annotate amplican.xml @ 0:71adaaace336 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
author iuc
date Wed, 22 Sep 2021 21:01:40 +0000
parents
children 8c1bba8d544a
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71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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1 <tool id='amplican' name='AmpliCan' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='20.01'>
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2 <description>analysis tool for genome editing </description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro='requirements' />
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7 <expand macro="bio_tools"/>
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8 <command detect_errors='exit_code'><![CDATA[
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9 #import re
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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10 mkdir ./fastq_folder ./output_folder
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11 #for $i in $fastq_files
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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12 #if str($i.element_identifier) != re.sub('[^\w\-_\.]', '_', str($i.element_identifier))
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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13 && echo "Please rename your datasets; only underscore (_) and alphanumeric characters are allowed."
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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14 && exit 1
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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15 #else
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16 && ln -s '${i}' ./fastq_folder/'${i.element_identifier}'
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17 #end if
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18 #end for
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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19 && Rscript '$amplican_script'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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20 #if 'knit_reports' in $output_options.outputs
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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21 && mv ./output_folder/reports/amplicon_report.html '${output_html.extra_files_path}'
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22 && mv ./output_folder/reports/barcode_report.html '${output_html.extra_files_path}'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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23 && mv ./output_folder/reports/group_report.html '${output_html.extra_files_path}'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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24 && mv ./output_folder/reports/guide_report.html '${output_html.extra_files_path}'
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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25 && mv ./output_folder/reports/id_report.html '${output_html.extra_files_path}'
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26 #end if
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27 ]]> </command>
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28 <configfiles>
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29 <configfile name="amplican_script"><![CDATA[
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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30 ## Setup R error handling to go to stderr
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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31 options(
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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32 show.error.messages = F,
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33 error = function() {
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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34 cat(geterrmessage(), file = stderr())
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35 q("no", 1, F)
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36 }
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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37 )
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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38 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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39 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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40
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41 suppressPackageStartupMessages({
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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42 library("amplican")
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43 })
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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44 #full analysis
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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45 amplicanPipeline(
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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46 '${config_file}',
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47 'fastq_folder',
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48 'output_folder',
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49 #if 'knit_reports' in $output_options.outputs
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50 knit_reports = TRUE,
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51 #else
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52 knit_reports = FALSE,
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53 #end if
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54 #if $output_options.write_alignment_format == 'fasta'
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55 write_alignments_format = "fasta",
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56 #else if $output_options.write_alignment_format == 'txt'
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57 write_alignments_format = "txt",
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58 #else
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59 write_alignments_format = "None",
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60 #end if
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61 average_quality = $quality_options.average_quality,
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62 min_quality = $quality_options.min_quality,
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63 use_parallel = FALSE,
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64 scoring_matrix = Biostrings::nucleotideSubstitutionMatrix(
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65 match = $alignment_options.scoring_matrix.match_scoring,
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66 mismatch = $alignment_options.scoring_matrix.mismatch_scoring,
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67 baseOnly = $alignment_options.scoring_matrix.base_only,
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68 type = "$alignment_options.scoring_matrix.scoring_type"
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69 ),
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70 gap_opening = $alignment_options.gap_opening,
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71 gap_extension = $alignment_options.gap_extension,
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72 fastqfiles = $advanced_options.fastq_use,
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73 primer_mismatch = $alignment_options.primer_mismatch,
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74 donor_mismatch = $alignment_options.donor_mismatch,
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75 PRIMER_DIMER = $advanced_options.primer_dimer,
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76 event_filter = $advanced_options.event_filter,
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77 cut_buffer = $advanced_options.cut_buffer,
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78 promiscuous_consensus = $advanced_options.promiscuous_consensus,
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79 normalize = c("guideRNA", "Group")
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80 )
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81 ]]></configfile>
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82 </configfiles>
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83 <inputs>
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84 <param name="config_file" type="data" format="txt" label="Configuration file"/>
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85 <param name="fastq_files" type="data" format="fastq, fastq.gz, fastqsanger, fastqsanger.gz"
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86 multiple="true" label="FASTQ files"/>
