Mercurial > repos > iuc > mmseqs2_taxonomy_assignment

annotate mmseqs2_taxonomy_assignment.xml @ 1:96b969571420 draft default tip

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author iuc
date Mon, 14 Apr 2025 18:39:04 +0000
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dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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1 <tool id="mmseqs2_taxonomy_assignment" name="MMseqs2 Taxonomy Assignments" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3 of sequences by comparing them to a reference database
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4 </description>
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5 <macros>
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6 <import>macro.xml</import>
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7 </macros>
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8 <expand macro="biotools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="version_command"/>
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11 <command detect_errors="exit_code"><![CDATA[
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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12 ln -s -f '${createdb.input_fasta}' 'input' &&
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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13 mmseqs createdb
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14 'input'
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15 'sequenceDB'
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16 --dbtype '$createdb.alph_type.dbtype'
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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17 --shuffle $createdb.shuffle &&
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18
1
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19 ##Used only for test
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
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20 #if str($download_tax_db) == 'true':
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
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21 cp -r '$database.database_type.mmseqs2_db_select.fields.path'/database* . &&
0
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22
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23 mmseqs createtaxdb
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24 database
1
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25 'tmp' &&
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
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26 #end if
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
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27 ##
0
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28
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29 #if $filtertaxseqdb.taxon_list
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30 mmseqs filtertaxseqdb
1
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
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31 ##Used only for test
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
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32 #if str($download_tax_db) == 'true':
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
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33 'database'
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
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34 ##
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35 #else
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
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36 '$database.database_type.mmseqs2_db_select.fields.path'/database
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
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37 #end if
0
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38 'database_filtered'
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39 --taxon-list '$filtertaxseqdb.taxon_list'
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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40 &&
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41 #end if
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42
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43 mmseqs taxonomy
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44 'sequenceDB'
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45 #if $filtertaxseqdb.taxon_list
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46 'database_filtered'
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47 #else
1
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48 ##Used only for test
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49 #if str($download_tax_db) == 'true':
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
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50 'database'
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51 ##
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52 #else
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53 '$database.database_type.mmseqs2_db_select.fields.path'/database
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54 #end if
0
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55 #end if
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56 'output_taxonomy'
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57 'tmp'
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58 #if str($createdb.alph_type.dbtype) == "1"
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59 --comp-bias-corr-scale $createdb.alph_type.comp_bias_corr_scale
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60 #elif str($createdb.alph_type.dbtype) == "2"
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61 --zdrop $createdb.alph_type.zdrop
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62 #end if
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63 ##Pre-filter options
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64 --add-self-matches $taxonomy.prefilter.add_self_matches
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65 -s $taxonomy.prefilter.sensitivity
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66 -k $taxonomy.prefilter.kmer_length
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67 --target-search-mode $taxonomy.prefilter.target_search_mode
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68 ##--k-score TWIN k-mer threshold for generating similar k-mer lists [seq:2147483647,prof:2147483647]
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69 --max-seqs $taxonomy.prefilter.max_seqs
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70 --split $taxonomy.prefilter.split
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71 --split-mode $taxonomy.prefilter.split_mode
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72 ##--split-memory-limit BYTE Set max memory per split. E.g. 800B, 5K, 10M, 1G. Default (0) to all available system memory [0]
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73 --diag-score $taxonomy.prefilter.diag_score
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74 --exact-kmer-matching $taxonomy.prefilter.exact_kmer_matching
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75 --mask $taxonomy.prefilter.mask
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76 --mask-prob $taxonomy.prefilter.mask_prob
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77 --mask-lower-case $taxonomy.prefilter.mask_lower_case
1
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78 --mask-n-repeat $taxonomy.prefilter.mask_n_repeat
0
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79 --min-ungapped-score $taxonomy.prefilter.min_ungapped_score
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80 --spaced-kmer-mode $taxonomy.prefilter.spaced_kmer_mode
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81 ##--spaced-kmer-pattern STR User-specified spaced k-mer pattern []
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82 ##--local-tmp STR Path where some of the temporary files will be created []
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83 ##--disk-space-limit BYTE Set max disk space to use for reverse profile searches. E.g. 800B, 5K, 10M, 1G. Default (0) to all available disk space in the temp folder [0]
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84
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85 ##Align options
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86 -a $taxonomy.align.convertalis
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87 ##The next 2 parameters seems to be the same
