: 8
diff changeset
88 #if str($alignment_options.splicing.C):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
89 -C $alignment_options.splicing.C
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
90 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
91 #if $alignment_options.splicing.u:
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
92 -u $alignment_options.splicing.u
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
93 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
94 $alignment_options.splicing.splice_flank
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
95 #if str($alignment_options.splicing.splice_site_annotations.use_annotations) == 'yes':
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
96 --junc-bed '$alignment_options.splicing.splice_site_annotations.junc_bed'
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
97 --junc-bonus $alignment_options.splicing.splice_site_annotations.junc_bonus
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
98 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
99 #elif str($mapping_options.F) and 'splice' not in str($fastq_input.analysis_type_selector):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
100 --frag=yes -F $mapping_options.F
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
101 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
102 #if str($alignment_options.A):
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
103 -A $alignment_options.A
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
104 #end if
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
105 #if str($alignment_options.B):
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
106 -B $alignment_options.B
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
107 #end if
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
108 #if str($alignment_options.O):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
109 #if str($alignment_options.O2):
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
110 -O $alignment_options.O,$alignment_options.O2
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
111 #else
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
112 -O $alignment_options.O
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
113 #end if
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
114 #end if
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
115 #if str($alignment_options.E):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
116 #if str($alignment_options.E2):
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
117 -E $alignment_options.E,$alignment_options.E2
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
118 #else
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
119 -E $alignment_options.E
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
120 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
121 #end if
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
122 #if str($alignment_options.z):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
123 #if str($alignment_options.z2):
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
124 -z $alignment_options.z,$alignment_options.z2
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
125 #else
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
126 -z $alignment_options.z
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
127 #end if
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
128 #end if
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
129 #if str($alignment_options.s):
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
130 -s $alignment_options.s
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
131 #end if
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
132 $alignment_options.no_end_flt
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
133 ## Output options
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
134 $io_options.Q
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
135 $io_options.L
8
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba"
iuc
parents: 7
diff changeset
136 $io_options.c
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
137 #if $io_options.cs:
14
09b53c1d4ab1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243"
iuc
parents: 13
diff changeset
138 --cs=$io_options.cs
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
139 #end if
3
1650a97189be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 1672eb3642d19c8502322115b86846297cd5a6b0
iuc
parents: 2
diff changeset
140 $io_options.Y
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
141 #if $io_options.K:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
142 -K $io_options.K
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
143 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
144 -t \${GALAXY_SLOTS:-4}
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
145 reference.fa
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
146 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
147 '$fastq_input.fastq_input1'
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
148 #else if $fastq_input.fastq_input_selector == 'paired':
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
149 '$fastq_input.fastq_input1' '$fastq_input.fastq_input2'
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
150 #else if $fastq_input.fastq_input_selector == 'paired_collection':
4
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
151 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
152 #end if
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
153 #if str($io_options.output_format) in ('BAM', 'CRAM'):
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
154 -a | samtools view --no-PG -hT reference.fa
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
155 #end if
4
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
156 #if $io_options.output_format == 'BAM':
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
157 | samtools sort
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
158 -@\${GALAXY_SLOTS:-2}
7
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
159 -T "\${TMPDIR:-.}"
4
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
160 -O $io_options.output_format
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
161 -o '$alignment_output'
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
162 #else if $io_options.output_format == 'CRAM':
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
163 | samtools sort
7
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
164 -T "\${TMPDIR:-.}"
4
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
165 -@\${GALAXY_SLOTS:-2}
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
166 -O $io_options.output_format
5
17e61517c166 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 31d0c015b36d7aa93f586c566ceeac56324863ad
iuc
parents: 4
diff changeset
167 $io_options.eqx
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
168 --reference reference.fa
2
4070f129540a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 79e4c4d7182a4d3f7b6d9a7e444a2bb34be588c0
iuc
parents: 1
diff changeset
169 --output-fmt-option no_ref
4
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
170 -o '$alignment_output'
11
f54f5baedfdd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 9eebe4bec24764deefcf7005abd588be29f4594f"
iuc
parents: 10
diff changeset
171 #else:
f54f5baedfdd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 9eebe4bec24764deefcf7005abd588be29f4594f"
iuc
parents: 10
diff changeset
172 > '$alignment_output'
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
173 #end if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
174 ]]>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
175 </command>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
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176 <inputs>
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177 <conditional name="reference_source">
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178 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
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179 <option value="cached">Use a built-in genome index</option>
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180 <option value="history">Use a genome from history and build index</option>
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181 </param>
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182 <when value="cached">
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183 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
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184 <options from_data_table="all_fasta">
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185 <filter type="sort_by" column="2" />
