Mercurial > repos > thanhlv > bbmap

annotate sendsketch.xml @ 3:abd4087dc088 draft

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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit e2d76780e87f3792d756ca65d6eb80e9d47f3234-dirty"
author thanhlv
date Mon, 25 Nov 2019 17:54:14 +0000
parents 68bea7cc680c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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1 <tool id="bbmap_sendsketch" name="sendsketch" version="@VERSION@">
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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2 <description> Identifying species using sketch</description>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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9 <command detect_errors="exit_code"><![CDATA[
1
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10 #import re
f285fe3f81ff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e-dirty"
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11 #set $safename = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
f285fe3f81ff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e-dirty"
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12 ln -sf '$input' '$safename' &&
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23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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13 sendsketch.sh
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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14 #if $printall
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15 printall=t
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16 #end if
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17 #if $translate
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18 translate=t
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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19 #end if
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68bea7cc680c "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit 34025d7211ff832f73481bbf9da4c901c99cb717"
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20 in='$safename'
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23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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21 out=output.txt
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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22 outsketch=sketch
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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23 minhits=$minhits
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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24 minani=$minani
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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25 format=$format
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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26 score=t
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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27 $db
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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28 ]]> </command>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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29
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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30 <inputs>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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31 <param name="input" type="data" format="fasta,fasta.gz" label="Input sequence"/>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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32 <param name="db" type="select" label="Sketch Database">
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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33 <option value="refseq" selected="true">Refseq</option>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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34 <option value="nt">nt</option>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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35 <option value="silva">silva</option>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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36 <option value="protein">RefSeq prokaryotic amino acid sketches</option>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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37 </param>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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38 <param name="format" type="select" label="Output Format">
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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39 <option value="2" selected="true">Default format with, per query, one query header line;
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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40 one column header line; and one reference line per hit</option>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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41 <option value="3">One line per hit, with columns query, reference, ANI,
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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42 and sizeRatio</option>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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43 <option value="4">JSON</option>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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44 </param>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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45 <param name="minhits" type="integer" min="1" value="3" label="Only report records with at least this many hits"/>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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46 <param name="minani" type="float" min="0" value="0.0" max="1" label="Only report records with at least this ANI"/>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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47 <param name="minwkid" type="float" min="0" value="0.0001" max="1" label="Only report records with at least this WKID"/>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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48 <param name="minbases" type="integer" min="0" value="0" label="Ignore ref sketches of sequences shortert than this"/>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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49 <param name="minsizeratio" type="float" min="0" value="0.0" max="1" label="Don't compare sketches if the smaller genome is less than
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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50 this fraction of the size of the larger"/>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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51 <param name="records" type="integer" min="1" value="20" label="Report at most this many best-matching records"/>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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52 <param name="write_sketch" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Write sketch?"/>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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53 <param name="translate" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Call genes and translate to proteins. Input should be
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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54 nucleotides"/>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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55 <param name="printall" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Print all column?"/>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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56 </inputs>
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57
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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58 <outputs>
3
abd4087dc088 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit e2d76780e87f3792d756ca65d6eb80e9d47f3234-dirty"
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59 <data name="Output" format="txt" label="${tool.name} on ${on_string} Results" from_work_dir="output.txt"/>
abd4087dc088 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit e2d76780e87f3792d756ca65d6eb80e9d47f3234-dirty"
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60 <data name="Sketch" format="binary" label="${tool.name} on ${on_string} Sketch" from_work_dir="sketch">
0
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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61 <filter>write_sketch is True</filter>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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62 </data>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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63 </outputs>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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64 <help><![CDATA[
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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65 Compares query sketches to reference sketches hosted on a
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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66 remote server via the Internet. The input can be sketches made by sketch.sh,
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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67 or fasta/fastq files from which SendSketch will generate sketches.
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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68 Only sketches will sent, not sequences.
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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69 ]]> </help>
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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70 <expand macro="citations" />
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71
23ecfa3e5eff "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit fec9224232f4fe1200df4f66e1fa064533b3f21e"
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72 </tool>