Mercurial > repos > iuc > bbtools_bbmap

annotate bbmap.xml @ 5:81cbb6a4c1ca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 08ae36bc77634de84d9613a71552a3e64a71a3f7"
author iuc
date Thu, 17 Mar 2022 07:44:30 +0000
parents 6d44c9f1a42b
children 858a65b52cf9
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rev   line source
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81cbb6a4c1ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 08ae36bc77634de84d9613a71552a3e64a71a3f7"
iuc
parents: 4
diff changeset
1 <tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy4" profile="@PROFILE@">
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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2 <description>short-read aligner</description>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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3 <macros>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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4 <import>macros.xml</import>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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5 </macros>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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6 <expand macro="requirements"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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7 <command detect_errors="exit_code"><![CDATA[
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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8 #import os
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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9 #import re
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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10
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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11 #if str($ref_source_cond.ref_source) == 'cached'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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12 #set ref = str($ref_source_cond.reference.fields.path)
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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13 #else:
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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14 #set ref = $ref_source_cond.reference
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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15 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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16
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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17 #if str($input_type_cond.input_type) in ['single', 'pair']:
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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18 #set read1 = $input_type_cond.read1
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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19 ## bbmap uses the file extension to determine the input format.
3
8157a81f511c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
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20 #set ext = '.fastq'
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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21 #if $read1.ext.endswith('.gz'):
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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22 #set ext = $ext + '.gz'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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23 #end if
3
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iuc
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24 #set read1_file = 'forward' + $ext
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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25 ln -s '${read1}' '${read1_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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26 #if str($input_type_cond.input_type) == 'pair':
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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27 #set read2 = $input_type_cond.read2
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iuc
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28 #set read2_file = 'reverse' + $ext
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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29 ln -s '${read2}' '${read2_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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30 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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31 #else:
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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32 #set read1 = $input_type_cond.reads_collection['forward']
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81cbb6a4c1ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 08ae36bc77634de84d9613a71552a3e64a71a3f7"
iuc
parents: 4
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33 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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34 ## bbmap uses the file extension to determine the input format.
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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35 #set ext = $read1_identifier + '.fastq'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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36 #if $read1.ext.endswith('.gz'):
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
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37 #set ext = $ext + '.gz'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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38 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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39 #set read1_file = $read1_identifier + $ext
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
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40 ln -s '${read1}' '${read1_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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41 #set read2 = $input_type_cond.reads_collection['reverse']
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81cbb6a4c1ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 08ae36bc77634de84d9613a71552a3e64a71a3f7"
iuc
parents: 4
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42 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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43 #set read2_file = $read2_identifier + $ext
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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44 ln -s '${read2}' '${read2_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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45 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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46
4
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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47 bbmap.sh
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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48
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
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49 #### Indexing Parameters
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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50 nodisk=f
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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51 ref='${ref}'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
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52 k=13
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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53 usemodulo=f
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
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54 rebuild=f
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
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55
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
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56 #### Input Parameters
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
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57 #if str($input_type_cond.input_type) == 'single':
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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58 in='${read1_file}'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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59 #else:
4
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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60 in='${read1_file}' in2='${read2_file}'
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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61 #end if
4
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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62 fastareadlen=500
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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63 unpigz=f
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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64 touppercase=t
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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65
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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66 #### Sampling Parameters