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186 <validator type="no_options" message="No reference genomes are available" />
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187 </options>
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188 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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189 </param>
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190 </when>
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191 <when value="history">
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192 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
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193 </when>
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194 </conditional>
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195 <!-- start unchanged copy from bwa-mem -->
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196 <conditional name="fastq_input">
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197 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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198 <option value="single">Single</option>
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199 <option value="paired">Paired</option>
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200 <option value="paired_collection">Paired Collection</option>
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201 <option value="paired_iv">Paired Interleaved</option>
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202 </param>
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203 <!-- below, preset options are only offered for single-end input
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204 because paired-end alignment in minimap2 is only enabled with -x sr
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205 (see https://github.com/lh3/minimap2/issues/190) -->
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206 <when value="single">
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207 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
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208 <param name="analysis_type_selector" type="select" optional="True"
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209 label="Select a profile of preset options"
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210 help="Each profile comes with the preconfigured settings mentioned in parentheses. You can customize each profile further in the indexing, mapping and alignment options sections below. If you do not select a profile here, the tool will use the per-parameter defaults listed in the below sections unless you customize them." >
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211 <option value="map-pb">PacBio/Oxford Nanopore read to reference mapping (-Hk19) (map-pb)</option>
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212 <option value="map-ont">Oxford Nanopore read to reference mapping. Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For PacBio reads, HPC minimizers consistently leads to faster performance and more sensitive results in comparison to normal minimizers. For Oxford Nanopore data, normal minimizers are better, though not much. The effectiveness of HPC is determined by the sequencing error mode. (map-ont)</option>
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213 <option value="map-hifi">PacBio HiFi reads vs reference mapping (-k19 -w19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1 -s200 ) (map-hifi)</option>
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214 <option value="ava-pb">PacBio all-vs-all overlap mapping (-Hk19 -Xw5 -m100 -g10000 --max-chain-skip 25) (ava-pb)</option>
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215 <option value="ava-ont">Oxford Nanopore all-vs-all overlap mapping (-k15 -Xw5 -m100 -g10000 -r2000 --max-chain-skip 25). Similarly, the major difference from ava-pb is that this preset is not using HPC minimizers. (ava-ont)</option>
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216 <option value="asm5">Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Only use this preset if the average divergence is far below 5%. (asm5)</option>
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217 <option value="asm10">Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 10% sequence divergence. (asm10)</option>
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218 <option value="asm20">Long assembly to reference mapping (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence. (asm20)</option>
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219 <option value="splice">Long-read spliced alignment (-k15 -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as the `N' CIGAR operator 2) long insertions are disabled 3) deletion and insertion gap costs are different during chaining 4) the computation of the `ms` tag ignores introns to demote hits to pseudogenes. (splice)</option>
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220 <option value="splice:hq">Long-read splice alignment for PacBio CCS reads (same as `splice` but with -C5 -O6,24 -B4) (splice:hq)</option>
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221 <option value="sr">Short single-end reads without splicing (-k21 -w11 --sr -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no) (sr)</option>
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222 <option value="self-homology">Construct a self-homology map - use same genome as query and reference (-DP -k19 -w19 -m200) (self-homology)</option>
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223 </param>
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224 </when>
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225 <when value="paired">
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226 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
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227 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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228 <expand macro="pe_anaylsis_fixed_selector" />
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229 </when>
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230 <when value="paired_collection">
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231 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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232 <expand macro="pe_anaylsis_fixed_selector" />
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233 </when>
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234 <when value="paired_iv">
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235 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
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236 <expand macro="pe_anaylsis_fixed_selector" />
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237 </when>
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238 </conditional>
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239 <section name="indexing_options" title="Indexing options">
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240 <param argument="-H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
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241 <param argument="-k" type="integer" min="4" max="28" optional="true" label="K-mer size" help=""/>
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242 <param argument="-w" type="integer" min="1" optional="true" label="Minimizer window size" help=""/>
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243 <param argument="-I" type="integer" min="1" optional="true" label="Split index for every N input gigabases" help=""/>
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244 </section>
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245 <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False">
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246 <param argument="-N" type="integer" min="0" optional="true" label="Retain at most INT secondary alignments" help="default=5"/>
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247 <param argument="-F" type="integer" min="0" value="" optional="true"
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248 label="Max fragment length for PE alignment"
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249 help="The maximum apparent fragment length up to which paired-end reads are aligned together; at higher fragment lengths the mates will be aligned independent of each other; effective only for paired-end data and when spliced alignment mode is turned off; default=800" />
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250 <param argument="-f" type="float" value="" optional="true" label="Filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
