annotate gffread.xml @ 24:8ec95406dfc1 draft default tip

Deleted selected files
author enios
date Thu, 27 May 2021 10:16:04 +0000
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1 <tool id="gffread" name="gffreadB" version="@VERSION@.0">
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2 <description>Filters and/or converts GFF3/GTF2 records</description>
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3 <requirements>
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4 <container type="docker">343307676715.dkr.ecr.eu-central-1.amazonaws.com/galaxy:gffread</container>
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5 </requirements>
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6 <macros>
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7 <token name="@VERSION@">0.11.6</token>
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8 <xml name="fasta_output_select">
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9 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">
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10 <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w exons.fa)</option>
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11 <option value="-x cds.fa">fasta file with spliced CDS for each GFF transcript (-x cds.fa)</option>
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12 <option value="-y pep.fa">protein fasta file with the translation of CDS for each record (-y pep.fa)</option>
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13 <option value="-W">for each fasta: record the exon coordinates projected onto the spliced sequence (-W)</option>
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14 </param>
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15 </xml>
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16 <xml name="ref_filtering_select">
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17 <param name="ref_filtering" type="select" display="checkboxes" multiple="true" label="reference based filters">
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18 <option value="-N">discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus, i.e. not GT-AG, GC-AG or AT-AC (-N)</option>
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19 <option value="-J">discard any mRNAs that either lack initial START codon or the terminal STOP codon, or have an in-frame stop codon (-J)</option>
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20 <option value="-V">discard any mRNAs with CDS having in-frame stop codons (-V)</option>
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21 <option value="-H">check and adjust the starting CDS phase if the original phase leads to a translation with an in-frame stop codon (-H with -V)</option>
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22 <!-- gffread bug: B not in missing from param to the arg parser
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23 <option value="-B">single-exon transcripts are also checked on the opposite strand (-B with -V)</option>
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24 -->
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25 </param>
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26 </xml>
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27 <xml name="trackname">
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28 <param name="tname" type="text" value="" optional="true" label="Trackname to use in the second column of each GFF output line" help="(-t track_name}">
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29 <validator type="regex">\w+</validator>
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30 </param>
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31 </xml>
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32 <xml name="merge_opts">
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33 <option value="-K">also collapse shorter, fully contained transcripts with fewer introns than the container (-K)</option>
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34 <option value="-Q">remove the containment restriction: multi-exon transcripts will be collapsed if just their introns match, while single-exon transcripts can partially overlap 80% (-Q)</option>
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35 <option value="-d dupinfo">output collapsing info (-d dupinfo)</option>
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36 </xml>
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37 <xml name="cluster_opts">
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38 <option value="--force-exons"> make sure that the lowest level GFF features are printed as 'exon' features (--force-exons)</option>
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39 <option value="-Z">merge close exons into a single exon (for intron size &lt; 4) (-Z)</option>
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40 </xml>
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41 <xml name="merge_opt_sel">
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42 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Merge options">
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43 <expand macro="cluster_opts" />
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44 <expand macro="merge_opts" />
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45 </param>
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46 </xml>
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47 <xml name="cluster_opt_sel">
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48 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options">
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49 <expand macro="cluster_opts" />
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50 </param>
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51 </xml>
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52 </macros>
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53 <command detect_errors="aggressive">
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54 <![CDATA[
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55 #if $reference_genome.source == 'history':
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56 ln -s '$reference_genome.genome_fasta' genomeref.fa &&
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57 #end if
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58 gffread '$input'
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59 #if $reference_genome.source == 'cached':
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60 -g '${reference_genome.fasta_indexes.fields.path}'
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61 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
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62 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
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63 #end if
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64 #elif $reference_genome.source == 'history':
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65 -g genomeref.fa
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66 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
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67 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
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68 #end if
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69 #end if
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70 #if $filtering and str($filtering) != '':
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71 #echo " "
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72 #echo ' '.join(str($filtering).split(','))
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73 #end if
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74 #if $maxintron and $maxintron > 0:
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75 -i $maxintron
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76 #end if
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77 #if $region.region_filter == 'filter':
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78 -r '$region.range' $region.discard_partial
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79 #end if
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80 #if $merging.merge_sel != 'none':
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81 $merging.merge_cmd
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82 #if $merging.merge_options:
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83 #echo ' '.join(str($merging.merge_options).split(','))
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84 #end if
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85 #end if
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86 #if $chr_replace:
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87 -m '$chr_replace'
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88 #end if
