Mercurial > repos > brinkmanlab > mash
annotate mash.xml @ 0:572587cbb1dd draft default tip
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
author | brinkmanlab |
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date | Fri, 24 Jan 2020 17:41:36 -0500 |
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572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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1 <tool id="mash" name="MASH" version="2.1" profile="18.09"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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2 <description>Fast genome and metagenome distance estimation using MinHash</description> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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3 <edam_topics> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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4 <edam_topic>topic_0091</edam_topic> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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5 </edam_topics> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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6 <edam_operations> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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7 <edam_operation>operation_0289</edam_operation> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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8 <edam_operation>operation_0296</edam_operation> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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9 </edam_operations> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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10 <macros> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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11 <xml name="sketching_options"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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12 <!-- sketching --> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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13 <param name="kmer_size" type="integer" min="1" max="32" value="21" argument="-k" label="K-mer size" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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14 <param name="sketch_size" type="integer" min="1" value="1000" argument="-s" label="Sketch size" help="Each sketch will have at most this many non-redundant min-hashes." /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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15 <param name="hash_seed" type="integer" min="0" max="4294967296" value="42" argument="-S" label="Seed to provide to the hash function" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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16 <param name="kmer_size_thresh" type="float" min="0" max="1" value="0.01" argument="-w" label="Probability threshold for warning about low k-mer size" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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17 <conditional name="input_option"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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18 <param name="individual_seq" type="boolean" checked="false" argument="-i" label="Sketch individual sequences" help="Sketch individual sequences, rather than whole files, e.g. for multi-fastas of single-chromosome genomes or pair-wise gene comparisons." /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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19 <when value="false"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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20 <param name="input_read_set" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Input is a read set" help="Sketch individual sequences, rather than whole files, e.g. for multi-fastas of single-chromosome genomes or pair-wise gene comparisons." /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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21 <!-- sketching reads --> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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22 <param name="bloom_size" type="text" argument="-b" optional="true" label="Use a Bloom filter of this size (raw bytes or with K/M/G/T)" help="Use a Bloom filter of this size (raw bytes or with K/M/G/T) to filter out unique k-mers. This is useful if exact filtering uses too much memory. However, some unique k-mers may pass erroneously, and copies cannot be counted beyond 2." > |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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23 <validator type="regex"><![CDATA[^[0-9]+[KMGT]?$]]></validator> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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24 </param> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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25 <param name="kmer_count" type="integer" min="0" value="1" argument="-m" label="Minimum copies of each k-mer required to pass noise filter for reads." /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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26 <param name="target_coverage" type="float" min="0" value="0" argument="-c" label="Target coverage" help="Sketching will conclude if this coverage is reached before the end of the input file (estimated by average k-mer multiplicity)." /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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27 <param name="genome_size" type="text" argument="-g" optional="true" label="Genome size (raw bases or with K/M/G/T)" help="If specified, will be used for p-value calculation instead of an estimated size from k-mer content." > |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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28 <validator type="regex"><![CDATA[^[0-9]+[KMGT]?$]]></validator> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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29 </param> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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30 </when> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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31 </conditional> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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32 <!-- alphabet --> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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33 <param name="preserve_strand" type="boolean" checked="false" truevalue="-n" falsevalue="" argument="-n" label="Preserve strand" help="By default, strand is ignored by using canonical DNA k-mers, which are alphabetical minima of forward-reverse pairs." /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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34 <param name="use_aaa" type="boolean" checked="false" truevalue="-a" falsevalue="" argument="-a" label="Use amino acid alphabet (A-Z, except BJOUXZ)" help="Implied kmer size of 9 and preserve strand" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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35 <param name="alphabet" type="text" area="false" argument="-z" label="Alphabet to base hashes on" > |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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36 <validator type="regex"><![CDATA[^[A-Za-z]*$]]></validator> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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37 </param> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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38 <param name="preserve_case" type="boolean" checked="false" truevalue="-Z" falsevalue="" argument="-Z" label="Preserve case in k-mers and alphabet" help="Sequence letters whose case is not in the current alphabet will be skipped when sketching." /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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39 </xml> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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40 </macros> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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41 <requirements> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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42 <requirement type="package" version="2.1">mash</requirement> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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43 </requirements> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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44 <version_command>mash --version</version_command> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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45 <command detect_errors="aggressive"><![CDATA[ |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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46 #import os |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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47 ## ===== Declare reusable parameter output for different modes === |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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48 #def sketching |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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49 -k $commands.kmer_size -s $commands.sketch_size |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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50 #if $commands.input_option.individual_seq |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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51 -i ##Hack around current conditional truevalue/falsevalue behavior |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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52 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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53 -S $commands.hash_seed -w $commands.kmer_size_thresh |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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54 #unless $commands.input_option.individual_seq |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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55 $commands.input_option.input_read_set |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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56 #if $commands.input_option.bloom_size |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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57 -b $commands.input_option.bloom_size |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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58 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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59 -m $commands.input_option.kmer_count |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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60 -c $commands.input_option.target_coverage |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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61 #if $commands.input_option.genome_size |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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62 -g $commands.input_option.genome_size |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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63 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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64 #end unless |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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65 $commands.preserve_strand $commands.use_aaa |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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66 #if $commands.alphabet |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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67 -z "$commands.alphabet" |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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68 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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69 $commands.preserve_case |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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70 #end def |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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|
71 |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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|
72 ## ===== Change to extension MASH expects ===== |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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73 #if $commands.command in ["dist", "screen"] and $commands.reference.is_of_type("msh") |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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74 ln -sf $commands.reference ${os.path.basename(str($commands.reference))}.msh && |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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75 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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76 #if $commands.command in ["dist", "sketch", "triangle"] |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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77 #for $input in $commands.inputs |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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78 #if $input.is_of_type("msh") |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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79 ln -sf $input ${os.path.basename(str($input))}.msh && |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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|
