Mercurial > repos > iuc > bbtools_bbduk

annotate bbduk.xml @ 1:60dd895841cd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
author iuc
date Tue, 01 Feb 2022 23:00:44 +0000
parents 204a131e47db
children 425dab0e057b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
1 <tool id="bbtools_bbduk" name="BBTools: BBduk" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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2 <description>decontamination using kmers</description>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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3 <macros>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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4 <import>macros.xml</import>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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5 </macros>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
6 <expand macro="requirements"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
7 <command detect_errors="exit_code"><![CDATA[
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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8 #import os
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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9 #import re
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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10
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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11 #if str($input_type_cond.input_type) in ['single', 'pair']:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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12 #set read1 = $input_type_cond.read1
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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13 ## bbduk uses the file extension to determine the input format.
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents: 0
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14 #set ext = '.fastq'
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
15 #if $read1.ext.endswith('.gz'):
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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16 #set ext = $ext + '.gz'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
17 #end if
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
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18 #set read1_file = 'forward' + $ext
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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19 ln -s '${read1}' '${read1_file}' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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20 #if str($input_type_cond.input_type) == 'pair':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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21 #set read2 = $input_type_cond.read2
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
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22 #set read2_file = 'reverse' + $ext
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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23 ln -s '${read2}' '${read2_file}' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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24 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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25 #else:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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26 #set read1 = $input_type_cond.reads_collection['forward']
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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27 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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28 ## bbduk uses the file extension to determine the input format.
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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29 #set ext = $read1_identifier + '.fastq'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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30 #if $read1.ext.endswith('.gz'):
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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31 #set ext = $ext + '.gz'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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32 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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33 #set read1_file = $read1_identifier + $ext
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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34 ln -s '${read1}' '${read1_file}' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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35 #set read2 = $input_type_cond.reads_collection['reverse']
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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36 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name))
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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37 #set read2_file = $read2_identifier + $ext
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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38 ln -s '${read2}' '${read2_file}' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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39 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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40
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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41 #if str($reference_type_cond.reference_type) == 'files':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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42 #set refs = list()
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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43 #for ref in $reference_type_cond.reference:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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44 ## bbduk looks at the file extension.
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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45 #set ref_name = str($os.path.basename($ref.file_name)) + '.fa'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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46 #if $ref.ext.endswith('.gz'):
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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47 gunzip -c '$ref' > '$ref_name' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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48 #else:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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49 ln -s '$ref' '$ref_name' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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50 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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51 $refs.append(str($ref_name))
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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52 #end for
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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53 #set refs = ','.join($refs)
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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54 #else if str($reference_type_cond.reference_type) == 'keywords':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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55 #set refs = str($reference_type_cond.reference)
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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56 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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57
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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58 bbduk.sh
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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59 in='${read1_file}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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60
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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61 #if str($input_type_cond.input_type) in ['pair', 'paired']:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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62 in2='${read2_file}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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63 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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64 #if str($outputs_select).find('outu') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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65 out='${outputu}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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66 #if str($input_type_cond.input_type) in ['pair', 'paired']:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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67 out2='${outputu2}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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68 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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69 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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70 #if str($outputs_select).find('outm') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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71 outm='${outputm}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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72 #if str($input_type_cond.input_type) in ['pair', 'paired']:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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73 outm2='${outputm2}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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74 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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75 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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76 #if str($outputs_select).find('outs') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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77 outs='${outputs}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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78 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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79