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89
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90 $full_gff_attribute_preservation
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91 $decode_url
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92 $expose
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93
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94 ##
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95 ## Although documented, does not appear to be used in the gffread code
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96 ## #if $seq_info:
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97 ## -A -s "$seq_info"
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98 ## #end if
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99 ##
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100 ## outputs
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101 #if $reference_genome.source != 'none':
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102 #if $reference_genome.fa_outputs and str($reference_genome.fa_outputs) != '':
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103 #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(','))
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104 #end if
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105 #end if
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106 #if $gffs.gff_fmt != 'none':
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107 #if $gffs.tname:
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108 -t '$gffs.tname'
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109 #end if
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110 #if $gffs.gff_fmt == 'gff':
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111 #if $input.datatype.file_ext == 'gft':
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112 $gffs.ensembl
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113 #end if
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114 $gffs.output_cmd
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115 #elif $gffs.gff_fmt == 'gtf':
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116 $gffs.output_cmd
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117 #end if
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118 #end if
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119 ]]>
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120 </command>
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121 <inputs>
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122 <param name="input" type="data" format="gff3,gtf" label="Input GFF3 or GTF feature file"/>
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123 <!-- filtering -->
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124 <param name="filtering" type="select" display="checkboxes" multiple="true" label="filters">
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125 <option value="-U">discard single-exon transcripts (-U)</option>
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126 <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option>
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127 <option value="-G">only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) (-G)</option>
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128 <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>
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129 <option value="--no-pseudo">filter out records matching the 'pseudo' keyword (--no-pseudo)</option>
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130 </param>
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131 <conditional name="region">
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132 <param name="region_filter" type="select" label="Filter by genome region">
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133 <option value="none">No</option>
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134 <option value="filter">Yes</option>
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135 </param>
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136 <when value="none"/>
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137 <when value="filter">
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138 <param name="range" type="text" value="" label="Only show transcripts overlapping coordinate range">
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139 <help><![CDATA[
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140 (-r [['strand']'chr':]'start'..'end') <br>
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141 examples: <br>
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142 1000..500000 <br>
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143 chr1:1000..500000 <br>
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144 +chr1:1000..500000 <br>
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145 -chr1:1000..500000
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146 ]]>
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147 </help>
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148 <validator type="regex">(([+-])?(\w+:))?\d+\.\.\d+</validator>
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149 </param>
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150 <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" checked="false"
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151 label="Discard all transcripts that are not fully contained within the given range" help="(-R)"/>
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152 </when>
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153 </conditional>
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154 <param name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns"
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155 help="If set, discard transcripts having an intron larger (-i max_intron)"/>
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156 <param name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names" >
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157 <help><![CDATA[(-m chr_replace) <br>
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158 chr_replace is a reference sequence replacement table consisting of 2 columns: "original_ref_ID" "new_ref_ID"<br>
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159 It is useful for switching between Ensembl and UCSC naming conventions <br>
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160 NOTE: GFF records on reference sequences that are not found among the "original_ref_ID" entries in this file will be filtered out
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161 ]]>
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162 </help>
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163 </param>
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164
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165 <!-- Although documented, does not appear to be used in the gffread code
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166 <param name="seq_info" type="data" format="tabular" optional="true" label="Use the description field as the value for a 'descr' attribute to the GFF record">
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167 <help>
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168 (-s seq_info.fsize -A) useful with mRNA/EST/protein mappings &lt;br&gt;
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169 seq_info input file is a 3 column tab-delimited file providing this info for each of the mapped sequences: &lt;br&gt;
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170 "seq-name" "seq-length" "seq-description" &lt;br&gt;
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171 </help>
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172 </param>
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173 -->
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174
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175 <!-- merging -->
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176 <conditional name="merging">
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177 <param name="merge_sel" type="select" label="Transcript merging" help="(-M/--merge or --cluster-only)">
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178 <option value="none">none</option>
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179 <option value="merge">merge: cluster the input transcripts into loci, collapsing matching transcripts</option>
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180 <option value="cluster">cluster-only: merge but without collapsing matching transcripts</option>
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181 </param>
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182 <when value="none"/>
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183 <when value="merge">
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184 <param name="merge_cmd" type="hidden" value="--merge"/>
