Mercurial > repos > estrain > bbmap_sendsketch

annotate bbmap_sendsketch.xml @ 0:e461ee9ba3a3 draft default tip

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