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251 <conditional name="kmer_ocurrence_interval">
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252 <param name="interval" argument="-U" type="select" label="Specify an interval of k-mer occurrences" help="Allows to specify an interval of k-mer occurrences with -U. For repeat-rich genomes, the automatic k-mer occurrence threshold determined by -f may be too large and makes alignment impractically slow. The new option protects against such cases. Enabled for asm* and map-hifi.">
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253 <option value="enabled">Enabled</option>
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254 <option value="" selected="true">Disabled</option>
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255 </param>
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256 <when value="enabled">
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257 <param name="lower_limit" type="integer" min="0" max="10000" value="" label="K-mer ocurrence lower limit"/>
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258 <param name="upper_limit" type="integer" min="0" max="10000" value="" label="K-mer ocurrence upper limit"/>
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259 </when>
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260 <when value="">
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261 </when>
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262 </conditional>
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263 <param argument="--min-occ-floor" type="integer" label="Force minimap2 to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" />
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264 <param argument="--q-occ-frac" type="float" value="0.01" label="Discard a query minimizer"
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265 help="Discard a query minimizer if its occurrence is higher than this fraction of query minimizers and than the reference occurrence threshold. It allows to avoid extremely long mapping time for pathologic reads with highly repeated k-mers not in the reference. Set to 0 to disable the new heuristic." />
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266
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267 <param argument="-g" type="integer" value="" optional="true" label="Stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/>
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268 <param argument="-r" type="integer" value="" optional="true" label="Bandwidth used in chaining and DP-based alignment" help="default=500" />
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269 <param argument="-n" type="integer" value="" optional="true" label="Minimal number of minimizers on a chain" help="default=3"/>
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270 <param argument="-m" type="integer" value="" optional="true" label="Minimal chaining score (matching bases minus log gap penalty)" help="default=40"/>
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271 <param argument="--max-chain-skip" type="integer" value="" optional="true"
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272 label="Maximum seed skips during chaining"
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273 help="A heuristics that stops chaining early. Minimap2 uses dynamic programming for chaining. The time complexity is quadratic in the number of seeds. This option makes minimap2 exit the inner loop if it repeatedly sees seeds already on chains. Set to a large number to switch off this heurstics effectively. default=25" />
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274 <param argument="--max-chain-iter" type="integer" value="" optional="true"
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275 label="Maximum number of partial chains checked during chaining"
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276 help="A heuristics to avoid quadratic time complexity in the worst case. default=5000" />
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277 <param argument="-X" type="boolean" truevalue="-X" falsevalue="" optional="true" label="Skip self and dual mappings (for the all-vs-all mode)"/>
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278 <param argument="-p" type="float" value="" max="1" optional="true" label="Min secondary-to-primary score ratio" help="default=0.8"/>
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279 <param argument="--mask-len" type="integer" min="0" max="10000" value="" optional="true" label="Fine control the removal of redundant hits" help="Keep an alignment if dropping it leaves an unaligned region on query longer than INT"/>
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280 </section>
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281 <section name="alignment_options" title="Alignment options" help="Sets -A, -B, -O, -E, -z, -s, and spliced alignments options." expanded="False">
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282 <conditional name="splicing">
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283 <param name="splice_mode" type="select"
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284 label="Customize spliced alignment mode?"
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285 help="Warning: Minimap2 cannot currently perform spliced alignments of read pairs. If you enable spliced alignment for paired-end data it will be treated as single-end!" >
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286 <option value="preset">No, use profile setting or leave turned off</option>
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287 <option value="">Disable spliced alignments (overwrite profile setting if necessary)</option>
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288 <option value="--splice">Yes, enable spliced alignments (--splice)</option>
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289 </param>
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290 <when value="preset" />
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291 <when value="" />
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292 <when value="--splice">
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293 <param argument="-G" type="integer" value="" optional="true"
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294 label="Maximum allowed gap on the reference"
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295 help="Higher values cause slower spliced alignment. When in use, this option causes -r (in mapping options) to be set to the same value. default=200k" />
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296 <param argument="-C" type="integer" min="0" optional="true"
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297 label="Cost of non-canonical (non-GT-AG) splicing"
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298 help="default=0" />
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299 <param argument="-u" type="select" optional="true"
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300 label="How to find GT-AG"
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301 help="default=n (don't match GT-AG)">
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302 <option value="n">Don't match GT-AG (-un)</option>
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303 <option value="f">Transcript strand (-uf)</option>
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304 <option value="b">Both strands (-ub)</option>
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305 </param>
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306 <param argument="--splice-flank" type="boolean" truevalue="--splice-flank=yes" falsevalue="--splice-flank=no" checked="true"
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307 label="Assume conserved flanking region of splice sites?"
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308 help="Assume the next base to a GT donor site tends to be A/G (91% in human and 92% in mouse) and the preceding base to a AG acceptor tends to be C/T. This trend is evolutionarily conserved, all the way to S. cerevisiae (PMID:18688272). Specifying this option generally leads to higher junction accuracy by several percents, so it is applied by default with --splice. However, the SIRV control does not honor this trend (only ~60%) so this option reduces accuracy. If you are benchmarking minimap2 on SIRV data, please disable this option." />
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309 <conditional name="splice_site_annotations">
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310 <param name="use_annotations" type="select"
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311 label="Use previously annotated splice sites to guide the alignment?"