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88 --alignment-mode $taxonomy.align.alignment_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
89 --alignment-output-mode $taxonomy.align.alignment_output_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
90 --wrapped-scoring $taxonomy.align.wrapped_scoring
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
91 -e $taxonomy.align.evalue
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
92 --min-seq-id $taxonomy.align.min_seq_id
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
93 --min-aln-len $taxonomy.align.min_aln_len
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
94 --seq-id-mode $taxonomy.align.seq_id_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
95 --alt-ali $taxonomy.align.alt_ali
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
96 -c $taxonomy.align.cov
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
97 --cov-mode $taxonomy.align.cov_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
98 --max-rejected $taxonomy.align.max_rejected
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
99 --max-accept $taxonomy.align.max_accept
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
100 --score-bias $taxonomy.align.score_bias
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
101 --realign $taxonomy.align.realign
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
102 --realign-score-bias $taxonomy.align.realign_score_bias
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
103 --realign-max-seqs $taxonomy.align.realign_max_seqs
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
104 --corr-score-weight $taxonomy.align.corr_score_weight
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
105 --exhaustive-search-filter $taxonomy.align.exhaustive_search_filter
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
106
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
107 ##Profile options
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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108 ##--pca Pseudo count admixture strength []
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
109 ##--pcb Pseudo counts: Neff at half of maximum admixture (range 0.0-inf) []
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
110 --mask-profile $taxonomy.profile.mask_profile
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
111 --e-profile $taxonomy.profile.e_profile
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
112 --wg $taxonomy.profile.wg
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
113 --filter-msa $taxonomy.profile.filter_msa
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
114 --filter-min-enable $taxonomy.profile.filter_min_enable
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
115 --max-seq-id $taxonomy.profile.max_seq_id
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
116 --qid $taxonomy.profile.qid
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
117 --qsc $taxonomy.profile.qsc
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
118 --cov $taxonomy.profile.cov
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
119 --diff $taxonomy.profile.diff
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
120 --pseudo-cnt-mode $taxonomy.profile.pseudo_cnt_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
121 --exhaustive-search $taxonomy.profile.exhaustive_search
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
122 --lca-search $taxonomy.profile.lca_search
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
123
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
124 ##Misc options
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
125 ##--orf-filter INT Prefilter query ORFs with non-selective search
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
126 ## Only used during nucleotide-vs-protein classification
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
127 ## NOTE: Consider disabling when classifying short reads [1]
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
128 --orf-filter-e $taxonomy.misc.orf_filter_e
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
129 --orf-filter-s $taxonomy.misc.orf_filter_s
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
130 --lca-mode $taxonomy.misc.lca_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
131 --tax-output-mode $taxonomy.misc.tax_output_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
132 --majority $taxonomy.misc.majority
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
133 --vote-mode $taxonomy.misc.vote_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
134 ##--lca-ranks STR Add column with specified ranks (',' separated) []
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
135 --tax-lineage $taxonomy.misc.tax_lineage
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
136 --blacklist $taxonomy.misc.blacklist
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
137 --taxon-list $taxonomy.misc.taxon_list
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
138 --rescore-mode $taxonomy.misc.rescore_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
139 --allow-deletion $taxonomy.misc.allow_deletion
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
140 --min-length $taxonomy.misc.min_length
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
141 --max-length $taxonomy.misc.max_length
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
142 --max-gaps $taxonomy.misc.max_gaps
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
143 --contig-start-mode $taxonomy.misc.contig_start_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
144 --contig-end-mode $taxonomy.misc.contig_end_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
145 --orf-start-mode $taxonomy.misc.orf_start_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
146 --forward-frames $taxonomy.misc.forward_frames
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
147 --reverse-frames $taxonomy.misc.reverse_frames
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
148 --translation-table $taxonomy.misc.translation_table
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
149 --translate $taxonomy.misc.translate
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
150 --use-all-table-starts $taxonomy.misc.use_all_table_starts
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
151 --id-offset $taxonomy.misc.id_offset
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
152 --sequence-overlap $taxonomy.misc.sequence_overlap
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
153 --sequence-split-mode $taxonomy.misc.sequence_split_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
154 --headers-split-mode $taxonomy.misc.headers_split_mode
1
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
155 --search-type $database.database_type.search_type
0
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
156 --prefilter-mode $taxonomy.misc.prefilter_mode
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
157
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
158 ##Common options
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
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159 ##--compressed INT Write compressed output [0]
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
160 --threads "\${GALAXY_SLOTS:-1}"
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
161 ##-v INT Verbosity level: 0: quiet, 1: +errors, 2: +warnings, 3: +info [3]
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
162 --max-seq-len $taxonomy.common.max_seq_len
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
163 ##--db-load-mode INT Database preload mode 0: auto, 1: fread, 2: mmap, 3: mmap+touch [0]
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
164 ##--mpi-runner STR Use MPI on compute cluster with this MPI command (e.g. "mpirun -np 42") []
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
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165 ##--force-reuse BOOL Reuse tmp filse in tmp/latest folder ignoring parameters and version changes [0]
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
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166 ##--remove-tmp-files BOOL Delete temporary files [0]
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
167
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
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diff changeset
168 ##Expert options
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
169 --filter-hits $taxonomy.expert.filter_hits
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
170 --sort-results $taxonomy.expert.sort_results
