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1 <tool id="gffread" name="gffread" version="@VERSION@.0">
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2 <description>Filters and/or converts GFF3/GTF2 records</description>
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3 <expand macro="requirements" />
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4 <expand macro="stdio" />
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5 <macros>
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6 <import>cuff_macros.xml</import>
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7 <xml name="fasta_output_select">
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8 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">
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9 <option value="-w exons.fa">(-w) a fasta file with spliced exons for each GFF transcript</option>
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10 <option value="-x cds.fa">(-x) a fasta file with spliced CDS for each GFF transcript</option>
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11 <option value="-y pep.fa">(-y) a protein fasta file with the translation of CDS for each record</option>
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12 <option value="-W">(-W) for each fasta record the exon coordinates projected onto the spliced sequence</option>
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13 </param>
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14 </xml>
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15 <xml name="ref_filtering_select">
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16 <param name="ref_filtering" type="select" display="checkboxes" multiple="true" label="reference based filters">
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17 <option value="-N">(-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)</option>
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18 <option value="-J">(-J) discard any mRNAs that either lack initial START codon or the terminal STOP codon, or have an in-frame stop codon (only print mRNAs with a fulll, valid CDS)</option>
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19 <option value="-V">(-V) discard any mRNAs with CDS having in-frame stop codons</option>
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20 <option value="-H">(-H with -V) check and adjust the starting CDS phase if the original phase leads to a translation with an in-frame stop codon</option>
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21 <option value="-B">(-B with -V) single-exon transcripts are also checked on the opposite strand</option>
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22 </param>
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23 </xml>
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24 <xml name="trackname">
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25 <param name="tname" type="text" value="" size="30" optional="true" label="(-t) Trackname to use in the second column of each GFF output line">
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26 <validator type="regex">\w+</validator>
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27 </param>
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28 </xml>
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29 <xml name="merge_opts">
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30 <option value="-K">(-K) also collapse shorter, fully contained transcripts with fewer introns than the container</option>
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31 <option value="-Q">(-Q) remove the containment restriction (multi-exon transcripts will be collapsed if just their introns match, while single-exon transcripts can partially overlap 80%)</option>
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32 <option value="-d dupinfo">(-d) output collapsing info</option>
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33 </xml>
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34 <xml name="cluster_opts">
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35 <option value="--force-exons">(--force-exons) make sure that the lowest level GFF features are printed as 'exon' features</option>
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36 <option value="-Z">(-Z) merge close exons into a single exon (for intron size < 4)</option>
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37 </xml>
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38 <xml name="merge_opt_sel">
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39 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Merge options">
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40 <expand macro="cluster_opts" />
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41 <expand macro="merge_opts" />
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42 </param>
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43 </xml>
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44 <xml name="cluster_opt_sel">
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45 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options">
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46 <expand macro="cluster_opts" />
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47 </param>
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48 </xml>
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49 </macros>
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50 <command>
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51 <![CDATA[
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52 #if $reference_genome.source == 'history':
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53 ln -s $reference_genome.genome_fasta genomeref.fa &&
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54 #end if
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55 gffread $input
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56 #if $reference_genome.source == 'cached':
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57 -g "${reference_genome.fasta_indexes.fields.path}"
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58 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
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59 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
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60 #end if
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61 #elif $reference_genome.source == 'history':
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62 -g genomeref.fa
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63 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
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64 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
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65 #end if
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66 #end if
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67 #if $filtering and str($filtering) != '':
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68 #echo " "
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69 #echo ' '.join(str($filtering).split(','))
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70 #end if
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71 #if $maxintron and $maxintron > 0:
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72 -i $maxintron
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73 #end if
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74 #if $region.region_filter == 'filter':
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75 -r $region.range $region.discard_partial
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76 #end if
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77 #if $merging.merge_sel != 'none':
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78 $merging.merge_cmd
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79 #echo ' '.join(str($merging.merge_options).split(','))
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80 #end if
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81 #if $chr_replace:
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82 -m "$chr_replace"
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83 #end if
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84 ##
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85 ## Although documented, does not appear to be used in the gffread code
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86 ## #if $seq_info:
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87 ## -A -s "$seq_info"
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88 ## #end if
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89 ##
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90 ## outputs
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91 #if $reference_genome.source != 'none':
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92 #if $reference_genome.fa_outputs and str($reference_genome.fa_outputs) != '':
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93 #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(','))
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94 #end if
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95 #end if
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96 #if $gffs.gff_fmt != 'none':
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97 #if $gffs.tname:
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98 -t "$gffs.tname"
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99 #end if
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100 #if $gffs.gff_fmt == 'gff':
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101 #if $input.datatype.file_ext == 'gft':
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102 $gffs.ensembl
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103 #end if
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104 $gffs.output_cmd
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105 #elif $gffs.gff_fmt == 'gtf':
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106 $gffs.output_cmd
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107 #end if