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87 <section name="quality_options" title="Sequence quality options">
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88 <param argument="average_quality" type="integer" min="0" max="93"
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89 value="0" label="Average quality"
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90 help="If the average quality of the reads fall below value of average_quality then sequence is filtered. Default is 0" />
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91 <param argument="min_quality" type="integer" min="0" max="93"
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92 value="20" label="Minimum quality"
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93 help="If one of nucleotides has quality below min_quality, then the sequence is filtered. Default is 20" />
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94 </section>
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95 <section name="alignment_options" title="Alignment options">
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96 <param argument="gap_opening" type="integer" min="0" max="40" value="25" label="Gap opening" help="The opening gap score" />
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97 <param argument="gap_extension" type="integer" min="0" max="40" value="0" label="Gap extension" help="The gap extension score" />
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98 <param argument="primer_mismatch" type="integer" min="0" max="40" value="0" label="Primer mismatch" help="Decide how many mismatches are allowed during primer matching of the reads, that groups reads by experiments. When primer_mismatch = 0 no mismatches are allowed, which can increase number of unasssigned read" />
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99 <param argument="donor_mismatch" type="integer" min="0" max="40" value="3" label="Donor mismatch" help="How many events of length 1 (mismatches, deletions and insertions of length 1) are allowed when aligning toward the donor template. This parameter is only used when donor template is specified. The higher the parameter the less strict will be algorithm accepting read as HDR. Set to 0 if only perfect alignments to the donor template marked as HDR, unadvised due to error rate of the sequencers" />
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100 <section name="scoring_matrix" title="Scoring matrix options" expanded="False">
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101 <param argument="match_scoring" type="integer" min="0" max="20" value="5" label="Match scoring" help="TODO" />
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102 <param argument="mismatch_scoring" type="integer" min="-20" max="0" value="-4" label="Mismatch scoring" help="TODO" />
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103 <param argument="base_only" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Base only" help="TODO" />
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104 <param argument="scoring_type" type="select" label="Scoring matrix type" help="TODO">
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105 <option value="DNA" selected="true">DNA</option>
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106 <option value="RNA">RNA</option>
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107 </param>
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108 </section>
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109 </section>
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110 <section name="advanced_options" title="Advanced options">
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111 <param argument="fastq_use" type="select" label="FASTQ files to use" help="Normally you want to use both FASTQ files. But in some special cases, you may want to use only the forward file, or only the reverse file">
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112 <option value="0">Use both FASTQ files</option>
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113 <option value="0.5">Use both FASTQ files, but only for one of the reads (forward or reverse) is required to have primer perfectly matched to sequence</option>
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114 <option value="1">Use only the forward FASTQ file</option>
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115 <option value="2">Use only the reverse FASTQ file</option>
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116 </param>
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117 <param argument="primer_dimer" type="integer" min="0" max="50" value="30" label="Primer dimer" help="Value specifying buffer for PRIMER DIMER detection. For a given read it will be recognized as PRIMER DIMER when alignment will introduce gap of size bigger than: length of amplicon - (lengths of PRIMERS + PRIMER_DIMER value)" />
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118 <param argument="event_filter" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Event filter" help="Whether detection of offtarget reads, should be enabled" />
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119 <param argument="cut_buffer" type="integer" min="0" max="30" value="5" label="Cut buffer" help="The number of bases by which extend expected cut sites (specified as UPPER case letters in the amplicon) in 5' and 3' directions" />
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120 <param argument="promiscuous_consensus" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Promiscuous consensus" help="Whether rules of amplicanConsensus should be promiscuous. When promiscuous, we allow indels that have no confirmation on the other strand" />
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121 </section>
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122 <section name="output_options" title="Output options">
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123 <param argument="write_alignment_format" type="select" label="Alignment format output" help="Whether it should write alignments results to separate files">
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124 <option value="None">None: don't write any alignments to files</option>
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125 <option value="txt" selected="true">Text file: read information followed by forward read and amplicon sequence followed by reverse read with its amplicon sequence</option>
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126 <option value="fasta">FASTA file: outputs alignments in fasta format where header indicates experiment ID, read id and number of reads</option>
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127 </param>
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128 <param name="outputs" type="select" label="Additional output files" display="checkboxes" multiple="true" help="Select the output files.">
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129 <option value="config_summary" selected="true">Configuration summary (config_summary.csv)</option>
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130 <option value="barcode_reads" selected="true">Barcode reads filters (barcode_reads_filters.csv)</option>
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131 <option value="knit_reports" selected="true" >Knitr HTML report</option>
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132 <option value="parameters" >Parameters (RunParameters.txt)</option>
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133 <option value="alignments_rds" selected="true">Alignments Rda file (AlignmentsExperimentSet.rds)</option>
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134 <option value="events_filtered_shifted" selected="true">Events filtered shifted (events_filtered_shifted.csv)</option>
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135 <option value="events_filtered_shifted_normalized" selected="true">Events filtered shifted normalized (events_filtered_shifted_normalized.csv)</option>
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136 <option value="raw_events" selected="true">Raw events (raw_events.csv)</option>
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137 <option value="unassigned_reads" selected="true">Unnasigned reads (unassigned_reads.csv) </option>
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138 </param>
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139 </section>
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140 </inputs>
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141 <outputs>
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142 <data name="config_summary" from_work_dir="./output_folder/config_summary.csv" format="csv" label="${tool.name} on ${on_string}: config summary">
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143 <filter>"config_summary" in output_options["outputs"]</filter>
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144 </data>
