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annotate flair_collapse.xml @ 0:5d17cf201540 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
author iuc
date Fri, 27 Nov 2020 18:45:47 +0000
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5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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1 <tool id="flair_collapse" name="FLAIR collapse" version="@TOOL_VERSION@" profile="20.01">
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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2 <description>defines high-confidence isoforms from flair-corrected reads</description>
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3
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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4 <macros>
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5 <import>flair_macros.xml</import>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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6 </macros>
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5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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8 <expand macro="requirements" />
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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9 <expand macro="version_command" />
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5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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11 <command detect_errors="exit_code"><![CDATA[
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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13 @PREPARE_REF@
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5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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15 ln -s '$input_query' query.bed &&
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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17 flair.py collapse
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5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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19 ###########
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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20 ## Input ##
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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21 ###########
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5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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23 -q query.bed
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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24 -r '$input_reads'
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25 -g reference.fa
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26 -f '$input_gtf'
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27
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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28 #if $input_promotors:
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29 -p '$input_promotors'
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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30 #end if
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31
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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32 ########################
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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33 ## Additional Options ##
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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34 ########################
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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35
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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36 -w $additional_options.window
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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37 -s $additional_options.support
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38 $additional_options.stringent
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39
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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40 #if str($additional_options.select_uniqueness):
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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41 -n str($additional_options.select_uniqueness)
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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42 #end if
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43
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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44 $additional_options.isoform
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45 --max_ends $additional_options.maxends
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46 $additional_options.trustends
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47
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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48 #if str($additional_options.select_filter):
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49 -e str($additional_options.select_filter)
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50 #end if
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51
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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52 #########
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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53 ## END ##
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54 #########
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55
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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56 ]]></command>
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57 <inputs>
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58 <param name="input_query" argument="-q" type="data" format="bed" label="Corrected Reads as BED file"/>
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59 <param name="input_reads" argument="-r" type="data" format="fasta,fastq" label="FASTA/FASTQ file of raw reads"/>
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60 <expand macro="reference_interface" />
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61 <param name="input_gtf" argument="-f" type="data" format="gtf" label="GTF annotation file"/>
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62 <param name="input_promotors" optional="true" argument="-p" type="data" format="bed" label="Promotor BED file to identify full-length reads" />
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63
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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64 <!-- Additional Options -->
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65 <section name="additional_options" title="Additional Options">
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66 <param name="window" argument="-w" type="integer" min="1" value="100" label="Window Size" help="Window size for comparing TSS/TES (Default=100)" />
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67 <param name="support" argument="-s" type="integer" min="1" value="3" label="Supporting Reads" help="Minimum number of supporting reads for an isoform (Default=3)" />
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68 <param name="stringent" argument="--stringent" type="boolean" checked="false" truevalue="--stringent" falsevalue="" label="Use Stringent Mode" help="Specify if all supporting reads need to be full-length (80% coverage and spanning 25 bp of the first and last exons) (Default=false)"/>
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69 <param name="select_uniqueness" argument="-n" type="select" label="Choose the TSS/TES for each unique set of splice junction." >
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70 <option value="" selected="true">No Selection</option>
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71 <option value="none">Best TSSs/TESs</option>
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72 <option value="longest">Single TSS/TES chosen to maximize length</option>
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73 <option value="best_only">Single most supported TSS/TES used in conjunction chosen</option>
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74 </param>
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75 <param name="isoform" argument="-i" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Use Isoform Mode" help="TSS/TES for each isoform will be determined from supporting reads for individual isoforms (Default=false)"/>
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76 <param name="maxends" argument="--max_ends" type="integer" min="0" value="2" label="Maximum Number of TSS/TES picked per isoform" help="(Default=2)" />
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77 <param name="trustends" argument="--trust_ends" type="boolean" checked="false" truevalue="--trust_ends" falsevalue="" label="Reads are generated from a long read method with minimal fragmentation?" />
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78 <param name="select_filter" argument="-e" type="select" label="Filter for isoforms." >
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79 <option value="" selected="true">No Filter</option>
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80 <option value="nosubset">Any isoforms that are a proper set of another isoform are removed</option>
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81 <option value="default">Subset isoforms are removed based on support</option>
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82 <option value="comprehensive">Default set + all subset isoforms</option>
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83 <option value="ginormous">Comprehensive set + single exon subset isoforms</option>
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84 </param>
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85 <param name="mapq" argument="--quality" type="integer" min="0" value="1" label="Minimum MAPQ of read assignment to an isoform" help="(Default=1)" />
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86 </section>
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87
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88 <section name="additional_outputs" title="Output Options">
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89 <param name="out_format" type="select" multiple="true" optional="true" display="checkboxes" label="Data types">
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90 <option value="bed">BED</option>