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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67 reads=-1
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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68 samplerate=1
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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69 skipreads=0
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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70
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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71 #### Mapping Parameters
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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72 maxindel=$mapping_options.maxindel
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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73 strictmaxindel='$mapping_options.strictmaxindel'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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74 tipsearch=$mapping_options.tipsearch
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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75 minid=$mapping_options.minid
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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76 minhits=$mapping_options.minhits
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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77 local='$mapping_options.local'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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78 perfectmode='$mapping_options.perfectmode'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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79 semiperfectmode='$mapping_options.semiperfectmode'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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80 threads=\${GALAXY_SLOTS:-4}
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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81 ambiguous='$mapping_options.ambiguous'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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82 samestrandpairs='$mapping_options.samestrandpairs'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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83 requirecorrectstrand='$mapping_options.requirecorrectstrand'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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84 killbadpairs='$mapping_options.killbadpairs'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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85 pairedonly='$mapping_options.pairedonly'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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86 rcomp='$mapping_options.rcomp'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
87 rcompmate='$mapping_options.rcompmate'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
88 pairlen=$mapping_options.pairlen
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
89 rescuedist=$mapping_options.rescuedist
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
90 rescuemismatches=$mapping_options.rescuemismatches
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
91 averagepairdist=$mapping_options.averagepairdist
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
92 deterministic='$mapping_options.deterministic'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
93 bandwidthratio='$mapping_options.bandwidthratio'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
94 bandwidth='$mapping_options.bandwidth'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
95 usejni='f'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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96 maxsites2=$mapping_options.maxsites2
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
97 ignorefrequentkmers='$mapping_options.ignorefrequentkmers'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
98 excludefraction=$mapping_options.excludefraction
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
99 greedy='$mapping_options.greedy'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
100 kfilter=$mapping_options.kfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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101
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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102 #### Quality and Trimming Parameters
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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103 qin='auto'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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104 qout='auto'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
105 qtrim='$qt_options.qtrim'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
106 untrim='$qt_options.untrim'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
107 trimq=$qt_options.trimq
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
108 mintrimlength=$qt_options.mintrimlength
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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109 fakefastaquality=$qt_options.fakefastaquality
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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diff changeset
110 ignorebadquality='$qt_options.ignorebadquality'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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111 usequality='$qt_options.usequality'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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112 minaveragequality=$qt_options.minaveragequality
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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113 maqb=$qt_options.maqb
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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114
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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115 #### Post-Filtering options
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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116 idfilter=$pf_options.idfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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117 subfilter=$pf_options.subfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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118 insfilter=$pf_options.insfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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119 delfilter=$pf_options.delfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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120 indelfilter=$pf_options.indelfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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121 editfilter=$pf_options.editfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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122 inslenfilter=$pf_options.inslenfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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123 dellenfilter=$pf_options.dellenfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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124 nfilter=$pf_options.nfilter
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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125
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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126 #### Output parameters
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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127 secondary='$output_options.secondary'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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128 maxsites=$output_options.maxsites
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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129 sssr=$output_options.sssr
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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130 ssao='$output_options.ssao'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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131 quickmatch='$output_options.quickmatch'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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132 trimreaddescriptions='$output_options.trimreaddescriptions'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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133 machineout='$output_options.machineout'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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134 printunmappedcount='$output_options.printunmappedcount'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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135 renamebyinsert='$output_options.renamebyinsert'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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136 #if str($output_options.output_sort) == 'coordinate':
