Mercurial > repos > thanhlv > centrifuge

annotate centrifuge.xml @ 0:a33c3356b8cf draft default tip

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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
author thanhlv
date Mon, 31 Jan 2022 11:17:00 +0000
parents
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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1 <tool id="centrifuge" name="Centrifuge" version="1.0.4_beta">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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2
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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3 <description>Read-based metagenome characterization</description>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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4
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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5 <!-- ***************************************************************** -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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6
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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7 <requirements>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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8 <requirement type="package" version="1.0.4_beta">centrifuge</requirement>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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9 </requirements>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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10
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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11 <!-- ***************************************************************** -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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12
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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13 <version_command>centrifuge --version | perl -wnE'print "$1\n" for /centrifuge\S+ version (\S+)/g'</version_command>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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14
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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15 <!-- ***************************************************************** -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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16
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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17 <command detect_errors="aggressive">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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18 <![CDATA[
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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19
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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20 centrifuge
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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21
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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22 ##--Output Options------------------------------
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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23
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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24 --out-fmt $outputs.out_fmt
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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25 --tab-fmt-cols $outputs.tab_fmt_cols
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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26
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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27 ##--General Options-----------------------------
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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28
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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29 --threads \${GALAXY_SLOTS:-1}
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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30
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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31 #if $general.skip != "":
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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32 --skip $general.skip
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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33 #end if
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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34 #if $general.upto != "":
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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35 --upto $general.upto
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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36 #end if
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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37 #if $general.trim5 != "":
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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38 --trim5 $general.trim5
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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39 #end if
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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40 #if $general.trim3 != "":
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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41 --trim3 $general.trim3
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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42 #end if
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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43
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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44 $general.ignore_quals
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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45 $general.nofw
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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46 $general.norc
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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47 $general.non_deterministic
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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48
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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49 #if $general.seed != "":
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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50 --seed $general.seed
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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51 #end if
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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52
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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53 ##--Classification------------------------------
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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54
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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55 --min-hitlen $classification.min_hitlen
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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56 -k $classification.k_distinct
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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57
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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58 #if $classification.min_totallen != "":
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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59 --min-totallen $classification.min_totallen
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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60 #end if
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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61
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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62 #if $classification.host_taxids != "":
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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63 --host-taxids $classification.host_taxids
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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64 #end if
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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65
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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66 #if $classification.exclude_taxids != "":
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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67 --exclude-taxids $classification.exclude_taxids
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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68 #end if
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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69
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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70 ##--Inputs--------------------------------------
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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71
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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72 -x '${inputs.db.fields.path}'
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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73
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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74 #for $s in $inputs.unpaired
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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75 -U '${s.u_reads}'
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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76 #end for
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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77
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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78 #for $s in $inputs.paired
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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79 -1 '${s.p_reads.forward}'
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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diff changeset
80 -2 '${s.p_reads.reverse}'
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
81 #end for
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
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82
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
83 #if $inputs.sra:
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
84 --sra-acc $inputs.sra
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
85 #end if
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
86
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
87 #if $outputs.out_fmt == "tab":
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
