Mercurial > repos > iuc > bbtools_bbduk

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
author iuc
date Tue, 27 Aug 2024 10:15:37 +0000
parents d1f62024a08b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
425dab0e057b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 1
diff changeset
1 <tool id="bbtools_bbduk" name="BBTools: BBduk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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"
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5 </macros>
3
425dab0e057b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
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6 <expand macro="edam_ontology"/>
8
d1f62024a08b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit e6a741fc2fe38e91a310e9c29467c814a2d34cac
iuc
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7 <expand macro="bio.tools"/>
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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8 <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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9 <command detect_errors="exit_code"><![CDATA[
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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10 #import os
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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11
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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12 #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"
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13 #set read1 = $input_type_cond.read1
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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14 ## 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"
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15 #set ext = '.fastq'
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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16 #if $read1.ext.endswith('.gz'):
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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17 #set ext = $ext + '.gz'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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18 #end if
1
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19 #set read1_file = 'forward' + $ext
0
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20 ln -s '${read1}' '${read1_file}' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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21 #if str($input_type_cond.input_type) == 'pair':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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22 #set read2 = $input_type_cond.read2
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23 #set read2_file = 'reverse' + $ext
0
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24 ln -s '${read2}' '${read2_file}' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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25 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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26 #else:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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27 #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"
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28 ## bbduk uses the file extension to determine the input format.
7
bf0cb5dd02f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
iuc
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29 #set ext = '.fastq'
0
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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"
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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"
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32 #end if
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bf0cb5dd02f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
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33 #set read1_file = 'forward' + $ext
0
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34 ln -s '${read1}' '${read1_file}' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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35 #set read2 = $input_type_cond.reads_collection['reverse']
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bf0cb5dd02f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
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36 #set read2_file = 'reverse' + $ext
0
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37 ln -s '${read2}' '${read2_file}' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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38 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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39
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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40 #if str($reference_type_cond.reference_type) == 'files':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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41 #set refs = list()
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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42 #for ref in $reference_type_cond.reference:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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43 ## bbduk looks at the file extension.
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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44 #set ref_name = str($os.path.basename($ref.file_name)) + '.fa'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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45 #if $ref.ext.endswith('.gz'):
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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46 gunzip -c '$ref' > '$ref_name' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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47 #else:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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48 ln -s '$ref' '$ref_name' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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49 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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50 $refs.append(str($ref_name))
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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51 #end for
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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52 #set refs = ','.join($refs)
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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53 #else if str($reference_type_cond.reference_type) == 'keywords':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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54 #set refs = str($reference_type_cond.reference)
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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55 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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56
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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57 bbduk.sh
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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58 in='${read1_file}'
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59
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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60 #if str($input_type_cond.input_type) in ['pair', 'paired']:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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61 in2='${read2_file}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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62 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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63 #if str($outputs_select).find('outu') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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64 out='${outputu}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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65 #if str($input_type_cond.input_type) in ['pair', 'paired']:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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66 out2='${outputu2}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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67 #end if
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"
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69 #if str($outputs_select).find('outm') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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70 outm='${outputm}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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71 #if str($input_type_cond.input_type) in ['pair', 'paired']:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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72 outm2='${outputm2}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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73 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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74 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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75 #if str($outputs_select).find('outs') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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76 outs='${outputs}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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77 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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78
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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79 #if str($reference_type_cond.reference_type) != 'no_reference':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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80 ref='$refs'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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81 #if str($reference_type_cond.ktrim_cond.ktrim_select) == 'yes':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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82 ktrim='${reference_type_cond.ktrim_cond.ktrim}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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83 minlength=$reference_type_cond.ktrim_cond.minlength