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185 <expand macro="merge_opt_sel" />
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186 </when>
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187 <when value="cluster">
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188 <param name="merge_cmd" type="hidden" value="--cluster-only"/>
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189 <expand macro="cluster_opt_sel" />
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diff changeset
190 </when>
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191 </conditional>
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diff changeset
192 <!-- reference sequence file -->
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193 <!-- Error: -g option is required for options -w, -x, -y, -V, -N, -M -->
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diff changeset
194 <conditional name="reference_genome">
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195 <param name="source" type="select" label="Reference Genome" help="(-g genome.fasta) NOTE: Required for fasta outputs">
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196 <option value="none">none</option>
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parents:
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197 <option value="cached"></option>
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198 <option value="history">From your history</option>
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199 </param>
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parents:
diff changeset
200 <when value="none">
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parents:
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201 </when>
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parents:
diff changeset
202 <when value="cached">
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parents:
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203 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
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parents:
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204 <options from_data_table="all_fasta"/>
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parents:
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205 </param>
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parents:
diff changeset
206 <expand macro="ref_filtering_select" />
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parents:
diff changeset
207 <expand macro="fasta_output_select" />
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parents:
diff changeset
208 </when>
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parents:
diff changeset
209 <when value="history">
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parents:
diff changeset
210 <param name="genome_fasta" type="data" format="fasta" label="Genome Reference Fasta"/>
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parents:
diff changeset
211 <expand macro="ref_filtering_select" />
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parents:
diff changeset
212 <expand macro="fasta_output_select" />
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213 </when>
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214 </conditional>
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215
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216 <!-- outputs -->
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diff changeset
217 <conditional name="gffs">
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218 <param name="gff_fmt" type="select" label="Feature File Output" help="(-o output.gff3|output.gtf)">
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parents:
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219 <option value="none">none</option>
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parents:
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220 <option value="gff">GFF</option>
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parents:
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221 <option value="gtf">GTF</option>
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222 </param>
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parents:
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223 <when value="none">
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parents:
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224 </when>
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parents:
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225 <when value="gff">
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226 <param name="output_cmd" type="hidden" value="-o output.gff3"/>
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parents:
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227 <param name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help="(-L)"/>
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parents:
diff changeset
228 <expand macro="trackname" />
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parents:
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229 </when>
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parents:
diff changeset
230 <when value="gtf">
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diff changeset
231 <param name="output_cmd" type="hidden" value="-T -o output.gtf"/>
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232 <expand macro="trackname" />
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233 </when>
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234 </conditional>
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235
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236 <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false"
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diff changeset
237 label="full GFF attribute preservation (all attributes are shown)" help="(-F)"/>
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parents:
diff changeset
238 <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" checked="false"
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parents:
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239 label="decode url encoded characters within attributes" help="(-D)"/>
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parents:
diff changeset
240 <param name="expose" type="boolean" truevalue="-E" falsevalue="" checked="false"
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parents:
diff changeset
241 label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help="(-E)"/>
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242
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243 </inputs>
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244 <outputs>
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parents:
diff changeset
245 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff3">
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parents:
diff changeset
246 <filter>gffs['gff_fmt'] == 'gff'</filter>
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parents:
diff changeset
247 </data>
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diff changeset
248 <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf">
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diff changeset
249 <filter>gffs['gff_fmt'] == 'gtf'</filter>
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parents:
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250 </data>
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251 <data name="output_exons" format="fasta" label="${tool.name} on ${on_string}: exons.fa" from_work_dir="exons.fa">
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diff changeset
252 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('exons.fa') > 0 </filter>
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253 </data>
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254 <data name="output_cds" format="fasta" label="${tool.name} on ${on_string}: cds.fa" from_work_dir="cds.fa">
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diff changeset
255 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('cds.fa') > 0</filter>
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256 </data>
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257 <data name="output_pep" format="fasta" label="${tool.name} on ${on_string}: pep.fa" from_work_dir="pep.fa">
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diff changeset
258 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('pep.fa') > 0</filter>
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diff changeset
259 </data>
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260 <data name="output_dupinfo" format="txt" label="${tool.name} on ${on_string}: dupinfo" from_work_dir="dupinfo">
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parents:
diff changeset
261 <filter>'merge_options' in merging and merging['merge_options'].find('dupinfo') > 0</filter>
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diff changeset
262 </data>
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263 </outputs>
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diff changeset
264 <tests>
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diff changeset
265 <test>
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parents:
diff changeset
266 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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diff changeset
267 <param name="gff_fmt" value="gff"/>
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parents:
diff changeset
268 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" />
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parents:
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269 </test>
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diff changeset
270 <test>
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parents:
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271 <param name="input" ftype="gtf" value="ecoli-k12.gff3"/>
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parents:
diff changeset
272 <param name="gff_fmt" value="gff"/>
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diff changeset
273 <param name="full_gff_attribute_preservation" value="-F"/>
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parents:
diff changeset
274 <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" />
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275 </test>
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diff changeset
276 <test>
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277 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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parents:
diff changeset
278 <param name="filtering" value="--no-pseudo"/>
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parents:
diff changeset
279 <param name="gff_fmt" value="gtf"/>
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parents:
diff changeset
280 <output name="output_gtf">
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diff changeset
281 <assert_contents>
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diff changeset
282 <not_has_text text="pseudo" />
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parents:
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283 </assert_contents>
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parents:
diff changeset
284 </output>
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285 </test>
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parents:
diff changeset
286 <test>
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parents:
diff changeset
287 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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parents:
diff changeset
288 <param name="region_filter" value="filter"/>
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parents:
diff changeset
289 <param name="range" value="19:496500..504965"/>
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parents:
diff changeset
290 <param name="gff_fmt" value="gtf"/>
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parents:
diff changeset
291 <output name="output_gtf">
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parents:
diff changeset
292 <assert_contents>
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parents:
diff changeset
293 <has_text text="ENST00000587541" />
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parents:
diff changeset
294 <has_text text="ENST00000382683" />
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parents:
diff changeset
295 </assert_contents>
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parents:
diff changeset
296 </output>
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297 </test>
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parents:
diff changeset
298 <test>
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parents:
diff changeset
299 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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parents:
diff changeset
300 <param name="region_filter" value="filter"/>
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parents:
diff changeset
301 <param name="range" value="19:496500..504965"/>
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parents:
diff changeset
302 <param name="discard_partial" value="true"/>
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parents:
diff changeset
303 <param name="gff_fmt" value="gtf"/>
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parents:
diff changeset
304 <output name="output_gtf">
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parents:
diff changeset
305 <assert_contents>
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parents:
diff changeset
306 <not_has_text text="ENST00000587541" />
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parents:
diff changeset
307 <has_text text="ENST00000382683" />
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parents:
diff changeset
308 </assert_contents>
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parents:
diff changeset
309 </output>
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parents:
diff changeset
310 </test>
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parents:
diff changeset
311 <test>
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parents:
diff changeset
312 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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parents:
diff changeset
313 <param name="filtering" value="-C"/>
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parents:
diff changeset
314 <param name="region_filter" value="filter"/>
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parents:
diff changeset
315 <param name="range" value="19:496500..504965"/>
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parents:
diff changeset
316 <param name="gff_fmt" value="gtf"/>
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parents:
diff changeset
317 <output name="output_gtf">
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parents:
diff changeset
318 <assert_contents>
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parents:
diff changeset
319 <not_has_text text="ENST00000587541" />
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parents:
diff changeset
320 <has_text text="ENST00000382683" />
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parents:
diff changeset
321 </assert_contents>
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parents:
diff changeset
322 </output>
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parents:
diff changeset
323 </test>
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parents:
diff changeset
324 <test>
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parents:
diff changeset
325 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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parents:
diff changeset
326 <param name="source" value="history"/>
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parents:
diff changeset
327 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
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parents:
diff changeset
328 <param name="fa_outputs" value="-w exons.fa,-x cds.fa,-y pep.fa"/>
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parents:
diff changeset
329 <param name="region_filter" value="filter"/>
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parents:
diff changeset
330 <param name="range" value="19:496500..504965"/>
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parents:
diff changeset
331 <param name="gff_fmt" value="gtf"/>
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parents:
diff changeset
332 <output name="output_gtf">
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parents:
diff changeset
333 <assert_contents>
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parents:
diff changeset
334 <has_text text="ENST00000587541" />
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parents:
diff changeset
335 <has_text text="ENST00000382683" />
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parents:
diff changeset
336 </assert_contents>
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parents:
diff changeset
337 </output>
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parents:
diff changeset
338 <output name="output_exons">
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parents:
diff changeset
339 <assert_contents>
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parents:
diff changeset
340 <has_text text="ENST00000346144 CDS=47-934" />
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enios
parents:
diff changeset
341 <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" />