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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171 ##--create-lookup INT Create database lookup file (can be very large) [0]
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
172 --chain-alignments $taxonomy.expert.chain_alignments
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
173 --merge-query $taxonomy.expert.merge_query
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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174 ##--strand INT Strand selection only works for DNA/DNA search 0: reverse, 1: forward, 2: both [1]
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175 &&
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176 mmseqs createtsv
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177 'sequenceDB'
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178 'output_taxonomy'
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179 'taxo_result.tsv'
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180
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181 --first-seq-as-repr $createtsv.first_seq_as_repr
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182 --target-column $createtsv.target_column
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183 --full-header $createtsv.full_header
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184 --idx-seq-src $createtsv.idx_seq_src
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185 --threads "\${GALAXY_SLOTS:-1}"
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186 ##--compressed INT Write compressed output [0]
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187 ##-v INT Verbosity level: 0: quiet, 1: +errors, 2: +warnings, 3: +info [3]
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188 ##--db-output BOOL Return a result DB instead of a text file [0]
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189
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190 #if str($kraken_report.keep_report) == "Yes"
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191 &&
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192 mmseqs taxonomyreport
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193 #if $filtertaxseqdb.taxon_list
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194 'database_filtered'
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195 #else
1
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196 ##Used only for test
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197 #if str($download_tax_db) == 'true':
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198 'database'
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199 ##
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200 #else
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201 '$database.database_type.mmseqs2_db_select.fields.path'/database
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202 #end if
0
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203 #end if
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204 'output_taxonomy'
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205 'taxo_result.txt'
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206 --report-mode 0
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207 --threads "\${GALAXY_SLOTS:-1}"
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208 #end if
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209 #if str($krona_report.keep_report) == "Yes"
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210 &&
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211 mmseqs taxonomyreport
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212 #if $filtertaxseqdb.taxon_list
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213 'database_filtered'
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214 #else
1
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215 ##Used only for test
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216 #if str($download_tax_db) == 'true':
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217 'database'
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218 ##
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219 #else
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220 '$database.database_type.mmseqs2_db_select.fields.path'/database
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221 #end if
0
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222 #end if
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223 'output_taxonomy'
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224 'taxo_result.html'
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225 --report-mode 1
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226 --threads "\${GALAXY_SLOTS:-1}"
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227 #end if
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228 ##-v INT Verbosity level: 0: quiet, 1: +errors, 2: +warnings, 3: +info [3]
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229
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230 ]]></command>
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231 <inputs>
1
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232 <!-- used only for tests, this makes it possible to download the taxonomy part of the db without having to have it in the test data directory, which is too large and cannot be reduced -->
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233 <param name="download_tax_db" type="hidden" value=""/>
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234 <!-- -->
0
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235 <section name="createdb" title="Convert FASTA/Q file(s) to MMseqs sequence DB format" expanded="true">
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236 <param name="input_fasta" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input fasta file" help="" />
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237 <conditional name="alph_type">
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238 <param argument="--dbtype" type="select" label="Input type" help="" >
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239 <option value="0" selected="true">Auto</option>
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240 <option value="1">Amino acid</option>
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241 <option value="2">Nucleotides</option>
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242 </param>
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243 <when value="0"/>
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244 <when value="1">
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245 <param argument="--comp-bias-corr-scale" type="float" min="0" max="1" value="1" label="Scale composition bias correction" help=""/>
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246 </when>
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247 <when value="2">
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248 <param argument="--zdrop" type="integer" min="0" value="40" label="Maximal allowed difference between score values before alignment is truncated" help=""/>
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249 </when>
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250 </conditional>
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251 <param argument="--shuffle" type="boolean" checked="true" label="Shuffle input database" truevalue="1" falsevalue="0" optional="true" help="" />
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252 </section>
1
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253 <section name="database" title="Choose the taxonomic reference database that you want to use" expanded="true">
0
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254 <conditional name="database_type">
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255 <param name="type" type="select" label="Database type" help="" >
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256 <option value="amino_acid_tax" selected="true">Amino acid with taxonomy information</option>
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257 <option value="nucleotides_tax">Nucleotides with taxonomy information</option>
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258 </param>
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259 <when value="amino_acid_tax">
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260 <param name="mmseqs2_db_select" type="select" label="MMseqs2 databases">
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261 <options from_data_table="mmseqs2_databases">
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262 <filter type="static_value" value="aminoacid" column="type"/>
