Mercurial > repos > iuc > adapter_removal

annotate adapter_removal.xml @ 1:40874f772ea1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit faa8c4bf004428988500537078264968ae05fa67
author iuc
date Mon, 26 Aug 2024 13:47:54 +0000
parents 04d05400d3a6
children
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04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
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1 <tool id="adapter_removal" name="AdapterRemoval: remove adapter sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
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2 <description>from HTS data</description>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
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3 <macros>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
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4 <import>macros.xml</import>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
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5 </macros>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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6 <expand macro="bio_tools"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
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7 <expand macro="requirements"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
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8 <command detect_errors="exit_code"><![CDATA[
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
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9 #import re
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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10
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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11 #if $input_type_cond.input_type in ['single', 'pair', 'interleaved']:
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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12 #set read1 = $input_type_cond.read1
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
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13 #if $input_type_cond.input_type == 'pair':
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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14 #set read2 = $input_type_cond.read2
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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15 #end if
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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16 #else:
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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17 #set read1 = $input_type_cond.reads_collection['forward']
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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18 #set read2 = $input_type_cond.reads_collection['reverse']
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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19 #end if
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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20
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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21 #set read1_identifier = 'read1' + $read1.ext
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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22 ln -s '${read1}' '${read1_identifier}' &&
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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23
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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24 #if $input_type_cond.input_type in ["pair", "paired"]:
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
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25 #set read2_identifier = 'read2' + $read2.ext
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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26 ln -s '${read2}' '${read2_identifier}' &&
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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27 #end if
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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28
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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29 AdapterRemoval
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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30 --file1 '${read1_identifier}'
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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31 #if str($input_type_cond.input_type) == 'interleaved':
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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32 --interleaved
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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33 --interleaved-input
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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34 #if str($input_type_cond.interleaved_output) == 'yes':
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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35 --interleaved-output '$output_interleaved_truncated'
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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36 #end if
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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37 $input_type_cond.combined_output
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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38 #else if str($input_type_cond.input_type) in ['pair', 'paired']:
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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39 --file2 '${read2_identifier}'
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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40 $input_type_cond.identify_adapters
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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41 #if str($input_type_cond.interleaved_output) == 'yes':
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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42 --interleaved-output
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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43 #end if
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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44 $input_type_cond.combined_output
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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45 #end if
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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46
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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47 --threads \${GALAXY_SLOTS:-8}
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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48
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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49 ###### FASTQ Options
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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50 --qualitybase '33'
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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51 --qualitybase-output '33'
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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52 --qualitymax $fastq_options.qualitymax
1
40874f772ea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit faa8c4bf004428988500537078264968ae05fa67
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53 $fastq_options.convert_uracils
40874f772ea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit faa8c4bf004428988500537078264968ae05fa67
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54 $fastq_options.mask_degenerate_bases
0
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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55
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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56 ###### FASTQ Trimming Options
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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57 --adapter1 '$fastq_trimming_options.adapter1'
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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58 --adapter2 '$fastq_trimming_options.adapter2'
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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59 #if $fastq_trimming_options.adapter_list:
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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60 --adapter-list '$fastq_trimming_options.adapter_list'
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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61 #end if
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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62 --minadapteroverlap $fastq_trimming_options.minadapteroverlap
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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63 --mm $fastq_trimming_options.mm
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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64 --shift $fastq_trimming_options.shift
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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65 #if str($fastq_trimming_options.trim5p_cond.trim5p_param) == 'yes':
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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66 --trim5p $fastq_trimming_options.trim5p_cond.trim5p_mate1 $fastq_trimming_options.trim5p_cond.trim5p_mate2
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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67 #end if
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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68 #if str($fastq_trimming_options.trim3p_cond.trim3p_param) == 'yes':
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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69 --trim3p $fastq_trimming_options.trim3p_cond.trim3p_mate1 $fastq_trimming_options.trim3p_cond.trim3p_mate2
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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70 #end if
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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71 $fastq_trimming_options.trimns
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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72 --maxns $fastq_trimming_options.maxns
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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73 $fastq_trimming_options.trimqualities
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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74 #if str($fastq_trimming_options.sliding_window_cond.sliding_window_param) == 'yes':
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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75 --trimwindows $fastq_trimming_options.sliding_window_cond.window_size
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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76 #end if
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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77 --minquality $fastq_trimming_options.minquality
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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78 $fastq_trimming_options.preserve5p
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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79 --minlength $fastq_trimming_options.minlength
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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80 --maxlength $fastq_trimming_options.maxlength
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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81
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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82 ###### FASTQ Merging Options
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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83 $fastq_merging_options.collapse
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84 --minalignmentlength $fastq_merging_options.minalignmentlength
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85 $fastq_merging_options.collapse_deterministic
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86 $fastq_merging_options.collapse_conservatively
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87
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88 ###### Output Options
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89 --settings '$output_settings'
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90 #if str($input_type_cond.input_type) == 'single':
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91 --output1 '$output_truncated'
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92 #else if str($input_type_cond.input_type) in ['pair', 'paired']:
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93 #if str($input_type_cond.interleaved_output) == 'no':
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94 --output1 '$output_forward_truncated'
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95 --output2 '$output_reverse_truncated'
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96 #else:
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97 --output1 '$output_interleaved_truncated'
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98 #end if
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99 #end if
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100
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101 ###### Outputs
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102 #if 'output_singleton' in $output_select:
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103 --singleton '$output_singleton_truncated'
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104 #end if
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105 #if 'output_collapsed' in $output_select:
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106 --outputcollapsed '$output_collapsed'
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107 #end if
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108 #if 'output_collapsed_truncated' in $output_select:
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109 --outputcollapsedtruncated '$output_collapsed_truncated'
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110 #end if
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111 #if 'output_discarded' in $output_select:
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112 --discarded '$output_discarded'
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113 #end if
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114 ]]></command>
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115 <inputs>
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116 <conditional name="input_type_cond">
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117 <param name="input_type" type="select" label="Choose the category of the reads files to be analyzed">
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118 <option value="single" selected="true">Single dataset containing reads</option>
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119 <option value="pair">Pair of forward and reverse reads in separate datasets</option>
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120 <option value="paired">Collection of paired reads</option>
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121 <option value="interleaved">Single dataset in which pairs of reads are written one after the other</option>
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122 </param>
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123 <when value="single">
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124 <param name="read1" type="data" format="@DATATYPES@" label="Read file"/>
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125 </when>
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126 <when value="pair">
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127 <param name="read1" type="data" format="@DATATYPES@" label="Forward read file"/>
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128 <param name="read2" type="data" format="@DATATYPES@" label="Reverse read file"/>
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129 <expand macro="identify_adapters_param"/>
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130 <expand macro="interleaved_output_param"/>
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131 <expand macro="combined_output_param"/>
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132 </when>
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133 <when value="paired">
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134 <param name="reads_collection" type="data_collection" format="@DATATYPES@" collection_type="paired" label="Collection of fastq paired read files"/>