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312 help="">
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313 <option value="no">No, perform unbiased alignment</option>
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314 <option value="yes">Yes, favor annotated splice sites</option>
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315 </param>
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316 <when value="no" />
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317 <when value="yes">
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318 <param argument="--junc-bed" type="data" format="bed"
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319 label="Dataset with annotated genes or introns"
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320 help="Gene annotations should be provided in BED12 (aka 12-column BED), intron positions in 5-column BED format." />
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321 <param argument="--junc-bonus" type="integer" min="1" value="1"
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322 label="Annotated splice site bonus"
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323 help="Score bonus for a splice donor or acceptor found in annotation." />
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324 </when>
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325 </conditional>
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326 </when>
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327 </conditional>
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328 <param argument="-A" type="integer" min="0" optional="true"
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329 label="Score for a sequence match" help="default=2"/>
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330 <param argument="-B" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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331 label="Penalty for a mismatch" help="-B; default=4" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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332 <param argument="-O" type="integer" min="1" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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diff changeset
333 label="Gap open penalties for deletions" help="-O; default=4"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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334 <param name="O2" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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diff changeset
335 label="Gap open penalties for insertions" help="-O; default=24"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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336 <param argument="-E" type="integer" min="1" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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diff changeset
337 label="Gap extension penalties; a gap of size k cost &#39;-O + -E*k&#39;. If two numbers are specified, the first is the penalty of extending a deletion and the second for extending an insertion"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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diff changeset
338 help="-E; default=2"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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339 <param name="E2" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
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diff changeset
340 label="Gap extension penalty for extending an insertion; if left empty uses the value specified for Gap extension penalties above"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
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341 help="-E; default=1"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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342 <param argument="-z" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
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diff changeset
343 label="Z-drop threshold for truncating an alignment"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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344 help="Increase to improve the contiguity of alignments at the cost of poorer alignments in the middle. default=400" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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345 <param name="z2" type="integer" min="0" optional="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
346 label="Z-drop threshold for reverse-complementing the query"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
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347 help="Decrease to find small inversions at the cost of performance and false positives. default=200" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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348 <param argument="-s" type="integer" min="0" optional="true"
12
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349 label="Minimal peak DP alignment score" help="default=80"/>
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
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350 <param name="no_end_flt" type="boolean" falsevalue="--no-end-flt" truevalue="" checked="true"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
351 label="Filter seeds towards the ends of chains before performing base-level alignment?" />
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
352 </section>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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353 <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False">
4
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iuc
parents: 3
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354 <param name="output_format" type="select" label="Select an output format">
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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355 <option value="BAM">BAM</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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356 <option value="CRAM">CRAM</option>
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
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357 <option value="paf">PAF</option>
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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358 </param>
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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359 <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" label="Don't output base quality"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
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parents: 11
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360 <param argument="-L" type="boolean" truevalue="-L" falsevalue="" label="Write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
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361 <param argument="-K" type="integer" optional="true" label="Minibatch size for mapping (in megabyte)" help="default=500M"/>
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
362 <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below.">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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363 <option value="none">no</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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364 <option value="short">short</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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365 <option value="long">long</option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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366 </param>
8
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba"
iuc
parents: 7
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367 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" label="Generate CIGAR"
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba"
iuc
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diff changeset
368 help="In PAF, the CIGAR is written to the ‘cg’ custom tag." />
53c0b7a1a0c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 4f9072805884196ffdc9ad1df93ecce08b7f08ba"
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diff changeset
369
12
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parents: 11
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370 <param argument="--eqx" type="boolean" truevalue="--eqx" falsevalue="" label="Write =/X CIGAR operators"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
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371 <param argument="-Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments ?"/>
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
372 </section>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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373 </inputs>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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374 <outputs>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
375 <data format="bam" name="alignment_output" label="${tool.name} on ${on_string} (mapped reads in ${io_options.output_format} format)">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
376 <actions>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
377 <conditional name="reference_source.reference_source_selector">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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378 <when value="cached">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
379 <action type="metadata" name="dbkey">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
380 <option type="from_data_table" name="all_fasta" column="1" offset="0">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
381 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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382 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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diff changeset
383 </option>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
384 </action>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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385 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