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108 #end if
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109 ]]>
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110 </command>
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111 <inputs>
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112 <param name="input" type="data" format="gff3,gtf" label="Input GFF3 or GTF feature file"/>
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113 <!-- filtering -->
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114 <param name="filtering" type="select" display="checkboxes" multiple="true" label="filters">
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115 <option value="-U">(-U) discard single-exon transcripts</option>
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116 <option value="-C">(-C) coding only: discard mRNAs that have no CDS feature</option>
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117 <option value="-G">(-G) only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input)</option>
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118 <option value="-O">(-O) process also non-transcript GFF records (by default non-transcript records are ignored)</option>
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119 <option value="--no-pseudo">(--no-pseudo) filter out records matching the 'pseudo' keyword</option>
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120 </param>
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121 <conditional name="region">
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122 <param name="region_filter" type="select" label="Filter by genome region">
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123 <option value="none">No</option>
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124 <option value="filter">Yes</option>
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125 </param>
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126 <when value="none"/>
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127 <when value="filter">
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128 <param name="range" type="text" value="" size="60" label="Only show transcripts overlapping coordinate range"
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129 help="-r [['strand']'chr':]'start'..'end' <br> examples: <br> 1000..500000 <br> chr1:1000..500000 <br> +chr1:1000..500000 <br> -chr1:1000..500000" >
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130 <validator type="regex">(([+-])?(\w+:))?\d+\.\.\d+</validator>
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131 </param>
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132 <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" check="false"
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133 label="(-R) and discard all transcripts that are not fully contained within the given range"/>
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134 </when>
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135 </conditional>
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136 <param name="maxintron" type="integer" value="" optional="true" min="0" label="(-i) max_intron - Filter out transcipts with large introns"
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137 help="If set, discard transcripts having an intron larger"/>
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138 <param name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names (e.g. chr1 with 1)" >
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139 <help>(-m chr_replace) <br>
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140 chr_replace is input file is a 2 column tab-delimited file containing a reference (genomic) sequence replacement table with this format: <br>
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141 "original_ref_ID" "new_ref_ID" <br>
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142 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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143 </help>
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144 </param>
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145
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146 <!-- Although documented, does not appear to be used in the gffread code
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147 <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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148 <help>
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149 (-s seq_info.fsize -A) useful with mRNA/EST/protein mappings <br>
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150 seq_info input file is a 3 column tab-delimited file providing this info for each of the mapped sequences: <br>
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151 "seq-name" "seq-length" "seq-description" <br>
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152 </help>
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153 </param>
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154 -->
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155
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156 <!-- merging -->
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157 <conditional name="merging">
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158 <param name="merge_sel" type="select" label="(-M) Transcript merging">
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159 <option value="none">none</option>
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160 <option value="merge">merge: cluster the input transcripts into loci, collapsing matching transcripts</option>
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161 <option value="cluster">cluster-only: merge but without collapsing matching transcripts</option>
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162 </param>
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163 <when value="none"/>
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164 <when value="merge">
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165 <param name="merge_cmd" type="hidden" value="--merge"/>
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166 <expand macro="merge_opt_sel" />
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167 </when>
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168 <when value="cluster">
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169 <param name="merge_cmd" type="hidden" value="--cluster-only"/>
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170 <expand macro="cluster_opt_sel" />
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171 </when>
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172 </conditional>
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173 <!-- reference sequence file -->
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174 <!-- Error: -g option is required for options -w, -x, -y, -V, -N, -M -->
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175 <conditional name="reference_genome">
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176 <param name="source" type="select" label="(-g) Reference Genome (Required for fasta outputs)">
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177 <option value="none">none</option>
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178 <option value="cached"></option>
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179 <option value="history">From your history</option>
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180 </param>
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181 <when value="none">
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182 </when>
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183 <when value="cached">
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184 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
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185 <options from_data_table="all_fasta"/>
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186 </param>
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187 <expand macro="ref_filtering_select" />
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188 <expand macro="fasta_output_select" />
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189 </when>
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190 <when value="history">
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191 <param name="genome_fasta" type="data" format="fasta" label="Genome Reference Fasta"/>
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192 <expand macro="ref_filtering_select" />
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193 <expand macro="fasta_output_select" />
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194 </when>
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195 </conditional>
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196
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197 <!-- outputs -->
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198 <conditional name="gffs">
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199 <param name="gff_fmt" type="select" optional="true" label="(-o) Feature File Output">
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200 <option value="none">none</option>
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201 <option value="gff">GFF</option>
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202 <option value="gtf">GTF</option>
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203 </param>
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204 <when value="none">
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205 </when>
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206 <when value="gff">
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207 <param name="output_cmd" type="hidden" value="-o output.gff3"/>
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208 <param name="ensembl" type="boolean" truevalue="-F" falsevalue="" check="false" label="(-L) Ensembl GTF to GFF3 conversion"/>
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209 <expand macro="trackname" />