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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137 out='all_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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138 outu='unmapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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139 outm='mapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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140 && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_all_reads' 'all_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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141 && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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142 && samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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143 #elif str($output_options.output_sort) == 'name':
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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144 out='all_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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145 outu='unmapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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146 outm='mapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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147 && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_all_reads' 'all_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
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148 && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_unmapped_reads' 'unmapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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149 && samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output_mapped_reads' 'mapped_reads.bam'
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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150 #else:
4
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151 out='all_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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152 outu='unmapped_reads.bam'
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153 outm='mapped_reads.bam'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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154 && mv 'all_reads.bam' '$output_all_reads'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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155 && mv 'unmapped_reads.bam' '$output_unmapped_reads'
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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156 && mv 'mapped_reads.bam' '$output_mapped_reads'
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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157 #end if
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158 ]]></command>
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159 <inputs>
2
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160 <expand macro="input_type_cond"/>
0
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161 <expand macro="reference_source_cond"/>
4
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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162 <section name="mapping_options" title="Mapping options">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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163 <param argument="maxindel" type="integer" value="16000" label="Maximum indel length" help="Don't look for indels longer than this (lower is faster)"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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164 <param argument="strictmaxindel" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Do not allow indels longer than the specified maximum indel length?" help="By default these are not sought, but may be found anyway"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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165 <param argument="tipsearch" type="integer" value="100" label="Look this far for read-end deletions with anchors shorter than K using brute force"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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166 <param argument="minid" type="float" value="0.76" label="Approximate minimum alignment identity to look for" help="Higher is faster and less sensitive"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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167 <param argument="minhits" type="integer" value="1" label="Minimum number of seed hits required for candidate sites" help="Higher is faster"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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168 <param argument="local" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Use local (rather than global) alignments?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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169 <param argument="perfectmode" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Allow only perfect mappings?"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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170 <param argument="semiperfectmode" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Allow only perfect and semiperfect (perfect except for N's in the reference) mappings?"/>
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171 <param name="ambiguous" type="select" label="Specify behavior on ambiguously-mapped reads with multiple top-scoring mapping locations">
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172 <option value="best" selected="true">Use the first best site</option>
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173 <option value="toss">Consider unmapped</option>
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174 <option value="random">Select one top-scoring site randomly</option>
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175 <option value="all">Retain all top-scoring sites</option>
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176 </param>
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177 <param argument="samestrandpairs" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Map paired reads to the same strand?" help="No value will map to opposite strands"/>
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178 <param argument="requirecorrectstrand" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Forbid pairing of reads without correct strand orientation?" help="Select No for long-mate-pair libraries"/>
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179 <param argument="killbadpairs" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Mark the read with the lower mapping quality as unmapped if a read pair is mapped with an inappropriate insert size or orientation?"/>
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180 <param argument="pairedonly" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Treat unpaired reads as unmapped?"/>
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181 <param argument="rcomp" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Reverse complement both reads prior to mapping (for LMP outward-facing libraries)?"/>
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182 <param argument="rcompmate" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Reverse complement read2 prior to mapping?"/>
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183 <param argument="pairlen" type="integer" value="32000" label="Maximum allowed distance between paired reads"/>
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184 <param argument="rescuedist" type="integer" value="1200" label="Maximum average insert size for trying to rescue paired reads" help="Lower is faster"/>
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185 <param argument="rescuemismatches" type="integer" value="32" label="Maximum mismatches allowed in a rescued read" help="Lower is faster"/>
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186 <param argument="averagepairdist" type="integer" value="100" label="Initial average distance between paired reads" help="Varies dynamically; does not need to be specified"/>
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187 <param argument="deterministic" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Run in deterministic mode?" help="BBMap is deterministic without this flag if using single-ended reads?"/>
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188 <param argument="bandwidthratio" type="integer" value="0" label="Restrict alignment band to this fraction of read length" help="Zero value ignores"/>
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189 <param argument="bandwidth" type="integer" value="0" label="Set the bandwidth directly to this fraction of read length" help="Faster but less accurate"/>
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190 <param argument="maxsites2" type="integer" value="800" label="Maximum number of alignments per read to output"/>
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191 <param argument="ignorefrequentkmers" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Discard low-information kmers that occur often?"/>
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192 <param argument="excludefraction" type="float" value="0.03" label="Fraction of kmers to ignore" help="For example, 0.03 will ignore the most common 3% of kmers"/>
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193 <param argument="greedy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use a greedy algorithm to discard the least-useful kmers on a per-read basis?"/>