386 <when value="history">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
387 <action type="metadata" name="dbkey">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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388 <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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389 </action>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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390 </when>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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391 </conditional>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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392 </actions>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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393 <change_format>
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diff changeset
394 <when input="io_options.output_format" value="paf" format="paf" />
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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395 <when input="io_options.output_format" value="CRAM" format="cram" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
396 </change_format>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
397 </data>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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398 </outputs>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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399 <tests>
20
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iuc
parents: 17
diff changeset
400 <test expect_num_outputs="1">
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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diff changeset
401 <!-- test single input -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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402 <param name="reference_source_selector" value="history" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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403 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
404 <param name="fastq_input_selector" value="single"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
405 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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406 <param name="analysis_type_selector" value="sr"/>
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
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parents: 12
diff changeset
407 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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408 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
409 <test expect_num_outputs="1">
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
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diff changeset
410 <!-- test cram output -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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411 <param name="reference_source_selector" value="history" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
412 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
413 <param name="fastq_input_selector" value="single"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
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diff changeset
414 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
415 <param name="analysis_type_selector" value="sr"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
416 <param name="output_format" value="CRAM"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
417 <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
418 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
419 <test expect_num_outputs="1">
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
420 <!-- test paired input -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
421 <param name="reference_source_selector" value="history" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
422 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
423 <param name="fastq_input_selector" value="paired"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
424 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
425 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
426 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
427 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
428 <test expect_num_outputs="1">
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
429 <!-- test paired input with one pair compressed -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
430 <param name="reference_source_selector" value="history" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
431 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
432 <param name="fastq_input_selector" value="paired"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
433 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
434 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
435 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
436 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
437 <test expect_num_outputs="1">
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
438 <!-- test collection input -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
439 <param name="reference_source_selector" value="history" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
440 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
441 <param name="fastq_input_selector" value="paired_collection"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
442 <param name="fastq_input1">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
443 <collection type="paired">
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
444 <element name="forward" value="bwa-mem-fastq1.fq" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
445 <element name="reverse" value="bwa-mem-fastq2.fq" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
446 </collection>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
447 </param>
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
448 <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" />
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
449 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
450 <test expect_num_outputs="1">
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
451 <!-- test data table reference -->
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
452 <param name="reference_source_selector" value="cached" />
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
453 <param name="ref_file" value="bwa-mem-mt-genome"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
454 <param name="fastq_input_selector" value="single"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
455 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
456 <param name="analysis_type_selector" value="sr"/>
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
457 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
458 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
459 <test expect_num_outputs="1">
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
460 <!-- test alignment options -->
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
461 <param name="reference_source_selector" value="cached" />
10
77b2770508f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit d7c1c96bd5297839271cf69ad2129a0f47a29b89"
iuc
parents: 9
diff changeset
462 <param name="min_occ_floor" value="1000"/>
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
463 <param name="ref_file" value="bwa-mem-mt-genome"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
464 <param name="fastq_input_selector" value="single"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
465 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
466 <param name="analysis_type_selector" value="sr"/>
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
467 <section name="alignment_options">
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
468 <!-- the folowing settings correspond to the defaults for "sr"
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
469 mode. The purpose is to check that all alignment params get
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
470 parsed correctly. -->
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
471 <param name="A" value="2" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
472 <param name="B" value="8" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
473 <param name="O" value="12" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
474 <param name="O2" value="32" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
475 <param name="E" value="2" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
476 <param name="E2" value="1" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
477 <param name="z" value="400" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
478 <param name="s" value="40" />
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
479 </section>
14
09b53c1d4ab1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243"
iuc
parents: 13
diff changeset
480 <section name="io_options">
09b53c1d4ab1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243"
iuc
parents: 13
diff changeset
481 <!-- the next setting is a noop for bam output, but tests that
09b53c1d4ab1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243"
iuc
parents: 13
diff changeset
482 a valid command line is formed for the cs option -->
09b53c1d4ab1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243"
iuc
parents: 13
diff changeset
483 <param name="cs" value="none" />
09b53c1d4ab1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 219f9463094519d9a97c3dfb93f0e1a2233c0243"
iuc
parents: 13
diff changeset
484 </section>
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
485 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
9
8c6cd2650d1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554"
iuc
parents: 8
diff changeset
486 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
487 <test expect_num_outputs="1">
4
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
488 <!-- test paf output -->
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
489 <param name="reference_source_selector" value="history" />