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91 <option value="fasta">FASTA</option>
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92 </param>
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93 </section>
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94 </inputs>
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95
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96 <outputs>
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97 <data name="outfile_isoforms_gtf" from_work_dir="flair.collapse.isoforms.gtf" format="gtf" label="${tool.name} on ${on_string}: Isoforms GTF" />
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98 <data name="outfile_isoforms_bed" from_work_dir="flair.collapse.isoforms.bed" format="bed" label="${tool.name} on ${on_string}: Isoforms BED">
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99 <filter>additional_outputs['out_format'] and 'bed' in additional_outputs['out_format']</filter>
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100 </data>
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101 <data name="outfile_isoforms_fasta" from_work_dir="flair.collapse.isoforms.fa" format="fasta" label="${tool.name} on ${on_string}: Isoforms FASTA">
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102 <filter>additional_outputs['out_format'] and 'fasta' in additional_outputs['out_format']</filter>
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103 </data>
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104 </outputs>
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105
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106 <tests>
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107 <test expect_num_outputs="3">
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108 <param name="input_query" ftype="bed" value="flair_all_corrected.bed" />
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109 <param name="input_reads" ftype="fastq.gz" value="chrM.fastq.gz" />
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110 <param name="ref_selector_genome" value="history" />
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111 <param name="reffile" ftype="fasta" value="chrM.fa" />
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112 <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" />
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113 <param name="out_format" value="bed,fasta" />
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114 <output name="outfile_isoforms_gtf" ftype="gtf" file="flair.collapse.isoforms.gtf" />
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115 <output name="outfile_isoforms_bed" ftype="bed" file="flair.collapse.isoforms.bed" />
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116 <output name="outfile_isoforms_fasta" ftype="fasta" file="flair.collapse.isoforms.fa" />
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117 </test>
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118 <!-- Test with cached genome -->
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119 <test expect_num_outputs="3">
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120 <param name="input_query" ftype="bed" value="flair_all_corrected.bed" />
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121 <param name="input_reads" ftype="fastq.gz" value="chrM.fastq.gz" />
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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122 <param name="ref_selector_genome" value="cached" />
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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123 <param name="reffile" value="chrM" />
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124 <param name="input_gtf" ftype="gtf" value="UCSC_Main_on_Human_knownGene_region_chrM.gtf" />
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125 <param name="out_format" value="bed,fasta" />
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126 <output name="outfile_isoforms_gtf" ftype="gtf" file="flair.collapse.isoforms.gtf" />
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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127 <output name="outfile_isoforms_bed" ftype="bed" file="flair.collapse.isoforms.bed" />
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128 <output name="outfile_isoforms_fasta" ftype="fasta" file="flair.collapse.isoforms.fa" />
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129 </test>
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130 </tests>
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131 <help><![CDATA[
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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132
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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133 .. class:: infomark
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134
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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135 **What it does**
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136
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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137 -------------------
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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138
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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139 @description@
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140
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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141 **flair collapse**
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142 Defines high-confidence isoforms from corrected reads.
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143
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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144 -------------------
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145
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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146 **Inputs**
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147
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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148 -------------------
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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149
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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150 (1) Corrected Reads as Bed12 File.
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151 (2) FASTA/FASTQ file of raw reads. All raw read fastq/fasta files should be concatenated into a single file.
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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152 (3) FASTA of Reference Genome.
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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153 (4) GTF annotation file.
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154 (5) Promoter regions bed file to identify full-length reads.
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155
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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156 -----------
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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157
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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158 **Outputs**
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159
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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160 -----------
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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161
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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162 Outputs the high-confidence isoforms in several formats:
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163 (1) bed,
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164 (2) gtf,
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165 (3) FASTA.
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166
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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167 --------------------
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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168
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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169 **More Information**
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170
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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171 --------------------
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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172
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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173 See the excellent `FLAIR documentation`_
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174
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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175 .. _`FLAIR documentation`: https://github.com/BrooksLabUCSC/flair
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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176
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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177
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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178 --------------------
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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179
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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180 **Galaxy Wrapper Development**
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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181
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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182 --------------------
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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183
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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184 @citation@
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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185
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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186 ]]></help>
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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187 <expand macro="citations" />
5d17cf201540 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair commit b80808c3c53775c3f323581efb44d124d6e8bd1a"
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188 </tool>