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145 <data name="barcode_reads" from_work_dir="./output_folder/barcode_reads_filters.csv" format="tabular" label="${tool.name} on ${on_string}: barcode reads filters">
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146 <filter>"barcode_reads" in output_options["outputs"]</filter>
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147 </data>
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148 <data name="output_html" from_work_dir="./output_folder/reports/index.html" format="html" label="${tool.name} on ${on_string}: report">
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149 <filter>"knit_reports" in output_options["outputs"]</filter>
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150 </data>
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151 <data name="parameters" from_work_dir="./output_folder/RunParameters.txt" format="txt" label="${tool.name} on ${on_string}: run parameters">
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152 <filter>"parameters" in output_options["outputs"]</filter>
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153 </data>
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154 <data name="alignments_rds" from_work_dir="./output_folder/alignments/AlignmentsExperimentSet.rds" format="rdata" label="${tool.name} on ${on_string}: alignments experiment set">
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155 <filter>"alignments_rds" in output_options["outputs"]</filter>
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156 </data>
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157 <data name="alignments_fasta" from_work_dir="./output_folder/alignments/alignments.fasta" format="fasta" label="${tool.name} on ${on_string}: alignments (FASTA)">
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158 <filter>output_options["write_alignment_format"] == "fasta"</filter>
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159 </data>
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160 <data name="alignments_txt" from_work_dir="./output_folder/alignments/alignments.txt" format="txt" label="${tool.name} on ${on_string}: alignments (txt)">
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161 <filter>output_options["write_alignment_format"] == "txt"</filter>
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162 </data>
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163 <data name="events_filtered_shifted" from_work_dir="./output_folder/alignments/events_filtered_shifted.csv" format="csv" label="${tool.name} on ${on_string}: evens filtered shifted">
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164 <filter>"events_filtered_shifted" in output_options["outputs"]</filter>
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165 </data>
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diff changeset
166 <data name="events_filtered_shifted_normalized" from_work_dir="./output_folder/alignments/events_filtered_shifted_normalized.csv" format="csv" label="${tool.name} on ${on_string}: events filtered shifted normalized">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
167 <filter>"events_filtered_shifted_normalized" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
168 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
169 <data name="raw_events" from_work_dir="./output_folder/alignments/raw_events.csv" format="csv" label="${tool.name} on ${on_string}: raw events">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
170 <filter>"raw_events" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
171 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
172 <data name="unassigned_reads" from_work_dir="./output_folder/alignments/unassigned_reads.csv" format="csv" label="${tool.name} on ${on_string}: unnasigned reads">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
173 <filter>"unassigned_reads" in output_options["outputs"]</filter>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
174 </data>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
175 </outputs>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
176 <tests>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
177 <!-- Test default inputs -->
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
178 <test expect_num_outputs="10">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
179 <param name="config_file" value="config.csv" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
180 <param name="fastq_files" value="R1_001.fastq,R1_002.fastq,R2_001.fastq,R2_002.fastq" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
181 <section name="quality_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
182 <param name="average_quality" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
183 <param name="min_quality" value="20"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
184 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
185 <section name="alignment_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
186 <param name="gap_opening" value="25"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
187 <param name="gap_extension" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
188 <param name="primer_mismatch" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
189 <param name="donor_mismatch" value="3"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
190 <section name="scoring_matrix">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
191 <param name="match_scoring" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
192 <param name="mismatch scoring" value="-4"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
193 <param name="base_only" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
194 <param name="scoring_type" value="DNA"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
195 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
196 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
197 <section name="advanced_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
198 <param name="fastq_use" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
199 <param name="primer_dimer" value="30"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
200 <param name="event_filter" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
201 <param name="cut_buffer" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
202 <param name="promiscuous_consensus" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
203 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
204 <section name="output_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
205 <param name="write_alignment_format" value="txt"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
206 <param name="outputs" value="config_summary,barcode_reads,knit_reports,parameters,alignments_rds,events_filtered_shifted,events_filtered_shifted_normalized,raw_events,unassigned_reads"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
207 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
208 <output name="config_summary" file="config_summary.csv" ftype="csv" lines_diff="10">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
209 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
210 <has_size value="2896" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
211 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
212 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
213 <output name="barcode_reads" file="barcode_reads_filtered.csv" ftype="tabular">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
214 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
215 <has_size value="212" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
216 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
217 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
218 <output name="output_html" file="output_html.html" ftype="html" lines_diff="17">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
219 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
220 <has_size value="1641557" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
221 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
222 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
223 <output name="parameters" file="RunParameters.txt" ftype="txt" lines_diff="4">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
224 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
225 <has_size value="418" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
226 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
227 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
228 <output name="alignments_rds" ftype="rdata">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
229 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
230 <has_size value="86527" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
231 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
232 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
233 <output name="alignments_txt" file="alignments.txt" ftype="txt">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
234 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
