Mercurial > repos > iuc > biotradis

annotate bacteria_tradis.xml @ 1:58234d95978d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 61c83ac999a040604915ff7cf92670b2635b967e"
author iuc
date Fri, 07 Feb 2020 05:20:39 -0500
parents 738e58ed9cc2
children 103bd59b3e33
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58234d95978d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 61c83ac999a040604915ff7cf92670b2635b967e"
iuc
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1 <tool id="bacteria_tradis" name="Bio-TraDis reads to counts" version="@TOOL_VERSION@+galaxy@VERSION@">
0
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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2 <description></description>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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3 <macros>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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4 <import>macros.xml</import>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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5 </macros>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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6 <expand macro="requirements" />
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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7 <command>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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8 <![CDATA[
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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9 ls '${input_fastq}' > file.txt &&
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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10 bacteria_tradis -v -f file.txt -r '${input_ref}'
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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11 #if str($map_parameters.map_options) == "modify":
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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12
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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13 #if str($map_parameters.set_kmers_options.set) == "yes":
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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14 --smalt_k '$map_parameters.set_kmers_options.kmer_length'
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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15 --smalt_s '$map_parameters.set_kmers_options.step_size'
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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16 #end if
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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18 --smalt_y '$map_parameters.min_percentage'
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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19 --smalt_r '$map_parameters.duplicate_reads'
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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20 -m '$map_parameters.min_quality'
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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22 #end if
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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23
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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24 #if str($tranposon_tag.use) == "yes":
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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25 -m '$tranposon_tag.nb_mismatches'
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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26 -t '$tranposon_tag.sequence'
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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27 #end if
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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28 2>&1
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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29 ]]>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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30 </command>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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31
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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32 <inputs>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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33 <param name="input_fastq" type="data" format="fastq" label="Fastq file containing TraDis reads"/>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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34 <param name="input_ref" type="data" format="fasta" label="Fasta File of the reference Genome"/>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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35
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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36 <conditional name="map_parameters">
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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37 <param name="map_options" type="select" label="Mapping Parameters" help="By default, the bacteria_tradis pipeline determines appropriate read mapping parameters automatically from the length of the first read in the fastq file. These parameters have been tested for data issue from TraDIS protocol of Barquist et al.">
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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38 <option value="default" selected="true">Use Default Parameters</option>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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39 <option value="modify">Set Mapping parameters</option>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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40
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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41 </param>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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42 <when value="modify">
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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43
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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44 <conditional name="set_kmers_options">
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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45 <param name="set" type="boolean" label="Modify kmers parameters" truevalue='yes' falsevalue='no' />
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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46 <when value="yes">
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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47 <param name="kmer_length" type="integer" value="" min="9" max="20" label=" Length of kmers hashed (--smalt_k)" help=" The minimum length of an exact match between a read and the genome needed to trigger an alignment attempt. Appropriate values are between ~10 and 20 for bacterial genomes depending on read length. Lower values lead to increased sensitivity at the expense of runtime." />
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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48 <param name="step_size" type="integer" value="" min="1" max="15" label="Step size for smalt kmers (--smalt_s)" help=" Distance between the start of hashed kmers. Appropriate values are between 1 and ~15, but should be less than --smalt_k to ensure kmers overlap. Lower values lead to increased sensitivity at the expense of runtime." />
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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49 </when>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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50 <when value="no">
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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51 </when>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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52 </conditional>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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53
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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54 <param name="min_percentage" type="float" value="0.96" min="0" max="1" label="Minimum percentage of identical bases between read and reference (--smalt_y)" help="May be lowered to improve sensitivity in the case of low quality or short reads." />
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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55 <param name="duplicate_reads" type="boolean" truevalue="-1" falsevalue="0" label="Randomly assign position to reads that align in multiple location (--smalt_r)" help="If not, reads mapping in multiples positions are ignored" />