88 -S $out_tab
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
89 #elif $outputs.out_fmt == "sam":
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
90 -S $out_sam
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
91 #end if
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
92
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
93 --report-file $report
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
94
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
95 ]]>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
96 </command>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
97
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
98 <!-- ***************************************************************** -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
99
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
100 <inputs>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
101
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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102 <section name="inputs" title="Inputs" expanded="True">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
103
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
104 <repeat name="unpaired" title="Unpaired reads" min="0" default="0">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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105 <param name="u_reads" type="data" format="fastq" label="Unpaired reads"/>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
106 </repeat>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
107
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
108 <repeat name="paired" title="Paired reads" min="0" default="0">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
109 <param name="p_reads" type="data_collection" collection_type="paired" format="fastq" label="Paired read collection"/>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
110 </repeat>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
111
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
112 <param name="sra" type="text" label="SRA accession">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
113 <sanitizer invalid_char="">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
114 <valid initial="string.letters,string.digits">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
115 <add value="," />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
116 </valid>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
117 </sanitizer>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
118 </param>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
119
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
120 <param name="db" type="select" label="Select a reference database">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
121 <options from_data_table="centrifuge_indices">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
122 <filter type="sort_by" column="2"/>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
123 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
124 </options>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
125 </param>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
126
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
127 </section>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
128
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
129 <section name="outputs" title="Outputs" expanded="False">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
130
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
131 <param argument="--out-fmt" name="out_fmt" type="select" label="Output format">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
132 <option value="tab" selected="true">tabular</option>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
133 <option value="sam">SAM</option>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
134 </param>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
135
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
136 <param argument="--tab-fmt-cols" name="tab_fmt_cols" type="text" label="Output columns" value="readID,seqID,taxID,score,2ndBestScore,hitLength,queryLength,numMatches">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
137 <sanitizer invalid_char="">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
138 <valid initial="string.letters,string.digits">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
139 <add value="," />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
140 </valid>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
141 </sanitizer>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
142 </param>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
143
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
144 </section>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
145
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
146 <section name="general" title="General options" expanded="False">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
147
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
148 <param argument="--skip" type="integer" value="" optional="true" label="Initial reads to skip" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
149 <param argument="--upto" type="integer" value="" optional="true" label="Stop after reads" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
150 <param argument="--trim5" type="integer" value="" optional="true" label="Trim 5' bases" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
151 <param argument="--trim3" type="integer" value="" optional="true" label="Trim 3' bases" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
152
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
153 <param argument="--ignore-quals" name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" checked="no" label="Ignore qualities" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
154
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
155 <param argument="--nofw" type="boolean" truevalue="--nofw" falsevalue="" checked="no" label="Don't map forward strand" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
156 <param argument="--norc" type="boolean" truevalue="--norc" falsevalue="" checked="no" label="Don't map rev-com strand" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
157
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
158 <param argument="--seed" type="integer" value="" min="0" optional="true" label="Starting seed" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
159 <param argument="--non-deterministic" name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" checked="no" label="Use non-deterministic seeding" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
160
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
161 </section>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
162
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
163 <section name="classification" title="Classification" expanded="True">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
164
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
165 <param argument="--min-hitlen" name="min_hitlen" type="integer" value="22" min="16" label="Minimum hit length" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
166 <param name="k_distinct" type="integer" value="5" min="5" label="Searching for at most k distinct, primary assignments for each read or pair." help="Primary assignments mean assignments whose assignment score is equal or higher than any other assignments. If there are more primary assignments than this value, the search will merge some of the assignments into a higher taxonomic rank. The assignment score for a paired-end assignment equals the sum of the assignment scores of the individual mates"/>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
167 <param argument="--min-totallen" name="min_totallen" type="integer" optional="true" min="0" label="Minimum summed length" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
168
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
169 <param argument="--host-taxids" name="host_taxids" type="text" label="Host taxonomic IDs">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
170 <sanitizer invalid_char="">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
171 <valid initial="string.digits">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
172 <add value="," />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
173 </valid>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
174 </sanitizer>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
175 </param>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
176 <param argument="--exclude-taxids" name="exclude_taxids" type="text" label="Excluded taxonomic IDs">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
177 <sanitizer invalid_char="">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
178 <valid initial="string.digits">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
179 <add value="," />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
180 </valid>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
181 </sanitizer>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
182 </param>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
183
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
184 </section>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
185
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
186 </inputs>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
187
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
188 <!-- ***************************************************************** -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
189
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
190 <outputs>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
191
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
192 <data name="out_tab" format="tabular" label="Centrifuge on ${on_string}: Output">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
193 <filter>(outputs['out_fmt'] == "tab")</filter>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
194 </data>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
195 <data name="out_sam" format="sam" label="Centrifuge on ${on_string}: Output">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
196 <filter>(outputs['out_fmt'] == "sam")</filter>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
197 </data>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
198 <data name="report" format="tabular" label="Centrifuge on ${on_string}: Report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
199
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
200 </outputs>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
201
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
202 <!-- ***************************************************************** -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
203
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
204 <tests>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
205 <!-- default unpaired -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
206 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
207 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
208 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