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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84 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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85 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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86
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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87 k=$advanced_options.k
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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88 rcomp='${advanced_options.rcomp}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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89 maskmiddle='${advanced_options.maskmiddle}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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90 minkmerhits='${advanced_options.minkmerhits}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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91 minkmerfraction=$advanced_options.minkmerfraction
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92 mincovfraction=$advanced_options.mincovfraction
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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93 hammingdistance=$advanced_options.hammingdistance
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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94 qhdist=$advanced_options.qhdist
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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95 editdistance=$advanced_options.editdistance
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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96 forbidn='${advanced_options.forbidn}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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97 trimfailures='${advanced_options.trimfailures}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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98 findbestmatch='${advanced_options.findbestmatch}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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99 skipr1='${advanced_options.skipr1}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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100 skipr2='${advanced_options.skipr2}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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101
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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102 #if str($output_stats_cond.output_stats) == 'yes':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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103 #if str($output_stats_cond.output_stats_select).find('stats') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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104 stats='${output_stats}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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105 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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106 #if str($output_stats_cond.output_stats_select).find('ref') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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107 refstats='${output_ref}'
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108 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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109 #if str($output_stats_cond.output_stats_select).find('rpkm') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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110 rpkm='${output_rpkm}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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111 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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112 #if str($output_stats_cond.output_stats_select).find('dump') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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113 dump='${output_dump}'
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114 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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115 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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116 #if str($output_hists_cond.output_hists) == 'yes':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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117 #if str($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"
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118 bhist='${output_bhist}'
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119 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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120 #if str($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"
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121 qhist='${output_quhist}'
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122 #end if
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123 #if str($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"
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124 qchist='${output_quchist}'
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125 #end if
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126 #if str($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"
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127 aqhist='${output_aqhist}'
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128 #end if
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129 #if str($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"
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130 bqhist='${output_bqhist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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131 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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132 #if str($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"
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133 lhist='${output_lhist}'
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134 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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135 #if str($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"
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136 phist='${output_phist}'
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137 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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138 #if str($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"
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139 gchist='${output_gchist}'
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140 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
141 #if str($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"
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142 enthist='${output_enthist}'
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iuc
parents:
diff changeset
143 #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
144 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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145 t=\${GALAXY_SLOTS:-4}
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iuc
parents:
diff changeset
146 ]]></command>
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147 <inputs>
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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148 <expand macro="input_type_cond"/>
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iuc
parents:
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149 <conditional name="reference_type_cond">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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150 <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:
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151 <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"
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152 <option value="files">files</option>
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153 <option value="keywords">keywords</option>
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iuc
parents:
diff changeset
154 </param>
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iuc
parents:
diff changeset
155 <when value="no_reference"/>
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iuc
parents:
diff changeset
156 <when value="files">
9
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diff changeset
157 <param name="reference" type="data" format="fasta,fasta.gz" optional="false" label="Select one or more fasta file" multiple="true"/>
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
158 <expand macro="ktrim_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
159 </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
160 <when value="keywords">
9
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parents: 8
diff changeset
161 <param name="reference" type="select" optional="false" label="Select one or more keywords" multiple="true">
0
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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162 <option value="adapters">adapters</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
163 <option value="artifacts">artifacts</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
164 <option value="phix">phix</option>
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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165 <option value="lambda">lambda</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
166 <option value="pjet">pjet</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
167 <option value="mtst">mtst</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
168 <option value="kapa">kapa</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
169 </param>
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diff changeset
170 <expand macro="ktrim_cond"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
171 </when>
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diff changeset
172 </conditional>
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parents:
diff changeset
173 <section name="advanced_options" title="Advanced options" expanded="false">
9
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parents: 8
diff changeset
174 <param argument="k" type="integer" min="1" value="27" label="Kmer length used for finding contaminants"/>
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
175 <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"