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135 <expand macro="identify_adapters_param"/>
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136 <expand macro="interleaved_output_param"/>
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137 <expand macro="combined_output_param"/>
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138 </when>
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139 <when value="interleaved">
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140 <param name="read1" type="data" format="@DATATYPES@" label="Interleaved read file"/>
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141 <expand macro="interleaved_output_param"/>
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142 <expand macro="combined_output_param"/>
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143 </when>
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144 </conditional>
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145 <!-- FASTQ Options -->
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146 <section name="fastq_options" title="FASTQ Options" expanded="false">
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147 <param argument="--qualitymax" type="integer" value="41" min="0" max="93" label="Maximum Phred score expected in input files and used when writing output files" help="Possible values are 0 to 93 for Phred+33 encoded files"/>
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148 <param argument="--mask-degenerate-bases" type="boolean" truevalue="--mask-degenerate-bases" falsevalue="" checked="false" label="Mask degenerate/ambiguous bases (B/D/H/K/M/N/R/S/V/W/Y)" help="This option will replace 'N's; if this option is not used, AdapterRemoval will abort upon encountering degenerate bases."/>
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149 <param argument="--convert-uracils" type="boolean" truevalue="--convert-uracils" falsevalue="" checked="false" label="Convert uracils (U) to thymine (T) " help="If this option is not used, AdapterRemoval will abort upon encountering uracils."/>
0
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150 </section>
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151 <!-- FASTQ Trimming Options -->
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152 <section name="fastq_trimming_options" title="FASTQ Trimming Options" expanded="false">
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153 <param argument="--adapter1" type="text" value="AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG" label="Adapter sequence expected to be found in mate 1 reads, specified in read direction">
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154 <expand macro="sanitizer"/>
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155 </param>
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156 <param argument="--adapter2" type="text" value="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" label="Adapter sequence expected to be found in mate 2 reads, specified in read direction">
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157 <expand macro="sanitizer"/>
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158 </param>
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159 <param argument="--adapter_list" type="data" format="tabular" optional="true" label="Tabular file containing adapter sequences" help="The first two columns of each line in the file must correspond to values passed to --adapter1 and --adapter2"/>
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160 <param argument="--minadapteroverlap" type="integer" value="0" min="0" label="Trim reads only if the overlap between read and the adapter is at least this number of bases long" help="Ignored unless input files are single-end reads"/>
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161 <param argument="--mm" type="float" value="3.0" label="The fraction of mismatches allowed in the aligned region" help="The value is used directly if less than 1, the rate s set to 1 / value if the value is greater than 1"/>
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162 <param argument="--shift" type="integer" value="2" min="0" max="93" label="Slip the alignment by this number of bases in the 5' end to allow for missing bases in the 5' end of the read"/>
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163 <conditional name="trim5p_cond">
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164 <param name="trim5p_param" type="select" label="Trim the 5' of reads by a fixed amount after removing adapters, but before carrying out quality based trimming?">
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165 <option value="no" selected="true">No</option>
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166 <option value="yes">Yes</option>
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167 </param>
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168 <when value="no"/>
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169 <when value="yes">
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170 <param name="trim5p_mate1" type="integer" value="0" min="0" label="Value for trimming the 5' of mate1 reads"/>
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171 <param name="trim5p_mate2" type="integer" value="0" min="0" label="Value for trimming the 5' of mate1 reads"/>
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172 </when>
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173 </conditional>
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174 <conditional name="trim3p_cond">
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175 <param name="trim3p_param" type="select" label="Trim the 3' of reads by a fixed amount after removing adapters, but before carrying out quality based trimming?">
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176 <option value="no" selected="true">No</option>
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177 <option value="yes">Yes</option>
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178 </param>
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179 <when value="no"/>
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180 <when value="yes">
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181 <param name="trim3p_mate1" type="integer" value="0" min="0" label="Value for trimming the 3' of mate1 reads"/>
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182 <param name="trim3p_mate2" type="integer" value="0" min="0" label="Value for trimming the 3' of mate1 reads"/>
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183 </when>
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184 </conditional>
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185 <param argument="--trimns" type="boolean" truevalue="--trimns" falsevalue="" checked="false" label="Trim consecutive Ns from the 5' and 3' termini?" help="If quality trimming is also enabled (--trimqualities), then stretches of mixed low-quality bases and/or Ns are trimmed"/>
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186 <param argument="--maxns" type="integer" value="1000" min="0" label="Discard reads containing more than this number of ambiguous bases ('N') after trimming"/>
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187 <param argument="--trimqualities" type="boolean" truevalue="--trimqualities" falsevalue="" checked="false" label="Trim consecutive stretches of low quality bases (threshold set by --minquality) from the 5' and 3' termini?" help="If trimming of Ns is also enabled (--trimns), then stretches of mixed low-quality bases and Ns are trimmed"/>
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188 <conditional name="sliding_window_cond">
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189 <param name="sliding_window_param" type="select" label="Perform sliding window approach to quality base-trimming inspired by sickle?">
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190 <option value="no" selected="true">No</option>
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191 <option value="yes">Yes</option>
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192 </param>
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193 <when value="no"/>
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194 <when value="yes">
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195 <param name="window_size" type="integer" value="0" min="0" label="Window size" help="See the Window based quality trimming section of the tool help below"/>
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196 </when>