209 <output name="out_tab" file="defaults.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
210 <output name="report" file="defaults.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
211 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
212 <!-- default paired -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
213 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
214 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
215 <param name="p_reads">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
216 <collection type="paired">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
217 <element name="forward" value="input_f.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
218 <element name="reverse" value="input_r.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
219 </collection>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
220 </param>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
221 <output name="out_tab" file="paired.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
222 <output name="report" file="paired.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
223 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
224 <!-- default combined -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
225 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
226 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
227 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
228 <param name="p_reads">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
229 <collection type="paired">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
230 <element name="forward" value="input_f.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
231 <element name="reverse" value="input_r.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
232 </collection>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
233 </param>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
234 <output name="out_tab" file="both.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
235 <output name="report" file="both.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
236 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
237 <!-- exclude IDs -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
238 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
239 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
240 <param name="exclude_taxids" value="9913" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
241 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
242 <output name="out_tab" file="exclude.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
243 <output name="report" file="exclude.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
244 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
245 <!-- specify host -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
246 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
247 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
248 <param name="host_taxids" value="9913" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
249 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
250 <output name="out_tab" file="host.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
251 <output name="report" file="host.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
252 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
253 <!-- minimum length -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
254 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
255 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
256 <param name="min_hitlen" value="83" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
257 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
258 <output name="out_tab" file="minlen83.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
259 <output name="report" file="minlen83.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
260 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
261 <!-- norc -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
262 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
263 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
264 <param name="norc" value="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
265 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
266 <output name="out_tab" file="norc.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
267 <output name="report" file="norc.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
268 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
269 <!-- nofw -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
270 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
271 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
272 <param name="nofw" value="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
273 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
274 <output name="out_tab" file="nofw.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
275 <output name="report" file="nofw.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
276 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
277 <!-- set seed -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
278 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
279 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
280 <param name="seed" value="123" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
281 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
282 <output name="out_tab" file="seed123.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
283 <output name="report" file="seed123.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
284 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
285 <!-- 5' trim -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
286 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
287 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
288 <param name="trim5" value="10" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
289 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
290 <output name="out_tab" file="trim5_10.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
291 <output name="report" file="trim5_10.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
292 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
293 <!-- 3' trim -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
294 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
295 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
296 <param name="trim3" value="5" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
297 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
298 <output name="out_tab" file="trim3_5.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
299 <output name="report" file="trim3_5.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
300 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
301 <!-- skip start -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
302 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
303 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
304 <param name="skip" value="3" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
305 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
306 <output name="out_tab" file="skip3.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
307 <output name="report" file="skip3.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
308 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
309 <!-- skip end -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
310 <test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
311 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
312 <param name="upto" value="6" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
313 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
314 <output name="out_tab" file="upto6.tsv" sort="true" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
315 <output name="report" file="upto6.report" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
316 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
317 <!-- invalid parameter value -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
318 <test expect_failure="true">
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
319 <param name="db" value="test_db" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
320 <param name="tab_fmt_cols" value="FooBar" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
321 <param name="u_reads" ftype="fastq" value="input_u.fq" />
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
322 </test>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
323
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
324 </tests>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
325
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
326 <!-- ***************************************************************** -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
327
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
328 <help>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
329 <![CDATA[
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
330
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
331 Overview
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
332 --------
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
333
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
334 **Credit**
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
335 This wrapper was modified from the original version at https://github.com/jvolkening/galaxy-tools
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
336
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
337 **Centrifuge** is a very rapid and memory-efficient system for the
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
338 classification of DNA sequences from microbial samples, with better
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
339 sensitivity than and comparable accuracy to other leading systems. The system
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
340 uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
341 the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
342 classification problem. Centrifuge requires a relatively small index (e.g.,
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
343 4.3 GB for ~4,100 bacterial genomes) yet provides very fast classification
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
344 speed, allowing it to process a typical DNA sequencing run within an hour.
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
345 Together these advances enable timely and accurate analysis of large
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
346 metagenomics data sets on conventional desktop computers.
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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diff changeset
347
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
348 Usage
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
349 -----
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
350
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
351 Following is the manpage for `centrifuge`, which can be linked with the
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
352 options above using the help text. Note that not all options are available in
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
353 the Galaxy wrapper.