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parents:
diff changeset
176 <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?"/>
9
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parents: 8
diff changeset
177 <param argument="minkmerhits" type="integer" min="1" value="1" label="Reads need at least this many matching kmers to be considered as matching the reference"/>
7beb76ffbc0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
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diff changeset
178 <param argument="minkmerfraction" type="float" min="0" value="0" label="A read needs at least this fraction of its total kmers to hit a ref in order to be considered a match"/>
7beb76ffbc0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
parents: 8
diff changeset
179 <param argument="mincovfraction" type="float" min="0" value="0" label="A read needs at least this fraction of its total bases to be covered by ref kmers to be considered a match"/>
7beb76ffbc0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
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diff changeset
180 <param argument="hammingdistance" type="integer" min="0" value="0" label="Maximum Hamming distance for ref kmers (subs only)"/>
7beb76ffbc0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
parents: 8
diff changeset
181 <param argument="qhdist" type="integer" min="0" value="0" label="Hamming distance for query kmers"/>
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182 <param argument="editdistance" type="integer" min="0" value="0" label="Maximum edit distance from ref kmers (subs and indels)"/>
0
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183 <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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184 <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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185 <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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diff changeset
186 <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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187 <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"
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188 </section>
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189 <param name="outputs_select" type="select" optional="false" label="Specify outputs" multiple="true">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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190 <option value="outu">Unmatched</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
191 <option value="outm">Matched</option>
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192 <option value="outs">Single</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
193 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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194 <conditional name="output_stats_cond">
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195 <param name="output_stats" type="select" label="Output statistics?">
0
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196 <option value="no" selected="true">No</option>
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197 <option value="yes">Yes</option>
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198 </param>
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199 <when value="no"/>
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200 <when value="yes">
9
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201 <param name="output_stats_select" type="select" optional="false" label="Specify statistics outputs" multiple="true">
0
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202 <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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203 <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"
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204 <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"
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diff changeset
205 <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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diff changeset
206 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
207 </when>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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208 </conditional>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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209 <conditional name="output_hists_cond">
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210 <param name="output_hists" type="select" label="Output histograms?">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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211 <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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212 <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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diff changeset
213 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
214 <when value="no"/>
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215 <when value="yes">
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parents: 8
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216 <param name="output_hists_select" type="select" optional="false" label="Specify statistics outputs" multiple="true">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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217 <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"
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218 <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"
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219 <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"
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220 <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"
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221 <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"
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222 <option value="lhist">Read length histogram</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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223 <option value="phist">Polymer length histogram</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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224 <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"
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225 <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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226 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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227 </when>
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228 </conditional>
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229 </inputs>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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230 <outputs>
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231 <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
9
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232 <filter>str(outputs_select).find('outu') &gt;= 0</filter>
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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233 <filter>'outu' in outputs_select</filter>
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234 </data>
1
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parents: 0
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235 <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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236 <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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237 </data>
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
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parents: 0
diff changeset
238 <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Matched)">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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239 <filter>'outm' in outputs_select</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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240 </data>
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
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parents: 0
diff changeset
241 <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Matched)">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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242 <filter>'outm' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
243 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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244 <data name="outputs" format="fastqsanger" label="${tool.name} on ${on_string} (Single)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
245 <filter>'outs' in outputs_select</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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246 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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247 <data name="output_stats" format="tabular" label="${tool.name} on ${on_string} (Detected contaminates stats)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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248 <filter>output_stats_cond['output_stats'] == 'yes' and 'stats' in output_stats_cond['output_stats_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
249 </data>
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parents:
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250 <data name="output_ref" format="tabular" label="${tool.name} on ${on_string} (Per reference file stats)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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251 <filter>output_stats_cond['output_stats'] == 'yes' and 'ref' in output_stats_cond['output_stats_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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252 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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253 <data name="output_rpkm" format="tabular" label="${tool.name} on ${on_string} (RPKM for each ref seq)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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254 <filter>output_stats_cond['output_stats'] == 'yes' and 'rpkm' in output_stats_cond['output_stats_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