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
490 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" />
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
491 <param name="fastq_input_selector" value="single"/>
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
492 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" />
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
493 <param name="analysis_type_selector" value="ava-ont"/>
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
494 <param name="output_format" value="paf"/>
15
7db8d4bc1eea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"
iuc
parents: 14
diff changeset
495 <output name="alignment_output" ftype="paf" file="mini_reads.paf" />
4
6f50f36e4481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
iuc
parents: 3
diff changeset
496 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
497 <test expect_num_outputs="1">
7
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
498 <!-- test self-homology mode -->
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
499 <param name="reference_source_selector" value="history" />
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
500 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
501 <param name="fastq_input_selector" value="single" />
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
502 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
503 <param name="analysis_type_selector" value="self-homology" />
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
504 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" />
7
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
505 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
506 <test expect_num_outputs="1">
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
507 <!-- test mask-len option -->
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
508 <param name="reference_source_selector" value="history" />
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
509 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
510 <param name="fastq_input_selector" value="single"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
511 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
512 <param name="analysis_type_selector" value="sr"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
513 <section name="mapping_options">
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
514 <param name="mask_len" value="100"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
515 </section>
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
516 <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" />
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
517 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
518 <test expect_num_outputs="1">
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
519 <!-- test map-hifi -->
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
520 <param name="reference_source_selector" value="history" />
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
521 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
522 <param name="fastq_input_selector" value="single"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
523 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
524 <param name="analysis_type_selector" value="map-hifi"/>
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
525 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" />
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
526 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
527 <test expect_num_outputs="1">
15
7db8d4bc1eea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"
iuc
parents: 14
diff changeset
528 <!-- test map-hifi uncompressed reference-->
7db8d4bc1eea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"
iuc
parents: 14
diff changeset
529 <param name="reference_source_selector" value="history" />
7db8d4bc1eea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"
iuc
parents: 14
diff changeset
530 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/>
7db8d4bc1eea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"
iuc
parents: 14
diff changeset
531 <param name="fastq_input_selector" value="single"/>
7db8d4bc1eea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"
iuc
parents: 14
diff changeset
532 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
7db8d4bc1eea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"
iuc
parents: 14
diff changeset
533 <param name="analysis_type_selector" value="map-hifi"/>
7db8d4bc1eea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"
iuc
parents: 14
diff changeset
534 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-2-fasta.bam" lines_diff="4" />
7db8d4bc1eea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"
iuc
parents: 14
diff changeset
535 </test>
20
92678fcb1a5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
iuc
parents: 17
diff changeset
536 <test expect_num_outputs="1">
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
537 <!-- test kmer ocurrence interval option -->
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
538 <param name="reference_source_selector" value="history" />
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
539 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
540 <param name="fastq_input_selector" value="single"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
541 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
542 <param name="analysis_type_selector" value="sr"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
543 <conditional name="kmer_ocurrence_interval">
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
544 <param name="interval" value="enabled"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
545 <param name="lower_limit" value="10"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
546 <param name="upper_limit" value="30"/>
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
547 </conditional>
13
1f06dccdc5d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
iuc
parents: 12
diff changeset
548 <output name="alignment_output" ftype="bam" file="minimap2-test-kmer_ocurrence.bam" lines_diff="4" />
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
549 </test>
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
550 </tests>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
551 <help>
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
552
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
553 Users’ Guide
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
554 ------------
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
555
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
556 Minimap2 is a versatile sequence alignment program that aligns DNA or
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
557 mRNA sequences against a large reference database. Typical use cases
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
558 include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
559 human genome; (2) finding overlaps between long reads with error rate up
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
560 to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
561 or Direct RNA reads against a reference genome; (4) aligning Illumina
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
562 single- or paired-end reads; (5) assembly-to-assembly alignment; (6)
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
563 full-genome alignment between two closely related species with
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
564 divergence below ~15%.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
565
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
566 For ~10kb noisy reads sequences, minimap2 is tens of times faster than
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
567 mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
568 is more accurate on simulated long reads and produces biologically
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
569 meaningful alignment ready for downstream analyses. For >100bp Illumina
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
570 short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
571 as accurate on simulated data. Detailed evaluations are available from
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
572 the `minimap2 preprint`.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
573
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
574 General usage
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
575 ~~~~~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
576
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
577 Minimap2 seamlessly works with gzip’d FASTA and FASTQ formats as input.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
578 You don’t need to convert between FASTA and FASTQ or decompress gzip’d
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
579 files first.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
580
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
581 For the human reference genome, minimap2 takes a few minutes to generate
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
582 a minimizer index for the reference before mapping. To reduce indexing
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
583 time, you can optionally save the index with option **-d** and replace
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
584 the reference sequence file with the index file on the minimap2 command
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
585 line:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
586
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
587 ***Importantly***, it should be noted that once you build the index,
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
588 indexing parameters such as **-k**, **-w**, **-H** and **-I** can’t be
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
589 changed during mapping. If you are running minimap2 for different data
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
590 types, you will probably need to keep multiple indexes generated with
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
591 different parameters. This makes minimap2 different from BWA which
