Mercurial > repos > iuc > bbtools_bbduk

annotate bbduk.xml @ 4:159b04e36791 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
author iuc
date Tue, 30 May 2023 09:02:48 +0000
parents 425dab0e057b
children bf0cb5dd02f2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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"
iuc
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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
parents: 1
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6 <expand macro="edam_ontology"/>
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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7 <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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8 <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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9 #import os
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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10 #import re
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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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18 #end if
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
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19 #set read1_file = 'forward' + $ext
0
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iuc
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20 ln -s '${read1}' '${read1_file}' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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21 #if str($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
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
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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 = $input_type_cond.reads_collection['forward']
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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28 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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29 ## 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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30 #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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31 #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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32 #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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33 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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34 #set read1_file = $read1_identifier + $ext
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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35 ln -s '${read1}' '${read1_file}' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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36 #set read2 = $input_type_cond.reads_collection['reverse']
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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37 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name))
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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38 #set read2_file = $read2_identifier + $ext
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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39 ln -s '${read2}' '${read2_file}' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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40 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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41
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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42 #if str($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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43 #set refs = list()
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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44 #for ref in $reference_type_cond.reference:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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45 ## bbduk looks at the file extension.
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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46 #set ref_name = str($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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47 #if $ref.ext.endswith('.gz'):
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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48 gunzip -c '$ref' > '$ref_name' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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49 #else:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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50 ln -s '$ref' '$ref_name' &&
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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51 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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52 $refs.append(str($ref_name))
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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53 #end for
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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54 #set refs = ','.join($refs)
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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55 #else if str($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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56 #set refs = str($reference_type_cond.reference)
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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57 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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58
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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59 bbduk.sh
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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60 in='${read1_file}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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61
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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62 #if str($input_type_cond.input_type) in ['pair', 'paired']:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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63 in2='${read2_file}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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64 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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65 #if str($outputs_select).find('outu') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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66 out='${outputu}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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67 #if str($input_type_cond.input_type) in ['pair', 'paired']:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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68 out2='${outputu2}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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69 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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70 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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71 #if str($outputs_select).find('outm') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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72 outm='${outputm}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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73 #if str($input_type_cond.input_type) in ['pair', 'paired']:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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74 outm2='${outputm2}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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75 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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76 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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77 #if str($outputs_select).find('outs') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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78 outs='${outputs}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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79 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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80
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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81 #if str($reference_type_cond.reference_type) != 'no_reference':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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82 ref='$refs'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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83 #if str($reference_type_cond.ktrim_cond.ktrim_select) == 'yes':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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84 ktrim='${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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85 minlength=$reference_type_cond.ktrim_cond.minlength
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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86 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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87 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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88
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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89 k=$advanced_options.k
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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90 rcomp='${advanced_options.rcomp}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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91 maskmiddle='${advanced_options.maskmiddle}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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92 minkmerhits='${advanced_options.minkmerhits}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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93 minkmerfraction=$advanced_options.minkmerfraction
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
94 mincovfraction=$advanced_options.mincovfraction
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
95 hammingdistance=$advanced_options.hammingdistance
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
96 qhdist=$advanced_options.qhdist
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
97 editdistance=$advanced_options.editdistance
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
98 forbidn='${advanced_options.forbidn}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
99 trimfailures='${advanced_options.trimfailures}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
100 findbestmatch='${advanced_options.findbestmatch}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
101 skipr1='${advanced_options.skipr1}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
102 skipr2='${advanced_options.skipr2}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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103
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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104 #if str($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