255 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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256 <data name="output_dump" format="fasta" label="${tool.name} on ${on_string} (kmer tables)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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257 <filter>output_stats_cond['output_stats'] == 'yes' and 'dump' in output_stats_cond['output_stats_select']</filter>
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parents:
diff changeset
258 </data>
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259 <data name="output_bhist" format="tabular" label="${tool.name} on ${on_string} (Base composition py poition)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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260 <filter>output_hists_cond['output_hists'] == 'yes' and 'bhist' in output_hists_cond['output_hists_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
261 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
262 <data name="output_quhist" format="tabular" label="${tool.name} on ${on_string} (Quality by position)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
263 <filter>output_hists_cond['output_hists'] == 'yes' and 'quhist' in output_hists_cond['output_hists_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
264 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
265 <data name="output_quchist" format="tabular" label="${tool.name} on ${on_string} (Bases w/ each quality value)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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266 <filter>output_hists_cond['output_hists'] == 'yes' and 'quchist' in output_hists_cond['output_hists_select']</filter>
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267 </data>
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268 <data name="output_aqhist" format="tabular" label="${tool.name} on ${on_string} (average read quality)">
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269 <filter>output_hists_cond['output_hists'] == 'yes' and 'aqhist' in output_hists_cond['output_hists_select']</filter>
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270 </data>
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271 <data name="output_bqhist" format="tabular" label="${tool.name} on ${on_string} (Quality for box plots)">
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272 <filter>output_hists_cond['output_hists'] == 'yes' and 'bqhist' in output_hists_cond['output_hists_select']</filter>
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273 </data>
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274 <data name="output_lhist" format="tabular" label="${tool.name} on ${on_string} (Read length)">
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275 <filter>output_hists_cond['output_hists'] == 'yes' and 'lhist' in output_hists_cond['output_hists_select']</filter>
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276 </data>
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277 <data name="output_phist" format="tabular" label="${tool.name} on ${on_string} (Polymer length)">
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278 <filter>output_hists_cond['output_hists'] == 'yes' and 'phist' in output_hists_cond['output_hists_select']</filter>
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279 </data>
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280 <data name="output_gchist" format="tabular" label="${tool.name} on ${on_string} (Read GC content)">
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281 <filter>output_hists_cond['output_hists'] == 'yes' and 'gchist' in output_hists_cond['output_hists_select']</filter>
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282 </data>
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283 <data name="output_enthist" format="tabular" label="${tool.name} on ${on_string} (Read entropy)">
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284 <filter>output_hists_cond['output_hists'] == 'yes' and 'enthist' in output_hists_cond['output_hists_select']</filter>
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285 </data>
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286 </outputs>
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287 <tests>
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288 <!-- Single read -->
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289 <test expect_num_outputs="1">
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290 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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291 <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
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292 <param name="reference_type" value="files"/>
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293 <param name="outputs_select" value="outu"/>
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294 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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295 </test>
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296 <!-- Paired reads in separate datasets -->
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297 <test expect_num_outputs="4">
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298 <param name="input_type" value="pair"/>
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299 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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300 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
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301 <param name="reference_type" value="files"/>
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302 <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
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303 <param name="outputs_select" value="outu"/>
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304 <param name="output_stats" value="yes"/>
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305 <param name="output_stats_select" value="dump"/>
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306 <param name="output_hists" value="yes"/>
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307 <param name="output_hists_select" value="quhist"/>
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308 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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309 <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/>
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310 <output name="output_dump" file="bduk_output_dump1.fasta" ftype="fasta" compare="contains"/>
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311 <output name="output_quhist" file="bduk_output_quhist1.tabular" ftype="tabular"/>
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312 </test>
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313 <!-- Collection of Paired reads -->
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314 <test expect_num_outputs="2">
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315 <param name="input_type" value="paired"/>
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316 <param name="reads_collection">
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317 <collection type="paired">
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318 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
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319 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
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320 </collection>
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321 </param>
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322 <param name="reference_type" value="keywords"/>
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323 <param name="reference" value="adapters,artifacts,phix,lambda,pjet,mtst,kapa"/>
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324 <param name="outputs_select" value="outu"/>
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325 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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326 <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/>
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327 </test>
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328 </tests>
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329 <help>
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330 **What it does**
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331
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332 BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single
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333 high-performance tool. It is capable of quality-trimming and filtering, adapter-trimming, contaminant-filtering via kmer
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334 matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation,
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335 subsampling, quality-score recalibration, kmer cardinality estimation, and various other operations in a single pass.
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336 Specifically, any combination of operations is possible in a single pass with the exception of kmer-based operations (kmer
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337 trimming, kmer masking, or kmer filtering). At most 1 kmer-based operation can be done in a single pass.
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338
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339 **Options**
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340
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341 * **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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342
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343 * **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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344
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345 **Outputs**
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346
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347 * **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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348 * **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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349 * **Single** - Singleton reads whose mate was trimmed shorter than the value of **Minimum read length**.
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350 </help>
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351 <expand macro="citations"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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352 </tool>