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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
author iuc
date Fri, 15 Dec 2023 19:39:24 +0000
parents 154d00cbbf2d
children
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1 <tool id="gffread" name="gffread" version="@GALAXY_TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>Filters and/or converts GFF3/GTF2 records</description>
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3 <macros>
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4 <!-- the version of this tool must not be lowered since in the past 2.x was used
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5 lets use small increments and hope that gffread catches up one day -->
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6 <token name="@GALAXY_TOOL_VERSION@">2.2.1.4</token>
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7 <token name="@TOOL_VERSION@">0.12.7</token>
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8 <token name="@VERSION_SUFFIX@">0</token>
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9 <xml name="fasta_output_select">
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10 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">
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11 <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w)</option>
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12 <option value="-x cds.fa">fasta file with spliced CDS for each GFF transcript (-x)</option>
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13 <option value="-y pep.fa">protein fasta file with the translation of CDS for each record (-y)</option>
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14 <option value="-W">for each fasta: record the exon coordinates projected onto the spliced sequence (-W)</option>
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15 <option value="-S">for protein fasta: use '*' instead of '.' as stop codon translation (-S)</option>
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16 </param>
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17 </xml>
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18 <xml name="ref_filtering_select">
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19 <param name="ref_filtering" type="select" display="checkboxes" multiple="true" label="reference based filters">
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20 <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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21 <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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22 <option value="-V">discard any mRNAs with CDS having in-frame stop codons (-V)</option>
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23 <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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24 <!-- gffread bug: B not in missing from param to the arg parser
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25 <option value="-B">single-exon transcripts are also checked on the opposite strand (-B with -V)</option>
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26 -->
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27 </param>
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28 </xml>
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29 <xml name="trackname">
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30 <param argument="-t" name="tname" type="text" value="" optional="true" label="Trackname to use in the second column of each GFF output line" help="">
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31 <validator type="regex">\w+</validator>
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32 </param>
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33 </xml>
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34 <xml name="merge_opts">
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35 <option value="-K">also collapse shorter, fully contained transcripts with fewer introns than the container (-K)</option>
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36 <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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37 <option value="-d dupinfo">output collapsing info (-d)</option>
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38 </xml>
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39 <xml name="cluster_opts">
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40 <option value="--force-exons"> make sure that the lowest level GFF features are printed as 'exon' features (--force-exons)</option>
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41 <option value="-Z">merge close exons into a single exon (for intron size &lt; 4) (-Z)</option>
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42 </xml>
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43 <xml name="merge_opt_sel">
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44 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Merge options">
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45 <expand macro="cluster_opts" />
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46 <expand macro="merge_opts" />
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47 </param>
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48 </xml>
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49 <xml name="cluster_opt_sel">
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50 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options">
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51 <expand macro="cluster_opts" />
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52 </param>
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53 </xml>
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54 </macros>
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55 <xrefs>
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56 <xref type="bio.tools">gffread</xref>
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57 </xrefs>
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58 <requirements>
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59 <requirement type="package" version="@TOOL_VERSION@">gffread</requirement>
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60 </requirements>
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61 <version_command>gffread --version</version_command>
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62 <command detect_errors="aggressive">
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63 <![CDATA[
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64 #if $reference_genome.source == 'history':
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65 ln -s '$reference_genome.genome_fasta' genomeref.fa &&
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66 #end if
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67
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68 gffread '$input'
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69 #if $input.ext.startswith("bed")
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70 --in-bed
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71 #end if
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72 #if $reference_genome.source == 'cached':
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73 -g '${reference_genome.fasta_indexes.fields.path}'
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74 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
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75 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
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76 #end if
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77 #elif $reference_genome.source == 'history':
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78 -g genomeref.fa
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79 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
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80 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
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81 #end if
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82 #end if
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83 #if $filtering and str($filtering) != '':
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84 #echo " "
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85 #echo ' '.join(str($filtering).split(','))
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86 #end if
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87 #if $maxintron and $maxintron > 0:
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88 -i $maxintron
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89 #end if
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90 #if $region.region_filter == 'filter':
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91 -r '$region.range' $region.discard_partial
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92 #end if
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93 #if $merging.merge_sel != 'none':
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94 $merging.merge_cmd
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95 #if $merging.merge_options:
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96 #echo ' '.join(str($merging.merge_options).split(','))
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97 #end if
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98 #end if
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99 #if $chr_replace:
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100 -m '$chr_replace'
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101 #end if
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102
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103 $full_gff_attribute_preservation
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104 $decode_url
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105 $expose
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106
0
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107 ##
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108 ## Although documented, does not appear to be used in the gffread code
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109 ## #if $seq_info:
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110 ## -A -s "$seq_info"
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111 ## #end if