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
592 always uses the same index regardless of query data types.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
593
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
594 Use cases
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
595 ~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
596
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
597 Minimap2 uses the same base algorithm for all applications. However, due
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
598 to the different data types it supports (e.g. short vs long reads; DNA
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
599 vs mRNA reads), minimap2 needs to be tuned for optimal performance and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
600 accuracy. It is usually recommended to choose a preset with option
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
601 **-x**, which sets multiple parameters at the same time. The default
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
602 setting is the same as ``map-ont``.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
603
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
604 Map long noisy genomic reads
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
605 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
606
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
607 The difference between ``map-pb`` and ``map-ont`` is that ``map-pb``
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
608 uses homopolymer-compressed (HPC) minimizers as seeds, while ``map-ont``
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
609 uses ordinary minimizers as seeds. Emperical evaluation suggests HPC
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
610 minimizers improve performance and sensitivity when aligning PacBio
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
611 reads, but hurt when aligning Nanopore reads.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
612
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
613 Map long mRNA/cDNA reads
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
614 ^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
615
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
616 There are different long-read RNA-seq technologies, including
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
617 tranditional full-length cDNA, EST, PacBio Iso-seq, Nanopore 2D cDNA-seq
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
618 and Direct RNA-seq. They produce data of varying quality and properties.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
619 By default, ``-x splice`` assumes the read orientation relative to the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
620 transcript strand is unknown. It tries two rounds of alignment to infer
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
621 the orientation and write the strand to the ``ts`` SAM/PAF tag if
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
622 possible. For Iso-seq, Direct RNA-seq and tranditional full-length
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
623 cDNAs, it would be desired to apply ``-u f`` to force minimap2 to
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
624 consider the forward transcript strand only. This speeds up alignment
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
625 with slight improvement to accuracy. For noisy Nanopore Direct RNA-seq
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
626 reads, it is recommended to use a smaller k-mer size for increased
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
627 sensitivity to the first or the last exons.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
628
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
629 It is worth noting that by default ``-x splice`` prefers
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
630 GT[A/G]..[C/T]AG over GT[C/T]..[A/G]AG, and then over other splicing
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
631 signals. Considering one additional base improves the junction accuracy
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
632 for noisy reads, but reduces the accuracy when aligning against the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
633 widely used SIRV control data. This is because SIRV does not honor the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
634 evolutionarily conservative splicing signal. If you are studying SIRV,
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
635 you may apply ``--splice-flank=no`` to let minimap2 only model GT..AG,
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
636 ignoring the additional base.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
637
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
638 Find overlaps between long reads
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
639 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
640
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
641 Similarly, ``ava-pb`` uses HPC minimizers while ``ava-ont`` uses
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
642 ordinary minimizers. It is usually not recommended to perform base-level
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
643 alignment in the overlapping mode because it is slow and may produce
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
644 false positive overlaps. However, if performance is not a concern, you
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
645 may try to add ``-a`` or ``-c`` anyway.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
646
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
647 Map short accurate genomic reads
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
648 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
649
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
650 When two read files are specified, minimap2 reads from each file in turn
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
651 and merge them into an interleaved stream internally. Two reads are
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
652 considered to be paired if they are adjacent in the input stream and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
653 have the same name (with the ``/[0-9]`` suffix trimmed if present).
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
654 Single- and paired-end reads can be mixed.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
655
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
656 Minimap2 does not work well with short spliced reads. There are many
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
657 capable RNA-seq mappers for short reads.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
658
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
659 Full genome/assembly alignment
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
660 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
661
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
662 For cross-species full-genome alignment, the scoring system needs to be
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
663 tuned according to the sequence divergence.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
664
7
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
665 Self-homology map creation
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
666 ^^^^^^^^^^^^^^^^^^^^^^^^^^
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
667
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
668 A self-homology map is created by mapping a genome (e.g. that of E. coli)
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
669 against itself. When this option is used the same FASTA file should
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
670 be used for reference and for the (single ended mode) query.
b3eab4b67562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4"
iuc
parents: 6
diff changeset
671
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
672 Advanced features
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
673 ~~~~~~~~~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
674
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
675 Working with >65535 CIGAR operations
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
676 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
677
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
678 Due to a design flaw, BAM does not work with CIGAR strings with >65535
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
679 operations (SAM and CRAM work). However, for ultra-long nanopore reads
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
680 minimap2 may align ~1% of read bases with long CIGARs beyond the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
681 capability of BAM. If you convert such SAM/CRAM to BAM, Picard and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
682 recent samtools will throw an error and abort. Older samtools and other
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
683 tools may create corrupted BAM.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
684
1
b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739
iuc
parents: 0
diff changeset
685 To avoid this issue, you can add option ``-L`` at the minimap2 command line.
b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739
iuc
parents: 0
diff changeset
686 This option moves a long CIGAR to the ``CG`` tag and leaves a fully clipped
b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739
iuc
parents: 0
diff changeset
687 CIGAR at the SAM CIGAR column. Current tools that don’t read CIGAR
b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739
iuc
parents: 0
diff changeset
688 (e.g. merging and sorting) still work with such BAM records; tools that read
b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739
iuc
parents: 0
diff changeset
689 CIGAR will effectively ignore these records. It has been decided that future
b103bc946f57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 160b3085e5c9152fc8eaeb2e8afc12cdc1abe739
iuc
parents: 0
diff changeset
690 tools will seamlessly recognize long-cigar records generated by option `-L`.