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197 </conditional>
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198 <param argument="--minquality" type="integer" value="2" min="0" label="Threshold for trimming low quality bases using --trimqualities and --trimwindows"/>
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199 <param argument="--preserve5p" type="boolean" truevalue="--preserve5p" falsevalue="" checked="false" label="Preserve (i.e., do not trim by --trimns, --trimqualities, and --trimwindows) bases at the 5p?" help="Collapsed reads will not be quality trimmed when this option is enabled"/>
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200 <param argument="--minlength" type="integer" value="15" min="0" label="Reads shorter than this length are discarded following trimming"/>
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201 <param argument="--maxlength" type="integer" value="4294967295" min="0" label="Reads longer than this length are discarded following trimming"/>
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202 </section>
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203 <!-- FASTQ Merging Options -->
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204 <section name="fastq_merging_options" title="FASTQ Merging Options" expanded="false">
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205 <param argument="--collapse" type="boolean" truevalue="--collapse" falsevalue="" checked="false" label="Output complete reads with an 'M_' name prefix and trimmed reads with an 'MT_' name prefix?"/>
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206 <param argument="--minalignmentlength" type="integer" value="11" min="0" label="Minimum overlap between mate 1 and mate 2 before the reads are collapsed into one when collapsing paired-end reads, or when attempting to identify complete template sequences in single-end mode"/>
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207 <param argument="--collapse_deterministic" type="boolean" truevalue="--collapse-deterministic" falsevalue="" checked="false" label="Collapse deterministically?" help="Setting this option also sets --collapse"/>
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208 <param argument="--collapse_conservatively" type="boolean" truevalue="--collapse-conservatively" falsevalue="" checked="false" label="Collapse conservatively?" help="Setting this option also sets --collapse"/>
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209 </section>
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210 <!-- Output Options -->
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211 <param name="output_select" type="select" multiple="true" label="Optionally select one or more of the following additional outputs">
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212 <option value="none" selected="true">No additional outputs</option>
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213 <option value="output_singleton">Output file containing paired reads for which the mate has been discarded</option>
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214 <option value="output_collapsed">Output file containing overlapping mate-pairs which have been merged into a single read (PE mode) or reads for which the adapter was identified by a minimum overlap</option>
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215 <option value="output_collapsed_truncated">Output collapsed reads (see param above) which were trimmed due the presence of low-quality or ambiguous nucleotides</option>
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216 <option value="output_discarded">Output reads reads discarded due to the --minlength, --maxlength or --maxns options</option>
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217 </param>
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218 </inputs>
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219 <outputs>
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220 <data name="output_settings" format="txt" label="${tool.name} on ${on_string} (settings)"/>
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221 <data name="output_truncated" format="fastqsanger" label="${tool.name} on ${on_string} (truncated)">
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222 <filter>input_type_cond['input_type'] == 'single'</filter>
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223 </data>
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224 <data name="output_forward_truncated" format="fastqsanger" label="${tool.name} on ${on_string} (forward truncated)">
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225 <filter>input_type_cond['input_type'] in ['pair', 'paired'] and input_type_cond['interleaved_output'] == 'no'</filter>
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226 </data>
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227 <data name="output_reverse_truncated" format="fastqsanger" label="${tool.name} on ${on_string} (reverse truncated)">
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228 <filter>input_type_cond['input_type'] in ['pair', 'paired'] and input_type_cond['interleaved_output'] == 'no'</filter>
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229 </data>
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230 <data name="output_interleaved_truncated" format="fastqsanger" label="${tool.name} on ${on_string} (interleaved truncated)">
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231 <filter>input_type_cond['input_type'] in ['pair', 'paired'] and input_type_cond['interleaved_output'] == 'yes'</filter>
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232 </data>
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233 <data name="output_singleton_truncated" format="fastqsanger" label="${tool.name} on ${on_string} (singleton truncated)">
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234 <filter>'output_singleton' in output_select</filter>
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235 </data>
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236 <data name="output_collapsed" format="fastqsanger" label="${tool.name} on ${on_string} (collapsed)">
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237 <filter>'output_collapsed' in output_select</filter>
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238 </data>
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239 <data name="output_collapsed_truncated" format="fastqsanger" label="${tool.name} on ${on_string} (collapsed truncated)">
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240 <filter>'output_collapsed_truncated' in output_select</filter>
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241 </data>
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242 <data name="output_discarded" format="fastqsanger" label="${tool.name} on ${on_string} (discarded)">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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243 <filter>'output_discarded' in output_select</filter>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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244 </data>
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245 </outputs>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
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246 <tests>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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247 <!-- Single dataset input, all defaults -->
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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248 <test expect_num_outputs="2">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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249 <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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250 <output name="output_settings" ftype="txt">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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251 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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252 <has_size value="2117" delta="10"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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253 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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254 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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255 <has_text text="AdapterRemoval"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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256 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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257 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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258 <output name="output_truncated" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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259 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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260 <has_size value="100731"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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261 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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262 <assert_contents>