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
354
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
355 ::
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
356
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
357 centrifuge [options]* -x <cf-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <filename>] [--report-file <report>]
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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diff changeset
358
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
359 <cf-idx> Index filename prefix (minus trailing .X.cf).
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
360 <m1> Files with #1 mates, paired with files in <m2>.
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
361 Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
362 <m2> Files with #2 mates, paired with files in <m1>.
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
363 Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
364 <r> Files with unpaired reads.
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
365 Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
366 <SRA accession number> Comma-separated list of SRA accession numbers, e.g. --sra-acc SRR353653,SRR353654.
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
367 <filename> File for classification output (default: stdout)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
368 <report> File for tabular report output (default: centrifuge_report.tsv)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
369
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
370 <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
371 specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
372
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
373 Options (defaults in parentheses):
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
374
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
375 Input:
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
376 -q query input files are FASTQ .fq/.fastq (default)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
377 --qseq query input files are in Illumina's qseq format
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
378 -f query input files are (multi-)FASTA .fa/.mfa
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
379 -r query input files are raw one-sequence-per-line
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
380 -c <m1>, <m2>, <r> are sequences themselves, not files
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
381 -s/--skip <int> skip the first <int> reads/pairs in the input (none)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
382 -u/--upto <int> stop after first <int> reads/pairs (no limit)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
383 -5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
384 -3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
385 --phred33 qualities are Phred+33 (default)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
386 --phred64 qualities are Phred+64
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
387 --int-quals qualities encoded as space-delimited integers
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
388 --ignore-quals treat all quality values as 30 on Phred scale (off)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
389 --nofw do not align forward (original) version of read (off)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
390 --norc do not align reverse-complement version of read (off)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
391 --sra-acc SRA accession ID
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
392
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
parents:
diff changeset
393 Classification:
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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394 --min-hitlen <int> minimum length of partial hits (default 22, must be greater than 15)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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395 --min-totallen <int> minimum summed length of partial hits per read (default 0)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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396 --host-taxids <taxids> comma-separated list of taxonomic IDs that will be preferred in classification
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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397 --exclude-taxids <taxids> comma-separated list of taxonomic IDs that will be excluded in classification
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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398
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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399 Output:
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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400 --out-fmt <str> define output format, either 'tab' or 'sam' (tab)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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401 --tab-fmt-cols <str> columns in tabular format, comma separated
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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402 default: readID,seqID,taxID,score,2ndBestScore,hitLength,queryLength,numMatches
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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403 -t/--time print wall-clock time taken by search phases
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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404 --un <path> write unpaired reads that didn't align to <path>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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405 --al <path> write unpaired reads that aligned at least once to <path>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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406 --un-conc <path> write pairs that didn't align concordantly to <path>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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407 --al-conc <path> write pairs that aligned concordantly at least once to <path>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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408 (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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409 --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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410 --quiet print nothing to stderr except serious errors
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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411 --met-file <path> send metrics to file at <path> (off)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
thanhlv
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412 --met-stderr send metrics to stderr (off)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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413 --met <int> report internal counters & metrics every <int> secs (1)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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414
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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415 Performance:
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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416 -o/--offrate <int> override offrate of index; must be >= index's offrate
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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417 -p/--threads <int> number of alignment threads to launch (1)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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418 --mm use memory-mapped I/O for index; many 'bowtie's can share
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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419
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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420 Other:
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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421 --qc-filter filter out reads that are bad according to QSEQ filter
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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422 --seed <int> seed for random number generator (0)
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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423 --non-deterministic seed rand. gen. arbitrarily instead of using read attributes
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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424 --version print version information and quit
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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425 -h/--help print this usage message
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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426
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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427 ]]>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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428 </help>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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429
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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430 <!-- ***************************************************************** -->
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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431
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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432 <citations>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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433 <citation type="doi">10.1101/gr.210641.116</citation>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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434 </citations>
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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435
a33c3356b8cf "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/centrifuge commit e7a2d92dc14da78e7ba641c603de75a985d037b6-dirty"
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436 </tool>