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
691
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
692 **TD;DR**: if you work with ultra-long reads and use tools that only
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
693 process BAM files, please add option ``-L``.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
694
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
695 The cs optional tag
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
696 ^^^^^^^^^^^^^^^^^^^
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
697
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
698 The ``cs`` SAM/PAF tag encodes bases at mismatches and INDELs. It
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
699 matches regular expression
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
700 ``/(:[0-9]+|\*[a-z][a-z]|[=\+\-][A-Za-z]+)+/``. Like CIGAR, ``cs``
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
701 consists of series of operations. Each leading character specifies the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
702 operation; the following sequence is the one involved in the operation.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
703
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
704 The ``cs`` tag is enabled by command line option ``--cs``. The following
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
705 alignment, for example:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
706
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
707 .. code::
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
708
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
709 CGATCGATAAATAGAGTAG---GAATAGCA
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
710 |||||| |||||||||| |||| |||
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
711 CGATCG---AATAGAGTAGGTCGAATtGCA
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
712
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
713 is represented as ``:6-ata:10+gtc:4*at:3``, where ``:[0-9]+`` represents
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
714 an identical block, ``-ata`` represents a deltion, ``+gtc`` an insertion
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
715 and ``*at`` indicates reference base ``a`` is substituted with a query
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
716 base ``t``. It is similar to the ``MD`` SAM tag but is standalone and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
717 easier to parse.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
718
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
719 If ``--cs=long`` is used, the ``cs`` string also contains identical
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
720 sequences in the alignment. The above example will become
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
721 ``=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA``. The long form of ``cs``
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
722 encodes both reference and query sequences in one string.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
723
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
724 Algorithm overview
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
725 ~~~~~~~~~~~~~~~~~~
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
726
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
727 In the following, minimap2 command line options have a dash ahead and
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
728 are highlighted in bold. The description may help to tune minimap2
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
729 parameters.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
730
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
731 1. Read **-I** [=*4G*] reference bases, extract
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
732 (**-k**,\ **-w**)-minimizers and index them in a hash table.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
733
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
734 2. Read **-K** [=*200M*] query bases. For each query sequence, do step 3
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
735 through 7:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
736
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
737 3. For each (**-k**,\ **-w**)-minimizer on the query, check against the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
738 reference index. If a reference minimizer is not among the top **-f**
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
739 [=*2e-4*] most frequent, collect its the occurrences in the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
740 reference, which are called *seeds*.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
741
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
742 4. Sort seeds by position in the reference. Chain them with dynamic
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
743 programming. Each chain represents a potential mapping. For read
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
744 overlapping, report all chains and then go to step 8. For reference
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
745 mapping, do step 5 through 7:
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
746
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
747 5. Let *P* be the set of primary mappings, which is an empty set
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
748 initially. For each chain from the best to the worst according to
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
749 their chaining scores: if on the query, the chain overlaps with a
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
750 chain in *P* by **–mask-level** [=*0.5*] or higher fraction of the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
751 shorter chain, mark the chain as *secondary* to the chain in *P*;
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
752 otherwise, add the chain to *P*.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
753
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
754 6. Retain all primary mappings. Also retain up to **-N** [=*5*] top
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
755 secondary mappings if their chaining scores are higher than **-p**
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
756 [=*0.8*] of their corresponding primary mappings.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
757
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
758 7. If alignment is requested, filter out an internal seed if it
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
759 potentially leads to both a long insertion and a long deletion.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
760 Extend from the left-most seed. Perform global alignments between
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
761 internal seeds. Split the chain if the accumulative score along the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
762 global alignment drops by **-z** [=*400*], disregarding long gaps.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
763 Extend from the right-most seed. Output chains and their alignments.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
764
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
765 8. If there are more query sequences in the input, go to step 2 until no
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
766 more queries are left.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
767
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
768 9. If there are more reference sequences, reopen the query file from the
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
769 start and go to step 1; otherwise stop.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
770
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
771 Limitations
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
772 -----------
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
773
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
774 - Minimap2 may produce suboptimal alignments through long
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
775 low-complexity regions where seed positions may be suboptimal. This
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
776 should not be a big concern because even the optimal alignment may be
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
777 wrong in such regions.
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
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778 </help>
12
037c6e54df11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 3617059cec3cc200dc22450347c070c4207b8852"
iuc
parents: 11
diff changeset
779 <expand macro="citations"/>
0
2445d53549ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 7cb87c310b34cb2af2547ad8a14679107fd86d5d
iuc
parents:
diff changeset
780 </tool>