annotate bbmap.xml @ 0:07a6e49c7d74 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
author iuc
date Mon, 04 Oct 2021 12:14:47 +0000
parents
children e0ca2ec4f5d9
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07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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1 <tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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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"
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3 <macros>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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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"
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5 </macros>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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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"
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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"
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8 #import os
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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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"
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11 #if str($ref_source_cond.ref_source) == 'cached'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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12 #set ref = str($ref_source_cond.reference.fields.path)
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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13 #else:
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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14 #set ref = $ref_source_cond.reference
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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15 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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16
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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17 #if str($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"
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18 #set read1 = $input_type_cond.read1
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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19 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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20 ## 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"
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21 #set ext = $read1_identifier + '.fastq'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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22 #if $read1.ext.endswith('.gz'):
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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23 #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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24 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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25 #set read1_file = $read1_identifier + $ext
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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26 ln -s '${read1}' '${read1_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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27 #if str($input_type_cond.input_type) == 'pair':
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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28 #set read2 = $input_type_cond.read2
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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29 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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30 #set read2_file = $read2_identifier + $ext
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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31 ln -s '${read2}' '${read2_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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32 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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33 #else:
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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34 #set read1 = $input_type_cond.reads_collection['forward']
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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35 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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36 ## 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"
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37 #set ext = $read1_identifier + '.fastq'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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38 #if $read1.ext.endswith('.gz'):
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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39 #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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40 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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41 #set read1_file = $read1_identifier + $ext
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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42 ln -s '${read1}' '${read1_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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43 #set read2 = $input_type_cond.reads_collection['reverse']
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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44 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name))
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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45 #set read2_file = $read2_identifier + $ext
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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46 ln -s '${read2}' '${read2_file}' &&
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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47 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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48
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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49 bbmap.sh t=\${GALAXY_SLOTS:-4} ref='${ref}'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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50 #if str($input_type_cond.input_type) == 'single':
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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51 in='${read1_file}'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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52 #else:
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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53 in1='${read1_file}' in2='${read2_file}'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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54 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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55 #if str($output_sort) == 'coordinate':
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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56 out='mapped.bam'; samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output' 'mapped.bam'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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57 #elif str($output_sort) == 'name':
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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58 out='mapped.bam'; samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output' 'mapped.bam'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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59 #else:
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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60 out='mapped.bam' && mv 'mapped.bam' '$output'
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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61 #end if
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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62 ]]></command>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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63 <inputs>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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64 <conditional name="input_type_cond">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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65 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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66 <option value="single" selected="true">Single dataset</option>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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67 <option value="pair">Dataset pair</option>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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68 <option value="paired">List of dataset pairs</option>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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69 </param>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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70 <when value="single">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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71 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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72 </when>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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73 <when value="pair">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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74 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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75 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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76 </when>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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77 <when value="paired">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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78 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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79 </when>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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80 </conditional>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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81 <expand macro="reference_source_cond"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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82 <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).">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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83 <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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84 <option value="name">Sort by read names</option>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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85 <option value="unsorted">Not sorted (sorted as input)</option>
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86 </param>
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87 </inputs>
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88 <outputs>
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89 <data format="bam" name="output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
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90 <expand macro="dbKeyActionsBBMap"/>
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91 <change_format>
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92 <when input="output_sort" value="name" format="qname_sorted.bam" />
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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93 <when input="output_sort" value="unsorted" format="qname_input_sorted.bam" />
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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94 </change_format>
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95 </data>
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96 </outputs>
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97 <tests>
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98 <!-- Single file, cached reference, output coordinate sorted -->
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99 <test expect_num_outputs="1">
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100 <param name="input_type" value="single"/>
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101 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
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102 <output name="output" file="output1.bam" ftype="bam" lines_diff="4">
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103 <metadata name="dbkey" value="89" />
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104 </output>
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105 </test>
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106 <!-- Paired reads in separate datasets, cached reference, output name sorted -->
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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107 <test expect_num_outputs="1">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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108 <param name="input_type" value="pair"/>
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109 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
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110 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
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111 <param name="output_sort" value="name"/>
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112 <output name="output" file="output2.bam" ftype="qname_sorted.bam" lines_diff="4">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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113 <metadata name="dbkey" value="89" />
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114 </output>
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115 </test>
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116 <!-- Collection of Paired reads, history reference, output unsorted -->
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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117 <test expect_num_outputs="1">
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118 <param name="input_type" value="paired"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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119 <param name="reads_collection">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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120 <collection type="paired">
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121 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
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122 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
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123 </collection>
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124 </param>
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125 <param name="ref_source" value="history"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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126 <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"
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127 <param name="output_sort" value="unsorted"/>
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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128 <output name="output" file="output3.bam" ftype="qname_input_sorted.bam" lines_diff="4">
07a6e49c7d74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa"
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129 <metadata name="dbkey" value="89" />
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130 </output>
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131 </test>
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132 </tests>
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133 <help>
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134 **What it does**
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135
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136 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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137 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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138 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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139 200 million contigs. the indexing phase is very fast compared to other aligners.
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140
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141 BBMap can output many different statistics files; an empirical read quality histogram, insert-size distribution, and genome
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142 coverage with or without generating a sam file. It is useful in quality control of libraries and sequencing runs or
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143 evaluating new sequencing platforms.
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144
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145 **Options**
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146
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147 *Bam sorting mode* - the generated bam files can be sorted according to three criteria: coordinates, names and input order.
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148
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149 * 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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150 chromosome are first in the file.
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151 * 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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152 * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file.
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153
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154 </help>
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155 <expand macro="citations"/>
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156 </tool>
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157