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194 <param argument="kfilter" type="integer" value="0" label="Potential mapping sites must have at least this many consecutive exact matches" help="Zero value ignores"/>
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195 </section>
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196 <section name="qt_options" title="Quality and trimming options">
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197 <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
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198 <option value="f" selected="true">No trimming</option>
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199 <option value="l">Trim left</option>
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200 <option value="r">Trim right</option>
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201 <option value="lr">Trim both</option>
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202 </param>
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203 <param argument="untrim" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Undo trimming after mapping?" help="Untrimmed bases will be soft-clipped in cigar strings"/>
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204 <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
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205 <param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
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206 <param argument="fakefastaquality" type="integer" value="-1" max="50" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/>
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207 <param argument="ignorebadquality" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Keep going, rather than crashing, if a read has out-of-range quality values?"/>
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208 <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
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209 <param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/>
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210 <param argument="maqb" type="integer" value="0" label="Calculate maq from this many initial bases" help="Zero value ignores"/>
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211 </section>
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212 <section name="output_options" title="Output options">
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213 <param argument="secondary" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Output secondary alignments?"/>
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214 <param argument="maxsites" type="integer" value="5" label="Maximum number of total alignments to output per read" help="Relevant only when outputting secondary alignments"/>
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215 <param argument="sssr" type="float" value="0.95" label="Output only secondary alignments with score of at least this fraction of primary"/>
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216 <param argument="ssao" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Only output secondary alignments for ambiguously-mapped reads?"/>
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217 <param argument="quickmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Generate cigar strings more quickly?"/>
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218 <param argument="trimreaddescriptions" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Truncate read and ref names at the first whitespace, assuming that the remainder is a comment or description?"/>
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219 <param argument="machineout" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Output statistics in machine-friendly (key=value) format?"/>
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220 <param argument="printunmappedcount" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Output the total number of unmapped reads and bases?" help="If input is paired, the number will be of pairs for which both reads are unmapped"/>
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221 <param argument="renamebyinsert" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Rename reads based on their mapped insert size?"/>
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222 <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can significantly extend the run time of the tool (it runs using a single thread)">
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223 <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
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224 <option value="name">Sort by read names</option>
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225 <option value="unsorted">Not sorted (sorted as input)</option>
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226 </param>
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227 </section>
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228 <section name="pf_options" title="Post-filtering options">
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229 <param argument="idfilter" type="integer" value="0" min="0" max="1" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/>
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230 <param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/>
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231 <param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/>
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232 <param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/>
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233 <param argument="indelfilter" type="integer" value="-1" label="Ban alignments with more than this many indels" help="Negative value ignores"/>
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234 <param argument="editfilter" type="integer" value="-1" label="Ban alignments with more than this many edits" help="Negative value ignores"/>
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235 <param argument="inslenfilter" type="integer" value="-1" label="Ban alignments with an insertion longer than this" help="Negative value ignores"/>
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236 <param argument="dellenfilter" type="integer" value="-1" label="Ban alignments with a deletion longer than this" help="Negative value ignores"/>
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237 <param argument="nfilter" type="integer" value="-1" label="Ban alignments with more than this many ns (includes nocall, noref, and off scaffold ends)" help="Negative value ignores"/>
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238 </section>
0
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239 </inputs>
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240 <outputs>
4
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241 <data format="bam" name="output_all_reads" label="${tool.name} on ${on_string} (all reads)">
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242 <expand macro="dbKeyActionsBBMap"/>
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diff changeset
243 <change_format>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
244 <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
245 <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
246 </change_format>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
247 </data>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
248 <data format="bam" name="output_unmapped_reads" label="${tool.name} on ${on_string} (unmapped reads)">
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
249 <expand macro="dbKeyActionsBBMap"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
250 <change_format>
4
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
251 <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
252 <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
253 </change_format>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
254 </data>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
255 <data format="bam" name="output_mapped_reads" label="${tool.name} on ${on_string} (mapped reads)">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
256 <expand macro="dbKeyActionsBBMap"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
257 <change_format>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
258 <when input="output_options.output_sort" value="name" format="qname_sorted.bam"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
259 <when input="output_options.output_sort" value="unsorted" format="qname_input_sorted.bam"/>
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
260 </change_format>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
261 </data>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
262 </outputs>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
263 <tests>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
264 <!-- Single file, cached reference, output coordinate sorted -->
4
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
265 <test expect_num_outputs="3">
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
266 <param name="input_type" value="single"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
267 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
4
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
268 <param name="output_sort" value="coordinate"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
