Mercurial > repos > estrain > bbmap_sendsketch
comparison bbmap_sendsketch.xml @ 0:e461ee9ba3a3 draft default tip
planemo upload commit 1b8023dc06967d4a0eba299c60afc7f09353360b
| author | estrain |
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| date | Thu, 12 Mar 2026 19:48:40 +0000 |
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| children |
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| -1:000000000000 | 0:e461ee9ba3a3 |
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| 1 <tool id="bbmap_sendsketch" name="bbmap_sendsketch" version="39.26+galaxy25"> | |
| 2 <description> Identifying species using sketch</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="39.37">bbmap</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 #import re | |
| 8 #set $safename = re.sub('[^\w\-_\.]', '_', $input.element_identifier) | |
| 9 ln -sf '$input' '$safename' && | |
| 10 sendsketch.sh | |
| 11 #if $printall | |
| 12 printall=t | |
| 13 #end if | |
| 14 #if $translate | |
| 15 translate=t | |
| 16 #end if | |
| 17 in='$safename' | |
| 18 out=output.txt | |
| 19 outsketch=sketch | |
| 20 minhits=$minhits | |
| 21 minani=$minani | |
| 22 format=$format | |
| 23 score=t | |
| 24 $db | |
| 25 ]]> </command> | |
| 26 | |
| 27 <inputs> | |
| 28 <param name="input" type="data" format="fasta,fasta.gz" label="Input sequence"/> | |
| 29 <param name="db" type="select" label="Sketch Database"> | |
| 30 <option value="refseq" selected="true">Refseq</option> | |
| 31 <option value="nt">nt</option> | |
| 32 <option value="silva">silva</option> | |
| 33 <option value="protein">RefSeq prokaryotic amino acid sketches</option> | |
| 34 </param> | |
| 35 <param name="format" type="select" label="Output Format"> | |
| 36 <option value="2" selected="true">Default format with, per query, one query header line; | |
| 37 one column header line; and one reference line per hit</option> | |
| 38 <option value="3">One line per hit, with columns query, reference, ANI, | |
| 39 and sizeRatio</option> | |
| 40 <option value="4">JSON</option> | |
| 41 </param> | |
| 42 <param name="minhits" type="integer" min="1" value="3" label="Only report records with at least this many hits"/> | |
| 43 <param name="minani" type="float" min="0" value="0.0" max="1" label="Only report records with at least this ANI"/> | |
| 44 <param name="minwkid" type="float" min="0" value="0.0001" max="1" label="Only report records with at least this WKID"/> | |
| 45 <param name="minbases" type="integer" min="0" value="0" label="Ignore ref sketches of sequences shortert than this"/> | |
| 46 <param name="minsizeratio" type="float" min="0" value="0.0" max="1" label="Don't compare sketches if the smaller genome is less than | |
| 47 this fraction of the size of the larger"/> | |
| 48 <param name="records" type="integer" min="1" value="20" label="Report at most this many best-matching records"/> | |
| 49 <param name="write_sketch" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Write sketch?"/> | |
| 50 <param name="translate" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Call genes and translate to proteins. Input should be | |
| 51 nucleotides"/> | |
| 52 <param name="printall" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Print all column?"/> | |
| 53 </inputs> | |
| 54 | |
| 55 <outputs> | |
| 56 <data name="Output" format="txt" label="${tool.name} on ${on_string} Results" from_work_dir="output.txt"/> | |
| 57 <data name="Sketch" format="binary" label="${tool.name} on ${on_string} Sketch" from_work_dir="sketch"> | |
| 58 <filter>write_sketch is True</filter> | |
| 59 </data> | |
| 60 </outputs> | |
| 61 <help><![CDATA[ | |
| 62 Compares query sketches to reference sketches hosted on a | |
| 63 remote server via the Internet. The input can be sketches made by sketch.sh, | |
| 64 or fasta/fastq files from which SendSketch will generate sketches. | |
| 65 Only sketches will sent, not sequences. | |
| 66 ]]> </help> | |
| 67 <expand macro="citations" /> | |
| 68 | |
| 69 </tool> |