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263 <filter type="static_value" value="yes" column="taxonomy"/>
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264 <validator message="No mmseqs2 database is available" type="no_options"/>
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265 </options>
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266 </param>
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267 <expand macro="search_type_aa" />
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268 </when>
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269 <when value="nucleotides_tax">
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270 <param name="mmseqs2_db_select" type="select" label="MMseqs2 databases">
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271 <options from_data_table="mmseqs2_databases">
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272 <filter type="static_value" value="nucleotide" column="type"/>
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273 <filter type="static_value" value="yes" column="taxonomy"/>
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274 <validator message="No mmseqs2 database is available" type="no_options"/>
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275 </options>
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276 </param>
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277 <expand macro="search_type_nt" />
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278 </when>
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279 </conditional>
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280 </section>
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281 <section name="filtertaxseqdb" title="Filter taxonomy sequence database">
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282 <param argument="--taxon-list" type="text" optional="true" value="" label="Taxonomy ID" help="Possibly multiple values separated by ','"/>
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283 </section>
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284 <section name="taxonomy" title="Taxonomy assignment by computing the lowest common ancestor of homologs">
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285 <section name="prefilter" title="Pre-filter">
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286 <expand macro="prefilter_common_parameters" />
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287 <param argument="--spaced-kmer-mode" type="select" label="Spaced k-mer mode" help="">
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288 <option value="0">Use consecutive positions in k-mers</option>
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289 <option value="1" selected="true">Use spaced k-mers</option>
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290 </param>
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291 <param argument="--min-ungapped-score" type="integer" min="0" value="15" label="Accept only matches with ungapped alignment score above threshold" help=""/>
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292 <param argument="-s" name="sensitivity" type="float" min="0" max="7.5" value="2" label="Sensitivity" help="1.0 faster; 4.0 fast; 7.5 sensitive"/>
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293 <param argument="--target-search-mode" type="select" label="Target search mode" help="" >
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294 <option value="0" selected="true">Regular k-mer</option>
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295 <option value="1">Similar k-mer</option>
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296 </param>
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297 <param argument="--max-seqs" type="integer" min="0" value="300" label="Maximum results per query sequence allowed to pass the prefilter" help="Affects sensitivity"/>
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298 <param argument="--split" type="integer" min="0" value="0" label="Split input into N equally distributed chunks" help="0: set the best split automatically"/>
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299 <param argument="--split-mode" type="select" label="Split mode" help="" >
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300 <option value="0">Split target db</option>
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301 <option value="1">Split query db</option>
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302 <option value="2" selected="true">Auto, depending on main memory</option>
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303 </param>
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304 <param argument="--diag-score" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Use ungapped diagonal scoring during prefilter" help=""/>
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305 <param argument="--exact-kmer-matching" type="integer" min="0" max="1" value="0" label="Extract only exact k-mers for matching" help=""/>
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306 </section>
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307 <section name="align" title="Align">
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308 <expand macro="align_common_parameters" />
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309 <param argument="--alignment-mode" type="select" label="Alignment mode : How to compute the alignment" help="" >
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310 <option value="0">Automatic</option>
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311 <option value="1" selected="true">Only score and end_pos</option>
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312 <option value="2">Also start_pos and cov</option>
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313 <option value="3">Also seq.id</option>
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314 <option value="4">Only ungapped alignment</option>
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315 </param>
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316 <param argument="-e" name="evalue" type="float" min="0" value="1" label="E-value threshold" help="List matches below this E-value"/>
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317 <param argument="--min-seq-id" type="float" min="0" max="1" value="0" label="Minimum sequence identity" help="List matches above this sequence identity for clustering"/>
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318 <param argument="-c" name="cov" type="float" min="0" value="0" label="List matches above this fraction of aligned (covered) residues" help=""/>
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319 <param argument="--cov-mode" type="select" label="Coverage mode" help="" >
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320 <option value="0" selected="true">Coverage of query and target</option>
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321 <option value="1">Coverage of target</option>
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322 <option value="2">Coverage of query</option>
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323 <option value="3">Target seq. length has to be at least x% of query length</option>
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324 <option value="4">Query seq. length has to be at least x% of target length</option>
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325 <option value="5">Short seq. needs to be at least x% of the other seq. length</option>
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326 </param>
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327 <param argument="--max-rejected" type="integer" min="0" value="5" label="Maximum rejected alignments before alignment calculation for a query is stopped" help=""/>
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328 <param argument="--max-accept" type="integer" min="0" value="30" label="Maximum accepted alignments before alignment calculation for a query is stopped" help=""/>
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329 <param argument="--exhaustive-search-filter" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Filter result during search ?" help=""/>
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330 </section>
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331 <section name="profile" title="Profile">
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332 <param argument="--mask-profile" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Mask query sequence of profile using tantan" help=""/>