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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80 #if str($reference_type_cond.reference_type) != 'no_reference':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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81 ref='$refs'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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82 #if str($reference_type_cond.ktrim_cond.ktrim_select) == 'yes':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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83 ktrim='${reference_type_cond.ktrim_cond.ktrim}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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84 minlength=$reference_type_cond.ktrim_cond.minlength
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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85 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
86 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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87
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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88 k=$advanced_options.k
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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89 rcomp='${advanced_options.rcomp}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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90 maskmiddle='${advanced_options.maskmiddle}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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91 minkmerhits='${advanced_options.minkmerhits}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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92 minkmerfraction=$advanced_options.minkmerfraction
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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93 mincovfraction=$advanced_options.mincovfraction
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
94 hammingdistance=$advanced_options.hammingdistance
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
95 qhdist=$advanced_options.qhdist
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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96 editdistance=$advanced_options.editdistance
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
97 forbidn='${advanced_options.forbidn}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
98 trimfailures='${advanced_options.trimfailures}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
99 findbestmatch='${advanced_options.findbestmatch}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
100 skipr1='${advanced_options.skipr1}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
101 skipr2='${advanced_options.skipr2}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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102
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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103 #if str($output_stats_cond.output_stats) == 'yes':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
104 #if str($output_stats_cond.output_stats_select).find('stats') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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105 stats='${output_stats}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
106 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
107 #if str($output_stats_cond.output_stats_select).find('ref') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
108 refstats='${output_ref}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
109 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
110 #if str($output_stats_cond.output_stats_select).find('rpkm') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
111 rpkm='${output_rpkm}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
112 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
113 #if str($output_stats_cond.output_stats_select).find('dump') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
114 dump='${output_dump}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
115 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
116 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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117 #if str($output_hists_cond.output_hists) == 'yes':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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118 #if str($output_hists_cond.output_hists_select).find('bhist') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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119 bhist='${output_bhist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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120 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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121 #if str($output_hists_cond.output_hists_select).find('quhist') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
122 qhist='${output_quhist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
123 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
124 #if str($output_hists_cond.output_hists_select).find('quchist') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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125 qchist='${output_quchist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
126 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
127 #if str($output_hists_cond.output_hists_select).find('aqhist') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
128 aqhist='${output_aqhist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
129 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
130 #if str($output_hists_cond.output_hists_select).find('bqhist') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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131 bqhist='${output_bqhist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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132 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
133 #if str($output_hists_cond.output_hists_select).find('lhist') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
134 lhist='${output_lhist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
135 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
136 #if str($output_hists_cond.output_hists_select).find('phist') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
137 phist='${output_phist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
138 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
139 #if str($output_hists_cond.output_hists_select).find('gchist') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
140 gchist='${output_gchist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
141 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
142 #if str($output_hists_cond.output_hists_select).find('enthist') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
143 enthist='${output_enthist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
144 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
145 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
146 t=\${GALAXY_SLOTS:-4}
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
147 ]]></command>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
148 <inputs>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
149 <expand macro="input_type_cond"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
150 <conditional name="reference_type_cond">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
151 <param name="reference_type" type="select" label="Choose the reference type" help="Optional, no reference is the default">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
152 <option value="no_reference" selected="true">No reference</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
153 <option value="files">files</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
154 <option value="keywords">keywords</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
155 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
156 <when value="no_reference"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
157 <when value="files">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
158 <param name="reference" type="data" format="fasta,fasta.gz" multiple="true" optional="false" label="Select one or more fasta file"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
159 <expand macro="ktrim_cond"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
160 </when>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
161 <when value="keywords">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
162 <param name="reference" type="select" multiple="true" optional="false" label="Select one or more keywords">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
163 <option value="adapters">adapters</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
164 <option value="artifacts">artifacts</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
165 <option value="phix">phix</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
166 <option value="lambda">lambda</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
167 <option value="pjet">pjet</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
168 <option value="mtst">mtst</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
169 <option value="kapa">kapa</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
170 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
171 <expand macro="ktrim_cond"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
172 </when>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
173 </conditional>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
174 <section name="advanced_options" title="Advanced options" expanded="false">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
175 <param argument="k" type="integer" value="27" min="1" label="Kmer length used for finding contaminants"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
176 <param argument="rcomp" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Look for reverse-complements of kmers in addition to forward kmers?"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
177 <param argument="maskmiddle" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Treat the middle base of a kmer as a wildcard to increase sensitivity in the presence of errors?"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