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iuc
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263 <has_text text="@read_150_1/1"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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264 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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265 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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266 </test>
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267 <!-- Dataset pair input, all defaults -->
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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268 <test expect_num_outputs="3">
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269 <param name="input_type" value="pair"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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270 <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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271 <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
1
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272 <section name="fastq_options">
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273 <param name="convert_uracils" value="false"/>
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274 <param name="mask_degenerate_bases" value="true"/>
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275 </section>
0
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276 <output name="output_settings" ftype="txt">
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277 <assert_contents>
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278 <has_size value="2594" delta="10"/>
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279 </assert_contents>
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280 <assert_contents>
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281 <has_text text="AdapterRemoval"/>
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282 </assert_contents>
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283 </output>
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parents:
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284 <output name="output_forward_truncated" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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285 <assert_contents>
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parents:
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286 <has_size value="101161"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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287 </assert_contents>
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288 <assert_contents>
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289 <has_text text="@read_150_1/1"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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290 </assert_contents>
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291 </output>
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parents:
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292 <output name="output_reverse_truncated" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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293 <assert_contents>
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parents:
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294 <has_size value="101161"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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295 </assert_contents>
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296 <assert_contents>
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iuc
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297 <has_text text="@read_150_1/2"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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298 </assert_contents>
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299 </output>
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300 </test>
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parents:
diff changeset
301 <!-- Dataset pair input, all defaults, interleaved output -->
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
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302 <test expect_num_outputs="2">
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diff changeset
303 <param name="input_type" value="pair"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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304 <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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diff changeset
305 <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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306 <param name="interleaved_output" value="yes"/>
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307 <output name="output_settings" ftype="txt">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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308 <assert_contents>
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309 <has_size value="2593" delta="10"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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310 </assert_contents>
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311 <assert_contents>
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parents:
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312 <has_text text="AdapterRemoval"/>
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313 </assert_contents>
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314 </output>
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parents:
diff changeset
315 <output name="output_interleaved_truncated" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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parents:
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316 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
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317 <has_size value="202322"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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318 </assert_contents>
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319 <assert_contents>
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iuc
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320 <has_text text="@read_150_1/1"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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321 </assert_contents>
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322 </output>
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iuc
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diff changeset
323 </test>
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324 <!-- Collection of dataset pairs input, all defaults -->
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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diff changeset
325 <test expect_num_outputs="3">
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diff changeset
326 <param name="input_type" value="paired"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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parents:
diff changeset
327 <param name="reads_collection">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
328 <collection type="paired">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
329 <element name="forward" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
330 <element name="reverse" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
331 </collection>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
332 </param>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
333 <output name="output_settings" ftype="txt">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