105 #if str($output_stats_cond.output_stats_select).find('stats') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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106 stats='${output_stats}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
107 #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
108 #if str($output_stats_cond.output_stats_select).find('ref') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
109 refstats='${output_ref}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
110 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
111 #if str($output_stats_cond.output_stats_select).find('rpkm') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
112 rpkm='${output_rpkm}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
113 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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114 #if str($output_stats_cond.output_stats_select).find('dump') >= 0:
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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115 dump='${output_dump}'
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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116 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
117 #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
118 #if str($output_hists_cond.output_hists) == 'yes':
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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119 #if str($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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120 bhist='${output_bhist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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121 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
122 #if str($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
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diff changeset
123 qhist='${output_quhist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
124 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
125 #if str($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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126 qchist='${output_quchist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
127 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
128 #if str($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
129 aqhist='${output_aqhist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
130 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
131 #if str($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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132 bqhist='${output_bqhist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
133 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
134 #if str($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
135 lhist='${output_lhist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
136 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
137 #if str($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
138 phist='${output_phist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
139 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
140 #if str($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
141 gchist='${output_gchist}'
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
142 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
143 #if str($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
144 enthist='${output_enthist}'
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 #end if
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
147 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
148 ]]></command>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
149 <inputs>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
150 <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
151 <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
152 <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
153 <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
154 <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
155 <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
156 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
157 <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
158 <when value="files">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
159 <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
160 <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
161 </when>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
162 <when value="keywords">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
163 <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
164 <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
165 <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
166 <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
167 <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
168 <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
169 <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
170 <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
171 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
172 <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
173 </when>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
174 </conditional>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
175 <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
176 <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
177 <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
178 <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
179 <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
180 <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
181 <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
182 <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"
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183 <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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parents:
diff changeset
184 <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"
iuc
parents:
diff changeset
185 <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"
iuc
parents:
diff changeset
186 <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"
iuc
parents:
diff changeset
187 <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"
iuc
parents:
diff changeset
188 <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"
iuc
parents:
diff changeset
189 <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
190 </section>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
191 <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"
iuc
parents:
diff changeset
192 <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
193 <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
194 <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
195 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
196 <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
197 <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"
iuc
parents:
diff changeset
198 <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
199 <option value="yes">Yes</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
200 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
201 <when value="no"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
202 <when value="yes">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
203 <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
204 <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"
iuc
parents:
diff changeset
205 <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
206 <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
207 <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
208 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
209 </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
210 </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
211 <conditional name="output_hists_cond">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
212 <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"
iuc
parents:
diff changeset
213 <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
214 <option value="yes">Yes</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
215 </param>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
216 <when value="no"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
217 <when value="yes">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
218 <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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219 <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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220 <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
221 <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
222 <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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223 <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
224 <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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225 <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
226 <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
227 <option value="enthist">Read entropy histogram</option>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
228 </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
229 </when>
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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230 </conditional>
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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231 </inputs>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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232 <outputs>
1
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iuc
parents: 0
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233 <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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234 <filter>str(outputs_select).find('outu') >= 0</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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235 <filter>'outu' in outputs_select</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
236 </data>
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents: 0
diff changeset
237 <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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diff changeset
238 <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
239 </data>
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents: 0
diff changeset
240 <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Matched)">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
241 <filter>'outm' in outputs_select</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
242 </data>
1
60dd895841cd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents: 0
diff changeset
243 <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Matched)">
0
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
244 <filter>'outm' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
245 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
246 <data name="outputs" format="fastqsanger" label="${tool.name} on ${on_string} (Single)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
247 <filter>'outs' in outputs_select</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
248 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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249 <data name="output_stats" format="tabular" label="${tool.name} on ${on_string} (Detected contaminates stats)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