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333 <param argument="--e-profile" type="float" min="0" value="1e-03" label="Include sequences matches with inf E-value threshold into the profile" help=""/>
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334 <param argument="--wg" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Use global sequence weighting for profile calculation" help=""/>
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335 <param argument="--filter-msa" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Filter MSA" help=""/>
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336 <param argument="--filter-min-enable" type="integer" min="0" value="0" label="Only filter MSAs with more than N sequences, 0 always filters" help=""/>
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337 <param argument="--max-seq-id" type="float" min="0" max="1" value="0.9" label="Reduce redundancy of output MSA using max. pairwise sequence identity" help=""/>
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338 <param argument="--qid" type="text" value="0" label="Reduce diversity of output MSAs using min.seq. identity with query sequences [0.0,1.0]" help="Alternatively, can be a list of multiple thresholds:
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339 E.g.: 0.15,0.30,0.50 to defines filter buckets of ]0.15-0.30] and ]0.30-0.50]"/>
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340 <param argument="--qsc" type="float" min="-50" max="100" value="-20" label="Reduce diversity of output MSAs using min. score per aligned residue with query sequences" help=""/>
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341 <param argument="--cov" type="float" min="0" max="1" value="0" label="Filter output MSAs using min. fraction of query residues covered by matched sequences" help=""/>
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342 <param argument="--diff" type="integer" min="0" value="1000" label="Filter MSAs by selecting most diverse set of sequences, keeping at least this many seqs in each MSA block of length 50" help=""/>
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343 <param argument="--pseudo-cnt-mode" type="select" label="Pseudo count mode" help="" >
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344 <option value="0" selected="true">Substitution-matrix</option>
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345 <option value="1">Context-specific pseudocounts</option>
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346 </param>
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347 <param argument="--exhaustive-search" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Exhaustive search" help=""/>
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348 <param argument="--lca-search" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Efficient search for LCA candidates" help=""/>
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349 </section>
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350 <section name="misc" title="Misc">
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351 <param argument="--orf-filter-e" type="float" min="0" value="1.000E+02" label="E-value threshold used for query ORF prefiltering" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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352 <param argument="--orf-filter-s" type="float" min="0" value="2" label="Sensitivity used for query ORF prefiltering" help=""/>
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353 <param argument="--lca-mode" type="select" label="LCA mode" help="" >
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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354 <option value="1">Single search LCA</option>
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355 <option value="3" selected="true">Approximate 2bLCA</option>
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356 <option value="4">Top hit</option>
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357 </param>
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358 <param argument="--tax-output-mode" type="select" label="Taxonomy output mode" help="" >
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359 <option value="0" selected="true">Output LCA</option>
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360 <option value="1">Output alignment</option>
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361 <option value="2">Output both</option>
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362 </param>
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363 <param argument="--majority" type="float" min="0" value="0.5" label="Minimal fraction of agreement among taxonomically assigned sequences of a set" help=""/>
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364 <param argument="--vote-mode" type="select" label="Mode of assigning weights to compute majority" help="" >
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365 <option value="0">Uniform</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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366 <option value="1" selected="true">Minus log E-value</option>
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367 <option value="2">Score</option>
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368 </param>
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369 <param argument="--tax-lineage" type="select" label="Taxonomy lineage" help="" >
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370 <option value="0" selected="true">Don't show</option>
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371 <option value="1">Add all lineage names</option>
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372 <option value="2">Add all lineage taxids</option>
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373 </param>
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374 <param argument="--blacklist" type="text" value="" label="Comma separated list of ignored taxa in LCA computation" help=""/>
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375 <param argument="--taxon-list" type="text" value="" label="Taxonomy ID, possibly multiple values separated by ','" help=""/>
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376 <param argument="--rescore-mode" type="select" label="Rescore diagonals with" help="" >
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377 <option value="0" selected="true">Hamming distance</option>
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378 <option value="1">Local alignment (score only)</option>
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379 <option value="2">Local alignment</option>
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380 <option value="3">Global alignment</option>
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381 <option value="4">Longest alignment fulfilling window quality criterion</option>
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382 </param>
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383 <param argument="--allow-deletion" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Allow deletions in a MSA" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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384 <param argument="--min-length" type="integer" min="0" value="30" label="Minimum codon number in open reading frames" help=""/>
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385 <param argument="--max-length" type="integer" min="0" value="32734" label="Maximum codon number in open reading frames" help=""/>
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386 <param argument="--max-gaps" type="integer" min="0" value="2147483647" label="Maximum number of codons with gaps or unknown residues before an open reading frame is rejected" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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387 <param argument="--contig-start-mode" type="select" label="Contig start can be" help="" >
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388 <option value="0">Incomplete</option>
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389 <option value="1">Complete</option>
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390 <option value="2" selected="true">Both</option>
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391 </param>
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392 <param argument="--contig-end-mode" type="select" label="Contig end can be" help="" >
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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393 <option value="0">Incomplete</option>