334 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
335 <has_size value="2594" delta="10"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
336 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
337 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
338 <has_text text="AdapterRemoval"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
339 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
340 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
341 <output name="output_forward_truncated" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
342 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
343 <has_size value="101161"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
344 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
345 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
346 <has_text text="@read_150_1/1"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
347 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
348 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
349 <output name="output_reverse_truncated" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
350 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
351 <has_size value="101161"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
352 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
353 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
354 <has_text text="@read_150_1/2"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
355 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
356 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
357 </test>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
358 <!-- Dataset pair input, all defaults, all optional outputs checked -->
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
359 <test expect_num_outputs="7">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
360 <param name="input_type" value="pair"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
361 <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
362 <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
363 <param name="output_select" value="output_singleton,output_collapsed,output_collapsed_truncated,output_discarded"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
364 <output name="output_settings" ftype="txt">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
365 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
366 <has_size value="2594" delta="10"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
367 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
368 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
369 <has_text text="AdapterRemoval"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
370 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
371 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
372 <output name="output_forward_truncated" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
373 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
374 <has_size value="101161"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
375 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
376 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
377 <has_text text="@read_150_1/1"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
378 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
379 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
380 <output name="output_reverse_truncated" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
381 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
382 <has_size value="101161"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
383 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
384 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
385 <has_text text="@read_150_1/2"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
386 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
387 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
388 <output name="output_singleton_truncated" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
389 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
390 <has_size value="0"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
391 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
392 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
393 <output name="output_collapsed" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
394 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
395 <has_size value="0"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
396 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
397 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
398 <output name="output_collapsed_truncated" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
399 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
400 <has_size value="0"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
401 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
402 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
403 <output name="output_discarded" ftype="fastqsanger">
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
404 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
405 <has_size value="270"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
406 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
407 <assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
408 <has_text text="@read_150_57/1"/>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
409 </assert_contents>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
410 </output>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
411 </test>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
412 </tests>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
413 <help>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
414 **What it does**
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
iuc
parents:
diff changeset
415
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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416 Searches for and removes adapter sequences from high-throughput sequencing (HTS) data and optionally trims low quality
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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417 bases from the 3' end of reads following adapter removal. This tool can analyze both single-end and paired-end data and
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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418 can be used to merge overlapping paired-end reads into longer consensus sequences. The tool can also construct a consensus
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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419 adapter sequence for paired-end reads.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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420
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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421 The following outputs, some of which are optional or are only produced under certain scenarios, are produced.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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422
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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423 * **settings** - File containing information on the parameters used in the run as well as verall statistics on the reads after trimming.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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424 * **truncated** - File containing trimmed single-end reads.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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425 * **forward truncated** - File containing trimmed mate1 reads.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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426 * **reverse truncated** - File containing trimmed mate2 reads.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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427 * **interleaved truncated** - File containing trimmed mate 2 reads when --interleaved-output is not enabled.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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428 * **singleton truncated** - File containing trimmed paired reads for which the mate has been discarded.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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429 * **collapsed** - If --collapsed is set, contains overlapping mate-pairs which have been merged into a single read (PE mode) or reads for which the adapter was identified by a minimum overlap, indicating that the entire template molecule is present. This does not include which have subsequently been trimmed due to low-quality or ambiguous nucleotides.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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430 * **collapsed truncated** - Collapsed reads (see --outputcollapsed) which were trimmed due the presence of low-quality or ambiguous nucleotides.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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431 * **discarded** - File containing reads discarded due to the --minlength, --maxlength or --maxns options.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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432