250 <filter>output_stats_cond['output_stats'] == 'yes' and 'stats' in output_stats_cond['output_stats_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
251 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
252 <data name="output_ref" format="tabular" label="${tool.name} on ${on_string} (Per reference file stats)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
253 <filter>output_stats_cond['output_stats'] == 'yes' and 'ref' in output_stats_cond['output_stats_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
254 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
255 <data name="output_rpkm" format="tabular" label="${tool.name} on ${on_string} (RPKM for each ref seq)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
256 <filter>output_stats_cond['output_stats'] == 'yes' and 'rpkm' in output_stats_cond['output_stats_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
257 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
258 <data name="output_dump" format="fasta" label="${tool.name} on ${on_string} (kmer tables)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
259 <filter>output_stats_cond['output_stats'] == 'yes' and 'dump' in output_stats_cond['output_stats_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
260 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
261 <data name="output_bhist" format="tabular" label="${tool.name} on ${on_string} (Base composition py poition)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
262 <filter>output_hists_cond['output_hists'] == 'yes' and 'bhist' in output_hists_cond['output_hists_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
263 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
264 <data name="output_quhist" format="tabular" label="${tool.name} on ${on_string} (Quality by position)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
265 <filter>output_hists_cond['output_hists'] == 'yes' and 'quhist' in output_hists_cond['output_hists_select']</filter>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
266 </data>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
267 <data name="output_quchist" format="tabular" label="${tool.name} on ${on_string} (Bases w/ each quality value)">
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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268 <filter>output_hists_cond['output_hists'] == 'yes' and 'quchist' in output_hists_cond['output_hists_select']</filter>
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269 </data>
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270 <data name="output_aqhist" format="tabular" label="${tool.name} on ${on_string} (average read quality)">
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271 <filter>output_hists_cond['output_hists'] == 'yes' and 'aqhist' in output_hists_cond['output_hists_select']</filter>
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272 </data>
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273 <data name="output_bqhist" format="tabular" label="${tool.name} on ${on_string} (Quality for box plots)">
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274 <filter>output_hists_cond['output_hists'] == 'yes' and 'bqhist' in output_hists_cond['output_hists_select']</filter>
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275 </data>
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276 <data name="output_lhist" format="tabular" label="${tool.name} on ${on_string} (Read length)">
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277 <filter>output_hists_cond['output_hists'] == 'yes' and 'lhist' in output_hists_cond['output_hists_select']</filter>
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278 </data>
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279 <data name="output_phist" format="tabular" label="${tool.name} on ${on_string} (Polymer length)">
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280 <filter>output_hists_cond['output_hists'] == 'yes' and 'phist' in output_hists_cond['output_hists_select']</filter>
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281 </data>
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282 <data name="output_gchist" format="tabular" label="${tool.name} on ${on_string} (Read GC content)">
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283 <filter>output_hists_cond['output_hists'] == 'yes' and 'gchist' in output_hists_cond['output_hists_select']</filter>
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284 </data>
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285 <data name="output_enthist" format="tabular" label="${tool.name} on ${on_string} (Read entropy)">
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286 <filter>output_hists_cond['output_hists'] == 'yes' and 'enthist' in output_hists_cond['output_hists_select']</filter>
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287 </data>
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288 </outputs>
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289 <tests>
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290 <!-- Single read -->
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291 <test expect_num_outputs="1">
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292 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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293 <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
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294 <param name="reference_type" value="files"/>
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295 <param name="outputs_select" value="outu"/>
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296 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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297 </test>
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298 <!-- Paired reads in separate datasets -->
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299 <test expect_num_outputs="4">
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300 <param name="input_type" value="pair"/>
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301 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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302 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
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303 <param name="reference_type" value="files"/>
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304 <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
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305 <param name="outputs_select" value="outu"/>
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306 <param name="output_stats" value="yes"/>
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307 <param name="output_stats_select" value="dump"/>
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308 <param name="output_hists" value="yes"/>
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309 <param name="output_hists_select" value="quhist"/>
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310 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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311 <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/>
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312 <output name="output_dump" file="bduk_output_dump1.fasta" ftype="fasta" compare="contains"/>
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313 <output name="output_quhist" file="bduk_output_quhist1.tabular" ftype="tabular"/>
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314 </test>
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315 <!-- Collection of Paired reads -->
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316 <test expect_num_outputs="2">
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317 <param name="input_type" value="paired"/>
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318 <param name="reads_collection">
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319 <collection type="paired">
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320 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
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321 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
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322 </collection>
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323 </param>
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324 <param name="reference_type" value="keywords"/>
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325 <param name="reference" value="adapters,artifacts,phix,lambda,pjet,mtst,kapa"/>
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326 <param name="outputs_select" value="outu"/>
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327 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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328 <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/>
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329 </test>
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330 </tests>
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331 <help>
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332 **What it does**
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333
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334 BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single
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335 high-performance tool. It is capable of quality-trimming and filtering, adapter-trimming, contaminant-filtering via kmer
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336 matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation,
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337 subsampling, quality-score recalibration, kmer cardinality estimation, and various other operations in a single pass.
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338 Specifically, any combination of operations is possible in a single pass with the exception of kmer-based operations (kmer
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339 trimming, kmer masking, or kmer filtering). At most 1 kmer-based operation can be done in a single pass.
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340
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341 **Options**
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342
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343 * **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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344
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345 * **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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346
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347 **Outputs**
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348
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349 * **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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350 * **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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351 * **Single** - Singleton reads whose mate was trimmed shorter than the value of **Minimum read length**.
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352 </help>
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353 <expand macro="citations"/>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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354 </tool>
204a131e47db "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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355