178 <param argument="minkmerhits" type="integer" value="1" min="1" label="Reads need at least this many matching kmers to be considered as matching the reference"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
179 <param argument="minkmerfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total kmers to hit a ref in order to be considered a match"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
180 <param argument="mincovfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total bases to be covered by ref kmers to be considered a match"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
181 <param argument="hammingdistance" type="integer" value="0" min="0" label="Maximum Hamming distance for ref kmers (subs only)"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
182 <param argument="qhdist" type="integer" value="0" min="0" label="Hamming distance for query kmers"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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183 <param argument="editdistance" type="integer" value="0" min="0" label="Maximum edit distance from ref kmers (subs and indels)"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
184 <param argument="forbidn" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Do not match kmers comntaining N?"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
185 <param argument="trimfailures" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim failed reads to 1bp instead of discarding them?"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
186 <param argument="findbestmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Associate read with sequence sharing most kmers if multiple matches?"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
187 <param argument="skipr1" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 1?"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
188 <param argument="skipr2" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 2?"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
189 </section>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
190 <param name="outputs_select" type="select" multiple="true" optional="false" label="Specify outputs">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
191 <option value="outu">Unmatched</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
192 <option value="outm">Matched</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
193 <option value="outs">Single</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
194 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
195 <conditional name="output_stats_cond">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
196 <param name="output_stats" type="select" label="Output statistics?">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
197 <option value="no" selected="true">No</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
198 <option value="yes">Yes</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
199 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
200 <when value="no"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
201 <when value="yes">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
202 <param name="output_stats_select" type="select" multiple="true" optional="false" label="Specify statistics outputs">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
203 <option value="stats">Statistics about which contamininants were detected</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
204 <option value="ref">Statistics on a per-reference-file basis</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
205 <option value="rpkm">RPKM for each reference sequence (for RNA-seq)</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
206 <option value="dump">kmer tables in fasta format</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
207 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
208 </when>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
209 </conditional>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
210 <conditional name="output_hists_cond">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
211 <param name="output_hists" type="select" label="Output histograms?">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
212 <option value="no" selected="true">No</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
213 <option value="yes">Yes</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
214 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
215 <when value="no"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
216 <when value="yes">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
217 <param name="output_hists_select" type="select" multiple="true" optional="false" label="Specify statistics outputs">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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218 <option value="bhist">Base composition histogram by position</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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219 <option value="quhist">Quality histogram by position</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
220 <option value="quchist">Count of bases with each quality value</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
221 <option value="aqhist">Histogram of average read quality</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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222 <option value="bqhist">Quality histogram designed for box plots</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
223 <option value="lhist">Read length histogram</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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224 <option value="phist">Polymer length histogram</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
225 <option value="gchist">Read GC content histogram</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
226 <option value="enthist">Read entropy histogram</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
227 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
228 </when>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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229 </conditional>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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230 </inputs>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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231 <outputs>
1
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iuc
parents: 0
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232 <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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233 <filter>str(outputs_select).find('outu') >= 0</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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234 <filter>'outu' in outputs_select</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
235 </data>
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents: 0
diff changeset
236 <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
237 <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
238 </data>
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents: 0
diff changeset
239 <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Matched)">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
240 <filter>'outm' in outputs_select</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
241 </data>
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents: 0
diff changeset
242 <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Matched)">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
243 <filter>'outm' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
244 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
245 <data name="outputs" format="fastqsanger" label="${tool.name} on ${on_string} (Single)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
246 <filter>'outs' in outputs_select</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
247 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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248 <data name="output_stats" format="tabular" label="${tool.name} on ${on_string} (Detected contaminates stats)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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249 <filter>output_stats_cond['output_stats'] == 'yes' and 'stats' in output_stats_cond['output_stats_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
250 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
251 <data name="output_ref" format="tabular" label="${tool.name} on ${on_string} (Per reference file stats)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
252 <filter>output_stats_cond['output_stats'] == 'yes' and 'ref' in output_stats_cond['output_stats_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
253 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
254 <data name="output_rpkm" format="tabular" label="${tool.name} on ${on_string} (RPKM for each ref seq)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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255 <filter>output_stats_cond['output_stats'] == 'yes' and 'rpkm' in output_stats_cond['output_stats_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
256 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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257 <data name="output_dump" format="fasta" label="${tool.name} on ${on_string} (kmer tables)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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258 <filter>output_stats_cond['output_stats'] == 'yes' and 'dump' in output_stats_cond['output_stats_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
259 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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260 <data name="output_bhist" format="tabular" label="${tool.name} on ${on_string} (Base composition py poition)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
261 <filter>output_hists_cond['output_hists'] == 'yes' and 'bhist' in output_hists_cond['output_hists_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
262 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
263 <data name="output_quhist" format="tabular" label="${tool.name} on ${on_string} (Quality by position)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