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394 <option value="1">Complete</option>
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395 <option value="2" selected="true">Both</option>
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396 </param>
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397 <param argument="--orf-start-mode" type="select" label="ORF fragment can be" help="" >
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398 <option value="0">From start to stop</option>
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399 <option value="1" selected="true">From any to stop</option>
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400 <option value="2">From last encountered start to stop (no start in the middle)</option>
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401 </param>
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402 <param argument="--forward-frames" type="text" value="1,2,3" label="Comma-separated list of frames on the forward strand to be extracted" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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403 <param argument="--reverse-frames" type="text" value="1,2,3" label="Comma-separated list of frames on the reverse strand to be extracted" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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404 <param argument="--translation-table" type="select" label="Translation table" help="">
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405 <option value="1" selected="true">Canonical</option>
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406 <option value="2">The Vertebrate Mitochondrial Code</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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407 <option value="3">The Yeast Mitochondrial Code</option>
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408 <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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409 <option value="5">The Invertebrate Mitochondrial Code</option>
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410 <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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411 <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option>
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412 <option value="10">The Euplotid Nuclear Code</option>
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413 <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option>
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414 <option value="12">The Alternative Yeast Nuclear Code</option>
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415 <option value="13">The Ascidian Mitochondrial Code</option>
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416 <option value="14">The Alternative Flatworm Mitochondrial Code</option>
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417 <option value="15">Blepharisma Nuclear Code</option>
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418 <option value="16">Chlorophycean Mitochondrial Code</option>
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419 <option value="21">Trematode Mitochondrial Code</option>
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420 <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
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421 <option value="23">Thraustochytrium Mitochondrial Code</option>
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422 <option value="24">Rhabdopleuridae Mitochondrial Code</option>
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423 <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>
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424 <option value="26">Pachysolen tannophilus Nuclear Code</option>
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425 <option value="27">Karyorelict Nuclear Code</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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426 <option value="28">Condylostoma Nuclear Code</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
427 <option value="29">Mesodinium Nuclear Code</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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428 <option value="30">Peritrich Nuclear Code</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
429 <option value="31">Blastocrithidia Nuclear Code</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
diff changeset
430 </param>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
431 <param argument="--translate" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Translate ORF to amino acid" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
diff changeset
432 <param argument="--use-all-table-starts" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Use all alternatives for a start codon in the genetic table, if false - only ATG (AUG)" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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433 <param argument="--id-offset" type="integer" min="0" value="0" label="Numeric ids in index file are offset by this value" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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434 <param argument="--sequence-overlap" type="integer" min="0" value="0" label="Overlap between sequences" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
diff changeset
435 <param argument="--sequence-split-mode" type="select" label="Sequence split mode" help="" >
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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436 <option value="0">Copy data</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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437 <option value="1" selected="true">Soft link data and write new index</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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438 </param>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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439 <param argument="--headers-split-mode" type="select" label="Headers split mode" help="" >
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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440 <option value="0" selected="true">Split position</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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441 <option value="1">Original header</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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442 </param>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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443 <param argument="--prefilter-mode" type="select" label="Prefilter mode" help="" >
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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444 <option value="0" selected="true">Kmer/ungapped</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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445 <option value="1">Ungapped</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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446 <option value="2">No filter</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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447 </param>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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448 </section>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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449 <expand macro="common_section"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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450 <section name="expert" title="Expert">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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451 <expand macro="expert_common_parameters" />
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
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452 <param argument="--chain-alignments" type="integer" min="0" value="0" label="Chain alignments" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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453 <param argument="--merge-query" type="integer" min="0" value="1" label="Combine ORFs/split sequences to a single entry" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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diff changeset