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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56 <param name="min_quality" type="integer" value="30" label="Minimum mapping quality score (-m) " help="Multi-mapping reads have a quality score of 0 by definition, so this parameter needs to be set to 0 for these reads to be properly processed. Can be lowered without dramatically affecting results in most cases, particularly if --smalt_y is set reasonably." />
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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57
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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58 </when>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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59 <when value="default">
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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60 </when>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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61 </conditional>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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62
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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63 <conditional name="tranposon_tag">
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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64 <param name="use" type="boolean" truevalue="yes" falsevalue="no" label="Search for a tranposon tag" help="Use with data containing a transposon tag attached to the reads. Only reads containing the transposon tag will be processed, and the tag will be removed before mapping." />
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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65
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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66 <when value="yes">
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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67
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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68 <param name="sequence" type="text" value="" help="" />
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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69 <param name="nb_mismatches" type="integer" value="2" min="0" max="1" help="If there is evidence for low-quality bases in the transposon tag (from FastQC, for instance), setting this to 1 or 2 may result in higher recovery of insertion sites. Higher than 2 is not advisable with the typical transposon tag lengths (10 - 12 bases) produced by TraDIS protocols, but may be appropriate with protocols that produce significantly longer transposon tags." />
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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70 <param name="tagdir" type="select" label="Direction of the transposon tag" help="" >
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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71 <option value="3" selected="true">3'</option>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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72 <option value="5">5bacteria_tradis.xml'</option>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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73 </param>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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74
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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75 </when>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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76 <when value="no">
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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77 </when>
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78 </conditional>
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79
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80
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81 </inputs>
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82
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83 <outputs>
1
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84 <data format="txt" name="Statistics" from_work_dir="file.stats" label="${tool.name} on ${on_string} : Statistics" />
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85 <data name="Counts" format="tabular.gz" from_work_dir="./*.gz" label="${tool.name} on ${on_string} : Counts" />
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86 <data name="Aligned_reads" format="bam" from_work_dir="./*.bam" label="${tool.name} on ${on_string} : Mapped Reads" />
0
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87 </outputs>
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88
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89 <tests>
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90 <test>
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91 <param name="input_fastq" ftype="fastq" value="tiny.fastq.gz"/>
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92 <param name="input_ref" ftype="fasta" value="tiny_ref.fasta"/>
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93 <param name="map_options" value="default"/>
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94 <param name="min_quality" ftype="float" value="0"/>
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95 <param name="use" value="no"/>
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96 <param name="set" ftype="select" value="no"/>
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97 <output name="Statistics" file="file.stats" lines_diff="2" />
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98 <output name="Counts" file="tiny.out.gz.CP009273.1_60_120.insert_site_plot.gz" compare="diff" decompress="true" lines_diff="0" />
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99 </test>
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100 <test>
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101 <param name="input_fastq" ftype="fastq" value="tiny.fastq.gz"/>
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102 <param name="input_ref" ftype="fasta" value="tiny_ref.fasta"/>
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103 <param name="min_quality" ftype="integer" value="0"/>
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104 <param name="map_options" value="modify"/>
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105 <param name="min_percentage" ftype="float" value="0.5"/>
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106 <param name="duplicate_reads" ftype="boolean" value="-1"/>
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107 <param name="min_quality" ftype="float" value="20"/>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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108 <param name="use" value="no"/>
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109 <param name="set" ftype="select" value="yes"/>
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110 <param name="kmer_length" ftype="integer" value="10"/>
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111 <param name="step_size" ftype="integer" value="5"/>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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112 <output name="Statistics" file="file.stats" lines_diff="2" />
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113 <output name="Counts" file="tiny_1.out.gz.CP009273.1_60_120.insert_site_plot.gz" compare="diff" decompress="true" lines_diff="0" />
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114 </test>
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115
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116 </tests>
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117 <help>
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118 <![CDATA[
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119
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120 **What is does**
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121
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122 Bio-TraDis provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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123
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124 -----
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125
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126 **Parameters**
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127
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128 The --smalt_r 0 and -m 0 options specify that we want to map reads with multiple best mappings to a random position and use these in our downstream analyses; by default these reads are left unmapped. Mapping and processing this library will take about 30 minutes to an hour on a typical desktop computer.
