Mercurial > repos > iuc > lexicmap
annotate lexicmap-index.xml @ 4:0004a511baff draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit eceb4b3a69c5a755feac55801e85eb914a669042
| author | iuc |
|---|---|
| date | Thu, 20 Nov 2025 19:38:27 +0000 |
| parents | 2e6641136004 |
| children |
| rev | line source |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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1 <tool id="lexicmap_index" name="LexicMap Index" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@"> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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2 <description>Builds LexicMap index</description> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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3 <macros> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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4 <import>macros.xml</import> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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5 </macros> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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6 <expand macro="bio_tools"/> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
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7 <expand macro="requirements"/> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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8 |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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9 <command detect_errors="exit_code"><![CDATA[ |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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10 |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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changeset
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11 echo '$input_genomes' | sed 's/,/\n/g' > fasta_list.tsv && |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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12 mkdir '$lexicmap_index.extra_files_path' && |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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13 lexicmap index |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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14 |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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15 --threads "\${GALAXY_SLOTS:-1}" |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
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16 |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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17 -X ./fasta_list.tsv -O '$lexicmap_index.extra_files_path' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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18 --big-genomes '$lexicmap_big_genomes' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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19 --batch-size '$batch_size' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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20 --contig-interval '$contig_interval' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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21 --kmer '$kmer' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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22 --masks '$masks' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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23 --max-genome '$max_genome' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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24 --min-seq-len '$min_seq_len' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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25 --rand-seed '$rand_seed' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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26 --seed-in-desert-dist '$seed_in_desert_dist' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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27 --seed-max-desert '$seed_max_desert' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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28 #if $mask_file |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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29 --mask-file '$mask_file' |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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30 #end if |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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31 |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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32 ]]></command> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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changeset
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33 <inputs> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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34 <param argument="--input-genomes" format="@FASTA_TYPES@" type="data" optional="false" multiple="true" label="FASTA files" help="Should be of datatype "fasta.gz" or "fasta"" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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changeset
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35 <section name="advanced_settings" title="Advanced settings" expanded="false"> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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changeset
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36 <param argument="--batch-size" value="5000" max="131072" type="integer" label="Batch Size" help="Maximum number of genomes in each batch (maximum value: 131072)" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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changeset
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37 <param argument="--contig-interval" min="1000" value="1000" type="integer" label="Contig interval" help="Length of interval (N's) between contigs in a genome. It can't betoo small (>1000) or some alignments might be fragmented" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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38 <param argument="--kmer" value="31" type="integer" min="2" max="32" label="Max k-mer size" help="Maximum k-mer size. K needs to be >= 32." /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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39 <param argument="--mask-file" format="txt" type="data" optional="true" label="Mask file" help="File of custom masks. This flag oversides -k/--kmer, -m/--masks, -s/--rand-seed etc." /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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40 <param argument="--masks" min="1" value="20000" type="integer" label="LexicHash masks" help="Number of LexicHash masks." /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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changeset
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41 <param argument="--max-genome" value="15000000" max="268435456" type="integer" label="Max genome size" help="Maximum genome size. Genomes with any single contig larger than the threshold will be skipped, while fragmented (with many contigs) genomes larger than the threshold will be split into chunks and alignments from these chunks will be merged in "lexicmap search". The value needs to be smaller than the maximum supported genome size: 268435456." /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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42 <param argument="--min-seq-len" value="-1" type="integer" label="Max sequence length" help="Maximum sequence length to index. The value would be equal to the kmer parameter value for values >= 0." /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff
changeset
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43 <param argument="--rand-seed" value="1" type="integer" label="Rand seed" help="Rand seed for generating random masks." /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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44 <param argument="--seed-in-desert-dist" value="50" type="integer" label="Seed in desert dist" help="Distance of k-mers to fill deserts." /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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45 <param argument="--seed-max-desert" value="100" type="integer" label="Seed max desert" help="Maximum length of sketching deserts, or maximum seed distance. Deserts with seed distance larger than this value will be filled by choosing k-mers roughly every --seed-in-desert-dist bases." /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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46 </section> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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47 </inputs> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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48 <outputs> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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49 <data name="lexicmap_index" format="lexicmap_index" label="index data" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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50 <data name="lexicmap_big_genomes" format="tsv" label="out file with metrics about skipped genomes" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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51 </outputs> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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52 <tests> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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53 <test expect_num_outputs="2"> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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54 <param name="input_genomes" value="genomes/GCF_001502155.1_ViralProj307776_genomic.fna.gz,genomes/GCF_001502175.1_ViralProj307780_genomic.fna.gz" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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55 <section name="advanced_settings"> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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56 <param name="max_genome" value="10000" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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57 </section> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
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58 <output name="lexicmap_index" ftype="lexicmap_index"> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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59 <extra_files name="genomes.chunks.bin" value="db.lmi/genomes.chunks.bin" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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60 <extra_files name="info.toml" value="db.lmi/info.toml" lines_diff="2"/> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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61 <extra_files name="masks.bin" value="db.lmi/masks.bin" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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62 <extra_files name="genomes.map.bin"> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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63 <assert_contents> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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64 <has_size value="54" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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65 </assert_contents> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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66 </extra_files> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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67 <expand macro="genomes_batch" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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68 <expand macro="seeds" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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69 </output> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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70 <output name="lexicmap_big_genomes" ftype="tsv" file="lexicmap_big_genomes.tsv" compare="re_match" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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71 </test> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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72 </tests> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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73 <help><![CDATA[ |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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74 |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
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75 Search sequences against an LexicMap index Database. For more information about settings |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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76 please visit: https://bioinf.shenwei.me/LexicMap/usage/index/ |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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77 |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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78 @info@ |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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79 ]]></help> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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80 <expand macro="citations" /> |
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2e6641136004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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81 </tool> |