454 </section>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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455 </section>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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456 <section name="createtsv" title="Create a tsv report from taxonomy output ">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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457 <param argument="--first-seq-as-repr" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Use the first sequence of the clustering result as representative sequence" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
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458 <param argument="--target-column" type="integer" min="0" value="1" label="Select a target column, 0 if no target id exists" help="" />
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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459 <param argument="--full-header" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Replace DB ID by its corresponding Full Header" help=""/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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460 <param argument="--idx-seq-src" type="select" label="Index sequences source" help="">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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461 <option value="0" selected="true">Auto</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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462 <option value="1">Split/translated sequences</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
463 <option value="2">Input sequences</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
diff changeset
464 </param>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
465 </section>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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466 <conditional name="kraken_report">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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467 <param name="keep_report" type="select" label="Do you want a Kraken style report" help="" >
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
468 <option value="Yes" selected="true">Yes</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
469 <option value="No">No</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
470 </param>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
471 <when value="Yes"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
472 <when value="No"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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473 </conditional>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
474 <conditional name="krona_report">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
475 <param name="keep_report" type="select" label="Do you want a Krona style report" help="" >
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
476 <option value="Yes" selected="true">Yes</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
477 <option value="No">No</option>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
478 </param>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
479 <when value="Yes"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
480 <when value="No"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
481 </conditional>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
482 </inputs>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
483 <outputs>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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484 <data name="output_taxonomy_tsv" format="tabular" from_work_dir="taxo_result.tsv" label="${tool.name} on ${on_string}: Taxonomy Report"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
485 <data name="output_taxonomy_kraken" format="txt" from_work_dir="taxo_result.txt" label="${tool.name} on ${on_string}: Kraken Report">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
486 <filter>kraken_report['keep_report'] == "Yes"</filter>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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487 </data>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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488 <data name="output_taxonomy_krona" format="html" from_work_dir="taxo_result.html" label="${tool.name} on ${on_string}: Krona Report">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
489 <filter>krona_report['keep_report'] == "Yes"</filter>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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490 </data>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
diff changeset
491 </outputs>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
492 <tests>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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493 <!-- Test with Kraken report -->
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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494 <test expect_num_outputs="2">
1
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
495 <param name="download_tax_db" value="true"/>
0
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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496 <section name="createdb">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
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497 <param name="input_fasta" value="light_mystery_reads.fasta" ftype="fasta"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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498 <conditional name="alph_type">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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499 <param name="dbtype" value="2"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
diff changeset
500 </conditional>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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501 </section>
1
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
502 <section name="database">
0
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
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503 <conditional name="database_type">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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504 <param name="type" value="amino_acid_tax"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
505 <param name="mmseqs2_db_select" value="UniProtKB/Swiss-Prot-15.6f452-10022025" />
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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506 </conditional>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
507 </section>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
508 <section name="filtertaxseqdb">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
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509 <param name="taxon_list" value="2" />
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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parents:
diff changeset
510 </section>
1
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
511 <section name="taxonomy">
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
512 <section name="prefilter">
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
513 <param name="mask_n_repeat" value="1" />
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
514 </section>
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
515 </section>
0
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
516 <conditional name="krona_report">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
517 <param name="keep_report" value="No"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
518 </conditional>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
519 <output name="output_taxonomy_tsv" ftype="tabular">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
520 <assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
521 <has_line line="MYSTERY.64&#009;119060&#009;family&#009;Burkholderiaceae&#009;1&#009;1&#009;1&#009;1.000"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
522 <has_n_columns n="8"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
523 </assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
524 </output>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
525 <output name="output_taxonomy_kraken" ftype="txt">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
526 <assert_contents>
1
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
527 <has_text text="kingdom"/>
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
528 <has_text text="Pseudomonadati"/>
0
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
529 </assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