235 <has_size value="13406" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
236 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
237 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
238 <output name="events_filtered_shifted" file="events_filtered_shifted.csv" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
239 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
240 <has_size value="4826" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
241 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
242 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
243 <output name="events_filtered_shifted_normalized" file="events_filtered_shifted_normalized.csv" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
244 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
245 <has_size value="4826" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
246 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
247 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
248 <output name="raw_events" file="raw_events.csv" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
249 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
250 <has_size value="4455" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
251 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
252 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
253 <output name="unassigned_reads" file="unassigned_reads.csv" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
254 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
255 <has_size value="1176" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
256 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
257 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
258 </test>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
259 <!-- Test alignment output in fasta format -->
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
260 <test expect_num_outputs="10">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
261 <param name="config_file" value="config.csv" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
262 <param name="fastq_files" value="R1_001.fastq,R1_002.fastq,R2_001.fastq,R2_002.fastq" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
263 <section name="quality_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
264 <param name="average_quality" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
265 <param name="min_quality" value="20"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
266 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
267 <section name="alignment_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
268 <param name="gap_opening" value="25"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
269 <param name="gap_extension" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
270 <param name="primer_mismatch" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
271 <param name="donor_mismatch" value="3"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
272 <section name="scoring_matrix">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
273 <param name="match_scoring" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
274 <param name="mismatch scoring" value="-4"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
275 <param name="base_only" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
276 <param name="scoring_type" value="DNA"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
277 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
278 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
279 <section name="advanced_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
280 <param name="fastq_use" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
281 <param name="primer_dimer" value="30"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
282 <param name="event_filter" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
283 <param name="cut_buffer" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
284 <param name="promiscuous_consensus" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
285 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
286 <section name="output_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
287 <param name="write_alignment_format" value="fasta"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
288 <param name="outputs" value="config_summary,barcode_reads,knit_reports,parameters,alignments_rds,events_filtered_shifted,events_filtered_shifted_normalized,raw_events,unassigned_reads"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
289 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
290 <output name="config_summary" ftype="csv" >
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
291 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
292 <has_size value="2896" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
293 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
294 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
295 <output name="barcode_reads" ftype="tabular">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
296 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
297 <has_size value="212" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
298 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
299 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
300 <output name="output_html" ftype="html">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
301 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
302 <has_size value="1641557" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
303 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
304 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
305 <output name="parameters" ftype="txt" lines_diff="2">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
306 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
307 <has_size value="418" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
308 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
309 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
310 <output name="alignments_rds" ftype="rdata">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
311 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
312 <has_size value="86527" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
313 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
314 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
315 <output name="alignments_fasta" ftype="fasta">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
316 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
317 <has_size value="16146" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
318 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
319 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
320 <output name="events_filtered_shifted" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
321 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
322 <has_size value="4826" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
323 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
324 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
325 <output name="events_filtered_shifted_normalized" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
326 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
327 <has_size value="4826" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
328 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
329 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
330 <output name="raw_events" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
331 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
332 <has_size value="4455" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
333 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
334 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
335 <output name="unassigned_reads" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
336 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
337 <has_size value="1176" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
338 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
339 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
340 </test>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
341 <!-- Test limit outputs -->
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
342 <test expect_num_outputs="2">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
343 <param name="config_file" value="config.csv" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
344 <param name="fastq_files" value="R1_001.fastq,R1_002.fastq,R2_001.fastq,R2_002.fastq" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
345 <section name="quality_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
346 <param name="average_quality" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
347 <param name="min_quality" value="20"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
348 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
349 <section name="alignment_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
350 <param name="gap_opening" value="25"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