80 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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81 #end for |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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82 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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83 #if $commands.command in ["sketch"] |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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84 ln -sf $output output.msh && |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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85 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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86 |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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87 ## ===== Execute MASH ===== |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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88 mash $commands.command |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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89 |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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90 ## ===== Enable threading ===== |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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91 #if False and $commands.command in ["dist", "screen", "sketch", "triangle"] |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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92 -p \${GALAXY_SLOTS:-1} ## -p seems broken at the time of writing |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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93 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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94 |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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95 ## ===== Select correct output parameters for selected mode ===== |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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96 #if $commands.command == "bounds" |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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97 >> $output |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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98 #else if $commands.command == "dist" |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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99 $commands.table_output -v $commands.max_p -d $commands.max_dist |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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100 #set $sketch=True |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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101 #for $input in $commands.inputs |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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102 #if $input.is_of_type("msh") |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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103 #set $sketch=False |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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104 #break |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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105 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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106 #end for |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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107 #if $sketch |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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108 $sketching() |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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109 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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110 #if $commands.reference.is_of_type("msh") |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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111 ${os.path.basename(str($commands.reference))}.msh |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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112 #else |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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113 $commands.reference |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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114 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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115 #for $input in $commands.inputs |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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116 #if $input.is_of_type("msh") |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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117 ${os.path.basename(str($input))}.msh |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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118 #else |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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119 $input |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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120 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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121 #end for |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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122 >> $output |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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123 #else if $commands.command == "info" |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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124 $commands.info_mode $commands.sketch >> $output |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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125 #else if $commands.command == "paste" |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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126 "$commands.out_prefix" |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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127 #for $sketch in $commands.sketches |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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128 $sketch |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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129 #end for |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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130 >> $output |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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131 #else if $commands.command == "screen" |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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132 $commands.winner_takes_all -i $commands.min_ident -v $commands.max_p |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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133 #if $commands.reference.is_of_type("msh") |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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134 ${os.path.basename(str($commands.reference))}.msh |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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135 #else |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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136 $commands.reference |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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137 #end if |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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138 #for $pool in $commands.pools |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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139 $pool |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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140 #end for |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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141 >> $output |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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142 #else if $commands.command == "sketch" |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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143 -o output |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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144 $sketching() |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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145 #for $input in $commands.inputs |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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146 $input |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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147 #end for |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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148 #else if $commands.command == "triangle" |
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149 $commands.comment_fields |
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150 $sketching() |
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151 #for $input in $commands.inputs |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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152 #if $input.is_of_type("msh") |
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153 ${os.path.basename(str($input))}.msh |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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154 #else |
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155 $input |
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156 #end if |
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157 #end for |
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158 >> $output |
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159 #end if |
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160 ]]></command> |
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161 <inputs> |
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162 <conditional name="commands"> |
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163 <param name="command" type="select" label="Mode"> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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164 <option value="bounds">Bounds: Print a table of Mash error bounds</option> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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165 <option value="dist">Dist: Estimate the distance of query sequences to references</option> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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166 <option value="info">Info: Display information about sketch files</option> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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167 <option value="paste">Paste: Create a single sketch file from multiple sketch files</option> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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168 <option value="screen">Screen: Determine whether query sequences are within a larger pool of sequences</option> |
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169 <option value="sketch">Sketch: Create sketches (reduced representations for fast operations)</option> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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170 <option value="triangle">Triangle: Estimate a lower-triangular distance matrix</option> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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171 </param> |
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172 <when value="bounds"> |
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173 <param name="kmer_size" type="integer" min="1" max="32" value="21" argument="-k" label="K-mer size" /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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174 <param name="error_bound" type="float" min="0" max="1" value="0.99" argument="-p" label="Mash distance estimates will be within the given error bounds with this probability" /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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175 </when> |
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176 <when value="dist"> |
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177 <!-- input --> |
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178 <param name="reference" type="data" format="fasta,fastq,fasta.gz,fastq.gz,msh" label="Reference" /> |
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179 <param name="inputs" type="data" format="fasta,fastq,fasta.gz,fastq.gz,msh" multiple="true" label="Queries" /> |
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180 <!-- output --> |