269 <output name="output_all_reads" ftype="bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
270 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
271 <assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
272 <has_size value="9433" delta="300"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
273 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
274 </output>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
275 <output name="output_unmapped_reads" ftype="bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
276 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
277 <assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
278 <has_size value="9432" delta="300"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
279 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
280 </output>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
281 <output name="output_mapped_reads" ftype="bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
282 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
283 <assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
284 <has_size value="938" delta="100"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
285 </assert_contents>
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
286 </output>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
287 </test>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
288 <!-- Paired reads in separate datasets, cached reference, output name sorted -->
4
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
289 <test expect_num_outputs="3">
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
290 <param name="input_type" value="pair"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
291 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
292 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
293 <param name="output_sort" value="name"/>
4
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
294 <output name="output_all_reads" ftype="qname_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
295 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
296 <assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
297 <has_size value="17103" delta="600"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
298 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
299 </output>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
300 <output name="output_unmapped_reads" ftype="qname_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
301 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
302 <assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
303 <has_size value="17105" delta="600"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
304 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
305 </output>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
306 <output name="output_mapped_reads" ftype="qname_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
307 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
308 <assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
309 <has_size value="967" delta="100"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
310 </assert_contents>
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
311 </output>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
312 </test>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
313 <!-- Collection of Paired reads, history reference, output unsorted -->
4
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
314 <test expect_num_outputs="3">
0
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
315 <param name="input_type" value="paired"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
316 <param name="reads_collection">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
317 <collection type="paired">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
318 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
319 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
320 </collection>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
321 </param>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
322 <param name="ref_source" value="history"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
323 <param name="reference" value="NC_002945v4.fasta" dbkey="89" ftype="fasta"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
iuc
parents:
diff changeset
324 <param name="output_sort" value="unsorted"/>
4
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
325 <output name="output_all_reads" ftype="qname_input_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
326 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
327 <assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
328 <has_size value="17059" delta="600"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
diff changeset
329 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
iuc
parents: 3
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330 </output>
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331 <output name="output_unmapped_reads" ftype="qname_input_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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332 <metadata name="dbkey" value="89"/>
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333 <assert_contents>
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334 <has_size value="17059" delta="600"/>
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335 </assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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336 </output>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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337 <output name="output_mapped_reads" ftype="qname_input_sorted.bam">
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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338 <metadata name="dbkey" value="89"/>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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339 <assert_contents>
6d44c9f1a42b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1800b13dcea155e96558f6b80989cf719071e300"
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340 <has_size value="906" delta="100"/>
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341 </assert_contents>
0
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342 </output>
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343 </test>
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344 </tests>
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345 <help>
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346 **What it does**
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347
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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348 BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. It is fast and extremely accurate, particularly
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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349 with highly mutated genomes or reads with long indels, even whole-gene deletions over 100kbp long. It has no upper limit
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350 to genome size or number of contigs and has been successfully used for mapping to an 85 gigabase soil metagenome with over
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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351 200 million contigs. the indexing phase is very fast compared to other aligners.
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352
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353 BBMap can output many different statistics files; an empirical read quality histogram, insert-size distribution, and genome
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354 coverage with or without generating a sam file. It is useful in quality control of libraries and sequencing runs or
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355 evaluating new sequencing platforms.
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356
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357 **Options**
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358
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359 *Bam sorting mode* - the generated bam files can be sorted according to three criteria: coordinates, names and input order.
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360
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361 * Sort by chromosomal coordinates - the file is sorted by coordinates (i.e., the reads from the beginning of the first
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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362 chromosome are first in the file.
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363 * Sort by read names - the file is sorted by the reference ID (i.e., the QNAME field).
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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364 * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file.
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365
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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366 </help>
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367 <expand macro="citations"/>
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368 </tool>
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369