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parents:
diff changeset
342 </assert_contents>
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parents:
diff changeset
343 </output>
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parents:
diff changeset
344 <output name="output_cds">
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parents:
diff changeset
345 <assert_contents>
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parents:
diff changeset
346 <has_text text="ENST00000346144" />
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parents:
diff changeset
347 <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" />
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parents:
diff changeset
348 </assert_contents>
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parents:
diff changeset
349 </output>
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parents:
diff changeset
350 <output name="output_pep">
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parents:
diff changeset
351 <assert_contents>
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parents:
diff changeset
352 <has_text text="ENST00000346144" />
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enios
parents:
diff changeset
353 <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" />
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parents:
diff changeset
354 </assert_contents>
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parents:
diff changeset
355 </output>
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parents:
diff changeset
356 </test>
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parents:
diff changeset
357
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parents:
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358 </tests>
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parents:
diff changeset
359 <help>
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parents:
diff changeset
360 <![CDATA[
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parents:
diff changeset
361 **gffread Filters and/or converts GFF3/GTF2 records**
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parents:
diff changeset
362
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parents:
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363 The gffread command is documented with the stringtie_ package.
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parents:
diff changeset
364
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parents:
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365 .. _stringtie: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
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parents:
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366
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parents:
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367
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parents:
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368 gffread v0.11.4. Usage: ::
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parents:
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369
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parents:
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370 gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>]
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parents:
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371 [-o <outfile>] [-t <trackname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]
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parents:
diff changeset
372 [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]
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parents:
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373 [-i <maxintron>] [--bed] [--table <attrlist>] [--sort-by <refseq_list.txt>]
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parents:
diff changeset
374
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parents:
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375 Filter, convert or cluster GFF/GTF/BED records, extract the sequence of
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enios
parents:
diff changeset
376 transcripts (exon or CDS) and more.
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parents:
diff changeset
377 By default (i.e. without -O) only transcripts are processed, discarding any
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parents:
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378 other non-transcript features. Default output is a simplified GFF3 with only
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379 the basic attributes.
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380
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381 <input_gff> is a GFF file, use '-' for stdin
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382
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383 Options:
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384
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385 -i discard transcripts having an intron larger than <maxintron>
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386 -l discard transcripts shorter than <minlen> bases
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387 -r only show transcripts overlapping coordinate range <start>..<end>
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388 (on chromosome/contig <chr>, strand <strand> if provided)
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389 -R for -r option, discard all transcripts that are not fully
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390 contained within the given range
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391 -U discard single-exon transcripts
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392 -C coding only: discard mRNAs that have no CDS features
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393 --nc non-coding only: discard mRNAs that have CDS features
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394 --ignore-locus : discard locus features and attributes found in the input
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395 -A use the description field from <seq_info.fsize> and add it
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396 as the value for a 'descr' attribute to the GFF record
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397 -s <seq_info.fsize> is a tab-delimited file providing this info
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398 for each of the mapped sequences:
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399 <seq-name> <seq-length> <seq-description>
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400 (useful for -A option with mRNA/EST/protein mappings)
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401
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402 Sorting: (by default, chromosomes are kept in the order they were found)
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403 --sort-alpha : chromosomes (reference sequences) are sorted alphabetically
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404 --sort-by : sort the reference sequences by the order in which their
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405 names are given in the <refseq.lst> file
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406
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407 Misc options:
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408 -F preserve all GFF attributes (for non-exon features)
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409 --keep-exon-attrs : for -F option, do not attempt to reduce redundant
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410 exon/CDS attributes
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411 -G do not keep exon attributes, move them to the transcript feature
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412 (for GFF3 output)
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413 --keep-genes : in transcript-only mode (default), also preserve gene records
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414 --keep-comments: for GFF3 input/output, try to preserve comments
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415 -O process other non-transcript GFF records (by default non-transcript
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416 records are ignored)
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417 -V discard any mRNAs with CDS having in-frame stop codons (requires -g)
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418 -H for -V option, check and adjust the starting CDS phase
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419 if the original phase leads to a translation with an
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420 in-frame stop codon
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421 -B for -V option, single-exon transcripts are also checked on the