530 </output>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
531 </test>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
532 <test expect_num_outputs="2">
1
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
533 <param name="download_tax_db" value="true"/>
0
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
534 <section name="createdb">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
535 <param name="input_fasta" value="light_mystery_reads.fasta" ftype="fasta"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
536 </section>
1
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
537 <section name="database">
0
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
538 <conditional name="database_type">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
539 <param name="type" value="amino_acid_tax"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
540 <param name="mmseqs2_db_select" value="UniProtKB/Swiss-Prot-15.6f452-10022025" />
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
541 </conditional>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
542 </section>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
543 <conditional name="kraken_report">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
544 <param name="keep_report" value="No"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
545 </conditional>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
546 <output name="output_taxonomy_tsv" ftype="tabular">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
547 <assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
548 <has_line line="MYSTERY.222&#009;1236&#009;class&#009;Gammaproteobacteria&#009;1&#009;1&#009;1&#009;1.000"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
549 <has_line line="MYSTERY.64&#009;119060&#009;family&#009;Burkholderiaceae&#009;1&#009;1&#009;1&#009;1.000"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
550 <has_n_columns n="8"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
551 </assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
552 </output>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
553 <output name="output_taxonomy_krona" ftype="html">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
554 <assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
555 <has_line line="// Krona is a flexible tool for exploring the relative proportions of"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
556 </assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
557 </output>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
558 </test>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
559 <test expect_num_outputs="3">
1
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
560 <param name="download_tax_db" value="true"/>
0
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
561 <section name="createdb">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
562 <param name="input_fasta" value="light_mystery_reads.fasta" ftype="fasta"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
563 </section>
1
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
564 <section name="database">
0
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
565 <conditional name="database_type">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
566 <param name="type" value="amino_acid_tax"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
567 <param name="mmseqs2_db_select" value="UniProtKB/Swiss-Prot-15.6f452-10022025" />
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
568 </conditional>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
569 </section>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
570 <output name="output_taxonomy_tsv" ftype="tabular">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
571 <assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
572 <has_line line="MYSTERY.222&#009;1236&#009;class&#009;Gammaproteobacteria&#009;1&#009;1&#009;1&#009;1.000"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
573 <has_line line="MYSTERY.64&#009;119060&#009;family&#009;Burkholderiaceae&#009;1&#009;1&#009;1&#009;1.000"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
574 <has_n_columns n="8"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
575 </assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
576 </output>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
577 <output name="output_taxonomy_krona" ftype="html">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
578 <assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
579 <has_line line="// Krona is a flexible tool for exploring the relative proportions of"/>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
580 </assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
581 </output>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
582 <output name="output_taxonomy_kraken" ftype="txt">
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
583 <assert_contents>
1
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
584 <has_text text="kingdom"/>
96b969571420 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053
iuc
parents: 0
diff changeset
585 <has_text text="Pseudomonadati"/>
0
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
586 </assert_contents>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
587 </output>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
588 </test>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
589 </tests>
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
590 <help><![CDATA[
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
591 **MMseqs2: ultra fast and sensitive sequence search and clustering suite**
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
592
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
593 MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
594 MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows.
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
595 The software is designed to run on multiple cores and servers and exhibits very good scalability.
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
596 MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity.
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
597 It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
598
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
iuc
parents:
diff changeset
599 **Usage**
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600
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601 * Convert FASTA/Q file(s) to MMseqs sequence DB format
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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602 *mmseqs createdb <i:fastaFile1[.gz|.bz2]> ... <i:fastaFileN[.gz|.bz2]>|<i:stdin> <o:sequenceDB> [options]*
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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603
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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604 * Filter taxonomy sequence database
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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605 *mmseqs filtertaxseqdb <i:taxSeqDB> <o:taxSeqDB> [options]*
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606
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607 * Taxonomy assignment by computing the lowest common ancestor of homologs
dbd5e2791f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 25b603890e8048ac7bbffb81eaaa440f87049521
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608 *mmseqs taxonomy <i:queryDB> <i:targetDB> <o:taxaDB> <tmpDir> [options]*
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609
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610 * Convert result DB to tab-separated flat file
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611 *mmseqs createtsv <i:queryDB> [<i:targetDB>] <i:resultDB> <o:tsvFile> [options]*
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612
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613 * Create a taxonomy report in Kraken or Krona format
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614 *mmseqs taxonomyreport <i:seqTaxDB> <i:taxResultDB/resultDB/sequenceDB> <o:taxonomyReport> [options]*
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615
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616 https://github.com/soedinglab/MMseqs2
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617
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618 ]]></help>
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619 <expand macro="citations"/>
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620 </tool>