264 <filter>output_hists_cond['output_hists'] == 'yes' and 'quhist' in output_hists_cond['output_hists_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
265 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
266 <data name="output_quchist" format="tabular" label="${tool.name} on ${on_string} (Bases w/ each quality value)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
267 <filter>output_hists_cond['output_hists'] == 'yes' and 'quchist' in output_hists_cond['output_hists_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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268 </data>
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269 <data name="output_aqhist" format="tabular" label="${tool.name} on ${on_string} (average read quality)">
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270 <filter>output_hists_cond['output_hists'] == 'yes' and 'aqhist' in output_hists_cond['output_hists_select']</filter>
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271 </data>
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272 <data name="output_bqhist" format="tabular" label="${tool.name} on ${on_string} (Quality for box plots)">
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273 <filter>output_hists_cond['output_hists'] == 'yes' and 'bqhist' in output_hists_cond['output_hists_select']</filter>
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274 </data>
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275 <data name="output_lhist" format="tabular" label="${tool.name} on ${on_string} (Read length)">
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276 <filter>output_hists_cond['output_hists'] == 'yes' and 'lhist' in output_hists_cond['output_hists_select']</filter>
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277 </data>
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278 <data name="output_phist" format="tabular" label="${tool.name} on ${on_string} (Polymer length)">
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279 <filter>output_hists_cond['output_hists'] == 'yes' and 'phist' in output_hists_cond['output_hists_select']</filter>
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280 </data>
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281 <data name="output_gchist" format="tabular" label="${tool.name} on ${on_string} (Read GC content)">
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282 <filter>output_hists_cond['output_hists'] == 'yes' and 'gchist' in output_hists_cond['output_hists_select']</filter>
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283 </data>
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284 <data name="output_enthist" format="tabular" label="${tool.name} on ${on_string} (Read entropy)">
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285 <filter>output_hists_cond['output_hists'] == 'yes' and 'enthist' in output_hists_cond['output_hists_select']</filter>
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286 </data>
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287 </outputs>
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288 <tests>
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289 <!-- Single read -->
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290 <test expect_num_outputs="1">
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291 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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292 <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
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293 <param name="reference_type" value="files"/>
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294 <param name="outputs_select" value="outu"/>
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295 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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296 </test>
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297 <!-- Paired reads in separate datasets -->
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298 <test expect_num_outputs="4">
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299 <param name="input_type" value="pair"/>
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300 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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301 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
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302 <param name="reference_type" value="files"/>
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303 <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
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304 <param name="outputs_select" value="outu"/>
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305 <param name="output_stats" value="yes"/>
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306 <param name="output_stats_select" value="dump"/>
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307 <param name="output_hists" value="yes"/>
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308 <param name="output_hists_select" value="quhist"/>
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309 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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310 <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/>
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311 <output name="output_dump" file="bduk_output_dump1.fasta" ftype="fasta" compare="contains"/>
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312 <output name="output_quhist" file="bduk_output_quhist1.tabular" ftype="tabular"/>
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313 </test>
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314 <!-- Collection of Paired reads -->
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315 <test expect_num_outputs="2">
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316 <param name="input_type" value="paired"/>
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317 <param name="reads_collection">
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318 <collection type="paired">
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319 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
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320 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
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321 </collection>
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322 </param>
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323 <param name="reference_type" value="keywords"/>
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324 <param name="reference" value="adapters,artifacts,phix,lambda,pjet,mtst,kapa"/>
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325 <param name="outputs_select" value="outu"/>
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326 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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327 <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/>
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328 </test>
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329 </tests>
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330 <help>
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331 **What it does**
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332
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333 BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single
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334 high-performance tool. It is capable of quality-trimming and filtering, adapter-trimming, contaminant-filtering via kmer
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335 matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation,
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336 subsampling, quality-score recalibration, kmer cardinality estimation, and various other operations in a single pass.
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337 Specifically, any combination of operations is possible in a single pass with the exception of kmer-based operations (kmer
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338 trimming, kmer masking, or kmer filtering). At most 1 kmer-based operation can be done in a single pass.
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339
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340 **Options**
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341
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342 * **Reference** - if a reference is specified, BBDuk will operate on kmers in one of 4 modes: right-trimming, left-trimming, masking, or filtering. The default is filtering - any read matching a reference kmer will be discarded.
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343
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344 * **Trim reads to remove bases matching reference kmers** - When trimming to the right, once a reference kmer is matched in a read, that kmer and all the bases to the right will be trimmed, leaving only the bases to the left. When trimming to the left, trimming will be done to the left instead.
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345
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346 **Outputs**
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347
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348 * **Unmatched** - All the reads that pass all filtering criteria. Reads will be at least as long as **Minimum read length** after any trimming operations and reads will not match any reference kmer if kmer-filtering is being performed. A read’s average quality will be at least as high as the specified **Minimum average quality**.
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349 * **Matched** - Reads failing any filter criteria (such as matching a reference kmer). By default, if either read in a pair fails, both will be included in *Matched*.
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350 * **Single** - Singleton reads whose mate was trimmed shorter than the value of **Minimum read length**.
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351 </help>
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352 <expand macro="citations"/>
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353 </tool>
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354