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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129
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130 By default, the ​bacteria_tradis​ pipeline determines appropriate read mapping parameters automatically from the length of the first read in the fastq file. It should be noted that the default parameters have been tested using the optimized TraDIS protocol of Barquist ​et al​., 20XX in the hands of an experienced sequencing specialist; these will need to be tuned for other protocols, or for pilot runs, etc. There are various other scenarios in which it would be appropriate to reduce the stringency of these parameters: in the case that read trimming has been applied, if there are quality issues in the library, for certain types of studies (particularly gene essentiality studies as above), or if the quality of the reference genome is low (or of a different strain).
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131
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132
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133 The *-mm* option specifies the number of mismatches allowed when matching the transposon tag; by default none are allowed. We sometimes observe one or two positions within the transposon tag that seem to have generally low quality. If there is evidence for low-quality bases in the transposon tag (from FastQC, for instance), setting this to 1 or 2 may result in higher recovery of insertion sites. Higher than 2 is not advisable with the typical transposon tag lengths (10 - 12 bases) produced by TraDIS protocols, but may be appropriate with protocols that produce significantly longer transposon tags.
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134
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135
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136 The *-m* option sets the minimum mapping quality score to use an alignment in downstream analysis (e.g. plot files); defaults to 30. Multi-mapping reads have a quality score of 0 by definition, so this parameter needs to be set to 0 for these reads to be properly processed. Can be lowered without dramatically affecting results in most cases, particularly if *smalt_y* is set reasonably.
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137
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138
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139 The other options specify parameters for the smalt mapper, which are discussed in more detail in the smalt manual (ftp.sanger.ac.uk/pub/resources/software/smalt/smalt-manual-0.7.4.pdf). We will discuss their effects on TraDIS mapping briefly here:
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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140
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141 *-smalt_k*: length of kmers hashed; roughly, the minimum length of an exact match between a read and the genome needed to trigger an alignment attempt. Appropriate values are between ~10 and 20 for bacterial genomes depending on read length. Lower values lead to increased sensitivity at the expense of runtime.
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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142
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143 *-smalt_s*: skipstep. Sampling step size, i.e. the distance between successive words that are hashed along the genomic reference sequence. With the option -s 1
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144 every word is hashed, with -s 2 every second word, with -s 3 very third etc. Appropriate values are between 1 and ~15, but should be less than --smalt_k to ensure kmers overlap. Lower values lead to increased sensitivity at the expense of runtime.
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145
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146
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147 *-smalt_y*: minimum percentage of identical bases between read and reference, defaults to .96 - 96% identity, or 4 mismatches allowed in a 100 base read. May be lowered to improve sensitivity in the case of low quality or short reads.
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148
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149
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150 *-smalt_r*: specifies what to do with reads that map equally well in multiple locations. By default this is set to -1, meaning that multi-mapping reads are left unmapped. This is appropriate in studies comparing insertion frequency in the same library passaged through multiple conditions, as in this case a change in frequency of one repetitive gene could lead to many genes appearing to be selected artifactually. For studies of gene essentiality in a newly created library, this should be set to 0 (randomly assign a position) to avoid repetitive elements (particularly insertion sequences and the like) artificially appearing to be essential.
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151
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152 -----
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154 **Output files**
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156 On completion, bacteria tradis ​produces a number of files. These include:
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157 **(input list name).stats**​ : Mapping statistics file. This is comma delimited, and includes one line for each library mapped along with a header. It can be easily opened in e.g. Excel or R.
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158 **(library name.replicon_name).insert_site_plot.gz**​: Plot files, one for each replicon and library. These contain insertion counts on each strand for every nucleotide position in the replicon. They can be opened as “user plots” in the Artemis genome browser, and will be used for further analysis.
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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159 **(library name).mapped.bam** : BAM file containing mapped reads.
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160
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161 -----
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162
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163 **More information**
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164
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165 .. class:: infomark
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166
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167 Additional information about Bio-TraDis can be found at https://github.com/sanger-pathogens/Bio-Tradis
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168 ]]>
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169 </help>
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170
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171 <expand macro="citations" />
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172
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173 </tool>
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176