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181 <param name="table_output" type="boolean" checked="false" truevalue="-t" falsevalue="" argument="-t" label="Table output" help="Table output (will not report p-values, but fields will be blank if they do not meet the p-value threshold)." /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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182 <param name="max_p" type="float" min="0" max="1" value="1" argument="-v" label="Maximum p-value to report" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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183 <param name="max_dist" type="float" min="0" max="1" value="1" argument="-d" label="Maximum distance to report" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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184 <expand macro="sketching_options" /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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185 </when> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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186 <when value="info"> |
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187 <param name="info_mode" type="select" label="Mode"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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188 <option value="" selected="true">Default</option> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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189 <option value="-H">Only show header info, do not list each sketch</option> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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190 <option value="-t">Tabular output (rather than padded), with no header</option> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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191 <option value="-c">Show hash count histograms for each sketch</option> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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192 <option value="-d">Dump sketches in JSON format</option> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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193 </param> |
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194 </when> |
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195 <when value="paste"> |
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196 <param name="sketches" type="data" format="msh" multiple="true" label="Sketches to merge" /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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197 <param name="out_prefix" type="text" area="false" label="Out prefix" /> |
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198 </when> |
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199 <when value="screen"> |
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200 <param name="reference" type="data" format="msh" label="inputs" help="Use the sketch command to combine multiple sketch inputs." /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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201 <param name="pools" type="data" format="fasta,fastq,fasta.gz,fastq.gz" multiple="true" label="Pools" help="The pool sequences are assumed to be nucleotides, and will be 6-frame translated if the inputs are amino acids." /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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202 <param name="winner_takes_all" type="boolean" checked="false" truevalue="-w" falsevalue="" argument="-w" label="Winner-takes-all strategy for identity estimates" help="After counting hashes for each query, hashes that appear in multiple inputs will be removed from all except the one with the best identity (ties broken by larger query), and other identities will be reduced. This removes output redundancy, providing a rough compositional outline." /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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203 <param name="min_ident" type="float" min="-1" max="1" value="0" argument="-i" label="Minimum identity to report" help="Inclusive unless set to zero, in which case only identities greater than zero (i.e. with at least one shared hash) will be reported. Set to -1 to output everything." /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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204 <param name="max_p" type="float" min="0" max="1" value="1" argument="-v" label="Maximum p-value to report" /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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205 </when> |
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206 <when value="sketch"> |
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207 <param name="inputs" type="data" format="fasta,fastq,fasta.gz,fastq.gz" multiple="true" label="Inputs" /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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208 <!-- TODO -I and -C --> |
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209 <expand macro="sketching_options" /> |
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210 </when> |
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211 <when value="triangle"> |
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212 <param name="inputs" type="data" format="fasta,fastq,fasta.gz,fastq.gz,msh" multiple="true" label="Input sequences" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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213 <param name="comment_fields" type="boolean" checked="false" truevalue="-C" falsevalue="" label="Use comment fields for sequence names instead of IDs" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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214 <expand macro="sketching_options" /> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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215 </when> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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216 </conditional> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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217 </inputs> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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218 <outputs> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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219 <data name="output" format="txt"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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220 <change_format> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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221 <when input="commands.command" value="bounds" format="tabular" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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222 <when input="commands.command" value="dist" format="tsv" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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223 <when input="commands.command" value="info" format="txt" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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224 <when input="commands.command" value="paste" format="msh" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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225 <when input="commands.command" value="screen" format="txt" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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226 <when input="commands.command" value="sketch" format="msh" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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227 <when input="commands.command" value="triangle" format="phylip" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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228 </change_format> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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229 </data> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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230 </outputs> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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231 <tests> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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232 <test expect_num_outputs="1"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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233 <conditional name="commands"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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234 <param name="command" value="bounds" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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235 </conditional> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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236 <output name="output" ftype="tabular"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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237 <assert_contents> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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238 <has_text text="Mash distance" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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239 <has_text text="Screen distance" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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240 </assert_contents> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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241 </output> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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242 </test> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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243 <test expect_num_outputs="1"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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244 <conditional name="commands"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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245 <param name="command" value="dist" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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246 <param name="reference" value="test-data/15600_genome.fasta" ftype="fasta" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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247 <param name="genomes" > |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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248 <collection type="list"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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249 <element name="test1" value="test-data/15596_genome.fasta" ftype="fasta" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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250 <element name="test2" value="test-data/15602_genome.fasta" ftype="fasta" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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251 <element name="test3" value="test-data/15599_genome.fasta" ftype="fasta" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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252 </collection> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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253 </param> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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254 <conditional name="input_option"> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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255 <param name="individual_seq" value="true" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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256 </conditional> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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257 </conditional> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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258 <output name="output" checksum="sha256:701ecc0d4fec3383267699ebd9d78dd7b84360ff57754aac4f2bc8bc00aee580" ftype="tsv" /> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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259 </test> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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260 </tests> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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261 <help><![CDATA[ |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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262 https://mash.readthedocs.io/en/latest/ |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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263 ]]></help> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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264 <citations> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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265 <citation type="doi">10.5281/zenodo.3364789</citation> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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266 <citation type="doi">10.1186/s13059-016-0997-x</citation> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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267 </citations> |
572587cbb1dd
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/<name of containing folder> commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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268 </tool> |