351 <param name="gap_extension" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
352 <param name="primer_mismatch" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
353 <param name="donor_mismatch" value="3"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
354 <section name="scoring_matrix">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
355 <param name="match_scoring" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
356 <param name="mismatch scoring" value="-4"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
357 <param name="base_only" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
358 <param name="scoring_type" value="DNA"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
359 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
360 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
361 <section name="advanced_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
362 <param name="fastq_use" value="0"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
363 <param name="primer_dimer" value="30"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
364 <param name="event_filter" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
365 <param name="cut_buffer" value="5"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
366 <param name="promiscuous_consensus" value="true"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
367 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
368 <section name="output_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
369 <param name="write_alignment_format" value="fasta"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
370 <param name="outputs" value="config_summary"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
371 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
372 <output name="config_summary" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
373 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
374 <has_size value="2896" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
375 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
376 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
377 <output name="alignments_fasta" ftype="fasta">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
378 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
379 <has_size value="16146" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
380 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
381 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
382 </test>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
383 <!-- Test gzip files -->
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
384 <test expect_num_outputs="2">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
385 <param name="config_file" value="config_gzip.csv" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
386 <param name="fastq_files" value="R1_001.fastq.gz,R1_002.fastq.gz,R2_001.fastq.gz,R2_002.fastq.gz" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
387 <section name="output_options">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
388 <param name="write_alignment_format" value="fasta"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
389 <param name="outputs" value="config_summary"/>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
390 </section>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
391 <output name="config_summary" ftype="csv">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
392 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
393 <has_size value="2896" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
394 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
395 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
396 <output name="alignments_fasta" ftype="fasta">
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
397 <assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
398 <has_size value="16146" delta="300" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
399 </assert_contents>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
400 </output>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
401 </test>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
402 </tests>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
403 <help><![CDATA[
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
404 .. class:: infomark
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
405
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
406 **Purpose**
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
407
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
408 AmpliCan is an analysis tool for genome editing that unites highly precise quantification and
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
409 visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
410 filtering of experimental artifacts, event-specific normalization, and off-target read detection
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
411 and quantifies insertions, deletions, HDR repair, as well as targeted base editing. It is
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
412 scalable to thousands of amplicon sequencing-based experiments from any genome editing experiment,
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
413 including CRISPR. It enables automated integration of controls and accounts for biases at every
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
414 step of the analysis.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
415
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
416 ----
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
417
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
418 .. class:: infomark
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
419
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
420 **Config file details**
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
421
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
422 Columns of the config file:
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
423
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
424 - ID - should be a unique identifier of your experiments.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
425 - Barcode - use this to group experiments with the same barcode.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
426 - Forward_Reads, Reverse_Reads - put names of your files in these fields, you can put here files compressed to .gz, we will unpack them for you.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
427 - Group - use this field if you want to group ID by other criteria, here for instance we will group by person that performed experiment, on later stage it is possible to generate report with breakdown using this field.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
428 - guideRNA - put your guideRNA in 5’ to 3’ fashion here, if he has to be reverse complemented to be found in the amplicon put “1” into Direction field, we will use this field to make sure your guideRNA is inside the amplicon and during plotting of the results.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
429 - Forward_Primer, Reverse_Primer - make sure these primers are correct for each of your IDs, Forward_Primer should be found in the amplicon as is, on the left side of the guide, Reverse_Primer reverse complement should be found on the amplicon on the right side of the guide.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
430 - Direction - here “0” means guide does not requires to be reverse complemented to be matched to the amplicon, “1” means it should be reverse complemented, this field is also used when plotting deletions, mismatches and insertions.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
431 - Amplicon - insert amplicon sequence as lower case letters, by putting UPPER CASE letters you can specify expected cut site, you should specify at least one cut site, here for example we specify in uppercase letter PAM sequence of the corresponding guideRNA.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
432 - Donor - insert donor template if you have designed HDR experiments or used base editors, otherwise leave empty, but keep the column. amplican will estimate HDR efficiency based on the events from aligning donor and amplicon sequences, donor and reads and reads and amplicon.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
433
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
434 If you have only forward primers leave column Reverse_Primer empty, leave empty also the Reverse_Reads column. You can still use amplican like normal.
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
iuc
parents:
diff changeset
435
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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436 ]]> </help>
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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437 <expand macro="citations" />
71adaaace336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc"
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438 </tool>