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422 opposite strand (requires -g)
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423 -P add transcript level GFF attributes about the coding status of each
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424 transcript, including partialness or in-frame stop codons (requires -g)
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425 --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
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426 that have CDS features
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427 --adj-stop stop codon adjustment: enables -P and performs automatic
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428 adjustment of the CDS stop coordinate if premature or downstream
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429 -N discard multi-exon mRNAs that have any intron with a non-canonical
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430 splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
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431 -J discard any mRNAs that either lack initial START codon
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432 or the terminal STOP codon, or have an in-frame stop codon
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433 (i.e. only print mRNAs with a complete CDS)
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434 --no-pseudo: filter out records matching the 'pseudo' keyword
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435 --in-bed: input should be parsed as BED format (automatic if the input
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436 filename ends with .bed*)
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437 --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
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438 features (see --tlf option below); automatic if the input
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439 filename ends with .tlf)
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440
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441 Clustering:
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442 -M/--merge : cluster the input transcripts into loci, discarding
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443 "duplicated" transcripts (those with the same exact introns
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444 and fully contained or equal boundaries)
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445 -d <dupinfo> : for -M option, write duplication info to file <dupinfo>
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446 --cluster-only: same as -M/--merge but without discarding any of the
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447 "duplicate" transcripts, only create "locus" features
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448 -K for -M option: also discard as redundant the shorter, fully contained
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449 transcripts (intron chains matching a part of the container)
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450 -Q for -M option, no longer require boundary containment when assessing
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451 redundancy (can be combined with -K); only introns have to match for
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452 multi-exon transcripts, and >=80% overlap for single-exon transcripts
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453 -Y for -M option, enforce -Q but also discard overlapping single-exon
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454 transcripts, even on the opposite strand (can be combined with -K)
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455
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456 Output options:
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457 --force-exons: make sure that the lowest level GFF features are considered
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458 "exon" features
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459 --gene2exon: for single-line genes not parenting any transcripts, add an
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460 exon feature spanning the entire gene (treat it as a transcript)
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461 --t-adopt: try to find a parent gene overlapping/containing a transcript
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462 that does not have any explicit gene Parent
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463 -D decode url encoded characters within attributes
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464 -Z merge very close exons into a single exon (when intron size<4)
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465 -g full path to a multi-fasta file with the genomic sequences
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466 for all input mappings, OR a directory with single-fasta files
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467 (one per genomic sequence, with file names matching sequence names)
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468 -w write a fasta file with spliced exons for each GFF transcript
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469 -x write a fasta file with spliced CDS for each GFF transcript
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470 -y write a protein fasta file with the translation of CDS for each record
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471 -W for -w and -x options, write in the FASTA defline the exon
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472 coordinates projected onto the spliced sequence;
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473 for -y option, write transcript attributes in the FASTA defline
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474 -S for -y option, use '*' instead of '.' as stop codon translation
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475 -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
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476 -m <chr_replace> is a name mapping table for converting reference
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477 sequence names, having this 2-column format:
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478 <original_ref_ID> <new_ref_ID>
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479 WARNING: all GFF records on reference sequences whose original IDs
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480 are not found in the 1st column of this table will be discarded!
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481 -t use <trackname> in the 2nd column of each GFF/GTF output line
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482 -o write the records into <outfile> instead of stdout
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483 -T main output will be GTF instead of GFF3
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484 --bed output records in BED format instead of default GFF3
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485 --tlf output "transcript line format" which is like GFF
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486 but exons, CDS features and related data are stored as GFF
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487 attributes in the transcript feature line, like this:
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488 exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords>
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489 <exons> is a comma-delimited list of exon_start-exon_end coordinates;
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490 <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>
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491 --table output a simple tab delimited format instead of GFF, with columns
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492 having the values of GFF attributes given in <attrlist>; special
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493 pseudo-attributes (prefixed by @) are recognized:
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494 @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen
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495 -v,-E expose (warn about) duplicate transcript IDs and other potential
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496 problems with the given GFF/GTF records
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497 ]]>
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498 </help>
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499 <citations>
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500 <citation type="doi">10.1038/nbt.1621</citation>
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501 </citations>
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502 </tool>
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503