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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433 **General Options**
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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434
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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435 * **Attempt to build a consensus adapter sequence from fully overlapping pairs of paired-end reads** - The minimum overlap is controlled by --minalignmentlength. The result will be compared with the values set using --adapter1 and --adapter2. No trimming is performed in this mode.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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436
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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437 **FASTQ Trimming Options**
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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438
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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439 * **Adapter sequence expected to be found in mate 1/2 reads, specified in read direction** - For a detailed description of how to provide the appropriate adapter sequences, see the "Adapters" section of the online documentation.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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440 * **Tabular file containing adapter sequences** - The first two columns of each line in the file are expected to correspond to values passed to --adapter1 and --adapter2. In single-end mode, only column one is required. Lines starting with # are ignored. When multiple rows are found in the table, AdapterRemoval will try each adapter (pair), and select the best aligning adapters for each FASTQ read processed.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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441 * **Trim reads only if the overlap between read and the adapter is at least this number of bases long** - In single-end mode, reads are only trimmed if the overlap between read and the adapter is at least X bases long, not counting ambiguous nucleotides (N); this is independent of the --minalignmentlength when using --collapse, allowing a conservative selection of putative complete inserts in single-end mode, while ensuring that all possible adapter contamination is trimmed.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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442 * **The fraction of mismatches allowed in the aligned region** - The allowed fraction of mismatches allowed in the aligned region. If the value is less than 1, then the value is used directly. If --mismatchrate is greater than 1, the rate is set to 1 / --mismatchrate. The default setting is 3 when trimming adapters, corresponding to a maximum mismatch rate of 1/3, and 10 when using --identify-adapters.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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443 * **Slip the alignment by this number of bases in the 5' end to allow for missing bases in the 5' end of the read** - To allow for missing bases in the 5' end of the read, the program can let the alignment slip --shift bases in the 5' end. This corresponds to starting the alignment maximum --shift nucleotides into read2 (for paired-end) or the adapter (for single-end).
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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444 * **Trim the 5' of reads by a fixed amount after removing adapters, but before carrying out quality based trimming** - Trim the 5' of reads by a fixed amount after removing adapters, but before carrying out quality based trimming. Specify one value to trim mate 1 and mate 2 reads the same amount, or two values separated by a space to trim each mate different amounts.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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445 * **Trim the 3' of reads by a fixed amount after removing adapters, but before carrying out quality based trimming** - Trim the 3' of reads by a fixed amount. See the descriptiuon of thetrim5p parameter immediately above.
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446 * **Trim consecutive Ns from the 5' and 3' termini** - If quality trimming is also enabled (--trimqualities), then stretches of mixed low-quality bases and/or Ns are trimmed.
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447 * **Window based quality trimming** - If window_size is greater than or equal to 1, that number is used as the window size for all reads. If window_size is greater than or equal to 0 and less than 1, then that number is multiplied by the length of individual reads to determine the window size. If the window length is zero or is greater than the current read length, then the read length is used instead. Reads are trimmed as follows for a given window size:
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448
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449 1. The new 5' is determined by locating the first window where both the average quality and the quality of the first base in the window is greater than --minquality.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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450 2. The new 3' is located by sliding the first window right, until the average quality becomes less than or equal to --minquality. The new 3' is placed at the last base in that window where the quality is greater than or equal to --minquality.
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451 3. If no 5' position could be determined, the read is discarded.
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452
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453 **FASTQ Merging Options**
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454
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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455 * **Output complete reads with an 'M\_' name prefix and trimmed reads with an 'MT\_' name prefix** - In paired-end mode, merge overlapping mates into a single and recalculate the quality scores. In single-end mode, attempt to identify templates for which the entire sequence is available. In both cases, complete "collapsed" reads are written with a 'M\_' name prefix, and "collapsed" reads which are trimmed due to quality settings are written with a 'MT\_' name prefix. The overlap needs to be at least --minalignmentlength nucleotides, with a maximum number of mismatches determined by --mm.
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456 * **Collapse deterministically** - Enable deterministic mode; currently only affects --collapse, different overlapping bases with equal quality are set to N quality 0, instead of being randomly sampled. Setting this option also sets --collapse.
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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457 * **Collapse conservatively** - Alternative merging algorithm inspired by FASTQ-join: For matching overlapping bases, the highest quality score is used. For mismatching overlapping bases, the highest quality base is used and the quality is set to the absolute difference in Phred-score between the two bases. For mismatching bases with identical quality scores, the base is set to 'N' and the quality score to 0 (Phred-encoded). Setting this option also sets --collapse.
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458 </help>
04d05400d3a6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f"
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459 <expand macro="citations"/>
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460 </tool>