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210 </when>
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211 <when value="gtf">
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212 <param name="output_cmd" type="hidden" value="-T -o output.gtf"/>
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213 <expand macro="trackname" />
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214 </when>
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215 </conditional>
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216
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217 <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" check="false"
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218 label="(-F) full GFF attribute preservation (all attributes are shown)"/>
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219 <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" check="false"
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220 label="(-D) decode url encoded characters within attributes"/>
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221 <param name="expose" type="boolean" truevalue="-E" falsevalue="" check="false"
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222 label="(-E) warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records"/>
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223
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224 </inputs>
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225 <outputs>
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226 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff3">
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227 <filter>gffs['gff_fmt'] == 'gff'</filter>
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228 </data>
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229 <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf">
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230 <filter>gffs['gff_fmt'] == 'gtf'</filter>
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231 </data>
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232 <data name="output_exons" format="fasta" label="${tool.name} on ${on_string}: exons.fa" from_work_dir="exons.fa">
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233 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('exons.fa') > 0 </filter>
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234 </data>
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235 <data name="output_cds" format="fasta" label="${tool.name} on ${on_string}: cds.fa" from_work_dir="cds.fa">
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236 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('cds.fa') > 0</filter>
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237 </data>
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238 <data name="output_pep" format="fasta" label="${tool.name} on ${on_string}: pep.fa" from_work_dir="pep.fa">
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239 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('pep.fa') > 0</filter>
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240 </data>
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241 <data name="output_dupinfo" format="txt" label="${tool.name} on ${on_string}: dupinfo" from_work_dir="dupinfo">
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242 <filter>'merge_options' in merging and merging['merge_options'].find('dupinfo') > 0</filter>
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243 </data>
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244 </outputs>
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245 <tests>
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246 <test>
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247 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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248 <param name="gff_fmt" value="gff"/>
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249 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" />
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250 </test>
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251
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252 <test>
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253 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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254 <param name="filtering" value="--no-pseudo"/>
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255 <param name="gff_fmt" value="gtf"/>
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256 <output name="output_gtf">
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257 <assert_contents>
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258 <not_has_text text="pseudo" />
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259 </assert_contents>
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260 </output>
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261 </test>
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262
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263 <test>
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264 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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265 <param name="region_filter" value="filter"/>
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266 <param name="range" value="19:496500..504965"/>
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267 <param name="gff_fmt" value="gtf"/>
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268 <output name="output_gtf">
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269 <assert_contents>
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270 <has_text text="ENST00000587541" />
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271 <has_text text="ENST00000382683" />
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272 </assert_contents>
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273 </output>
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274 </test>
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275
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276 <test>
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277 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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278 <param name="region_filter" value="filter"/>
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279 <param name="range" value="19:496500..504965"/>
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280 <param name="discard_partial" value="true"/>
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281 <param name="gff_fmt" value="gtf"/>
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282 <output name="output_gtf">
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283 <assert_contents>
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284 <has_text text="ENST00000587541" />
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285 <has_text text="ENST00000382683" />
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286 </assert_contents>
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287 </output>
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288 </test>
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289
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290 <test>
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291 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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292 <param name="filtering" value="-C"/>
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293 <param name="region_filter" value="filter"/>
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294 <param name="range" value="19:496500..504965"/>
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295 <param name="gff_fmt" value="gtf"/>
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296 <output name="output_gtf">
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297 <assert_contents>
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298 <not_has_text text="ENST00000587541" />
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299 <has_text text="ENST00000382683" />
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300 </assert_contents>
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301 </output>
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302 </test>
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303
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304 <test>
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305 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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306 <param name="source" value="history"/>
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307 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
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308 <param name="fa_outputs" value="-w exons.f,-x cds.fa,-y pep.fa"/>
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309 <param name="region_filter" value="filter"/>
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310 <param name="range" value="19:496500..504965"/>
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311 <param name="gff_fmt" value="gtf"/>
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312 <output name="output_gtf">
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313 <assert_contents>
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314 <not_has_text text="ENST00000587541" />
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315 <has_text text="ENST00000382683" />
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316 </assert_contents>
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317 </output>
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318 <output name="output_exons">
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319 <assert_contents>
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320 <has_text text="ENST00000346144 gene=MADCAM1 CDS=47-932" />
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321 <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" />
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322 </assert_contents>
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323 </output>
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324 <output name="output_cds">
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325 <assert_contents>
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326 <has_text text="ENST00000346144 gene=MADCAM1" />
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327 <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" />
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328 </assert_contents>
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329 </output>
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330 <output name="output_pep">
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331 <assert_contents>
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332 <has_text text="ENST00000346144 gene=MADCAM1" />
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333 <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" />
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334 </assert_contents>
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335 </output>
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336 </test>
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337
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338 </tests>
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339 <help>
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340 <![CDATA[
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341 **gffread Filters and/or converts GFF3/GTF2 records**
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342
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343 Usage: ::
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344
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345 gffread "input_gff" [-g "genomic_seqs_fasta" | "dir"][-s "seq_info.fsize"]
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346 [-o "outfile.gff"] [-t "tname"] [-r [["strand"]"chr":]"start".."end" [-R]]
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347 [-CTVNJMKQAFGUBHZWTOLE] [-w "exons.fa"] [-x "cds.fa"] [-y "tr_cds.fa"]
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348 [-i "maxintron"]
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349
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350 Options: ::
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351
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352 -g full path to a multi-fasta file with the genomic sequences
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353 for all input mappings, OR a directory with single-fasta files
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354 (one per genomic sequence, with file names matching sequence names)
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355 -s <seq_info.fsize> is a tab-delimited file providing this info
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356 for each of the mapped sequences:
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357 <seq-name> <seq-length> <seq-description>
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358 (useful for -A option with mRNA/EST/protein mappings)
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359 -i discard transcripts having an intron larger than <maxintron>
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360 -r only show transcripts overlapping coordinate range <start>..<end>
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361 (on chromosome/contig <chr>, strand <strand> if provided)
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362 -R for -r option, discard all transcripts that are not fully
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363 contained within the given range
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364 -U discard single-exon transcripts
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365 -C coding only: discard mRNAs that have no CDS feature
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366 -F full GFF attribute preservation (all attributes are shown)
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367 -G only parse additional exon attributes from the first exon
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368 and move them to the mRNA level (useful for GTF input)
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369 -A use the description field from <seq_info.fsize> and add it
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370 as the value for a 'descr' attribute to the GFF record
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371
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372 -O process also non-transcript GFF records (by default non-transcript
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373 records are ignored)
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374 -V discard any mRNAs with CDS having in-frame stop codons
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375 -H for -V option, check and adjust the starting CDS phase
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376 if the original phase leads to a translation with an
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377 in-frame stop codon
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378 -B for -V option, single-exon transcripts are also checked on the
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379 opposite strand
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380 -N discard multi-exon mRNAs that have any intron with a non-canonical
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381 splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
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382 -J discard any mRNAs that either lack initial START codon
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383 or the terminal STOP codon, or have an in-frame stop codon
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384 (only print mRNAs with a fulll, valid CDS)
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385 --no-pseudo: filter out records matching the 'pseudo' keyword
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386
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387 -M/--merge : cluster the input transcripts into loci, collapsing matching
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388 transcripts (those with the same exact introns and fully contained)
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389 -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>
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390 --cluster-only: same as --merge but without collapsing matching transcripts
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391 -K for -M option: also collapse shorter, fully contained transcripts
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392 with fewer introns than the container
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393 -Q for -M option, remove the containment restriction:
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394 (multi-exon transcripts will be collapsed if just their introns match,
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395 while single-exon transcripts can partially overlap (80%))
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396
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397 --force-exons: make sure that the lowest level GFF features are printed as
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398 "exon" features
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399 -E expose (warn about) duplicate transcript IDs and other potential
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400 problems with the given GFF/GTF records
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401 -D decode url encoded characters within attributes
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402 -Z merge close exons into a single exon (for intron size<4)
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403 -w write a fasta file with spliced exons for each GFF transcript
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404 -x write a fasta file with spliced CDS for each GFF transcript
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405 -W for -w and -x options, also write for each fasta record the exon
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406 coordinates projected onto the spliced sequence
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407 -y write a protein fasta file with the translation of CDS for each record
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408 -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
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409 -m <chr_replace> is a reference (genomic) sequence replacement table with
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410 this format:
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411 <original_ref_ID> <new_ref_ID>
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412 GFF records on reference sequences that are not found among the
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413 <original_ref_ID> entries in this file will be filtered out
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414 -o the "filtered" GFF records will be written to <outfile.gff>
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415 (use -o- for printing to stdout)
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416 -t use <trackname> in the second column of each GFF output line
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417 -T -o option will output GTF format instead of GFF3
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418
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419
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420
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421
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422
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423 ]]>
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424 </help>
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425 </tool>
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