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112 ##
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113 ## outputs
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114 #if $reference_genome.source != 'none':
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115 #if $reference_genome.fa_outputs and str($reference_genome.fa_outputs) != '':
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116 #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(','))
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117 #end if
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118 #end if
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119
0
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120 #if $gffs.gff_fmt != 'none':
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121 #if $gffs.gff_fmt != 'bed' and $gffs.tname:
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122 -t '$gffs.tname'
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123 #end if
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124 #if $gffs.gff_fmt == 'gff':
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125 #if $input.datatype.file_ext == 'gtf':
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126 $gffs.ensembl
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127 #end if
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128 #end if
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129 #if $gffs.gff_fmt == 'gtf'
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130 -T
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131 #elif $gffs.gff_fmt == 'bed'
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132 --bed
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133 #end if
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134 -o output.$gffs.gff_fmt
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135 #else if 'fa_outputs' not in $reference_genome or '.fa' not in str($reference_genome['fa_outputs'])
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136 -o output.gff
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137 #end if
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138
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139 ## Missing options
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140 ##
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141 ## --ids
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142 ## --nids
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143 ## -l
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144 ## --jmatch
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145 ## --nc
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146 ## --ignore-locus
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147 ## -A -s (see above)
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148 ## --sort-alpha : chromosomes (reference sequences) are sorted alphabetically
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149 ## --sort-by : sort the reference sequences by the order in which their
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150 ## names are given in the <refseq.lst> file
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151 ## Misc
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152 ## --keep-exon-attrs : for -F option, do not attempt to reduce redundant
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153 ## --attrs
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154 ## --keep-genes : in transcript-only mode (default), also preserve gene records
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155 ## --keep-comments: for GFF3 input/output, try to preserve comments
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156 ## -B (see above)
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157 ## -P
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158 ## --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
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159 ## that have CDS features
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160 ## --adj-stop stop codon adjustment: enables -P and performs automatic
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161 ## adjustment of the CDS stop coordinate if premature or downstream
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162
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163 ## --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
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164 ## features (see --tlf option below); automatic if the input
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165 ## filename ends with .tlf)
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166 ## --stream: fast processing of input GFF/BED transcripts as they are received
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167 ## ((no sorting, exons must be grouped by transcript in the input data)
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168
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169 ## Clustering
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170
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171 ## -Y
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172
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173 ## Output
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174
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175 ## --gene2exon
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176 ## --t-adopt
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177 ## -j
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178 ## --w-add
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179 ## --w-nocds
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180 ]]>
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181 </command>
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182 <inputs>
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183 <param name="input" type="data" format="bed,gff3,gtf" label="Input BED, GFF3 or GTF feature file"/>
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184 <!-- filtering -->
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185 <param name="filtering" type="select" display="checkboxes" multiple="true" label="filters">
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186 <option value="-U">discard single-exon transcripts (-U)</option>
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187 <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option>
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188 <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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189 <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>
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190 <option value="--no-pseudo">filter out records matching the 'pseudo' keyword (--no-pseudo)</option>
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191 </param>
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192 <conditional name="region">
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193 <param name="region_filter" type="select" label="Filter by genome region">
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194 <option value="none">No</option>
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195 <option value="filter">Yes</option>
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196 </param>
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197 <when value="none"/>
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198 <when value="filter">
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199 <param argument="-r" name="range" type="text" value="" label="Only show transcripts overlapping coordinate range">
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200 <help><![CDATA[
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201 [['strand']'chr':]'start'..'end' <br>
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202 examples: <br>
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203 1000..500000 <br>
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204 chr1:1000..500000 <br>
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205 +chr1:1000..500000 <br>
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206 -chr1:1000..500000
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207 ]]>
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208 </help>
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209 <validator type="regex">(([+-])?(\w+:))?\d+\.\.\d+</validator>
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210 </param>
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211 <param argument="-R" name="discard_partial" type="boolean" truevalue="-R" falsevalue="" checked="false"
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212 label="Discard all transcripts that are not fully contained within the given range" help=""/>
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213 </when>
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214 </conditional>
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215 <param argument="-i" name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns"
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216 help="If set, discard transcripts having an intron larger"/>
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217 <param argument="-m" name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names" >
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218 <help><![CDATA[
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219 chr_replace is a reference sequence replacement table consisting of 2 columns: "original_ref_ID" "new_ref_ID"<br>
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220 It is useful for switching between Ensembl and UCSC naming conventions <br>
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221 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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222 ]]>
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223 </help>
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224 </param>
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225
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226 <!-- Although documented, does not appear to be used in the gffread code
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227 <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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228 <help>
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229 (-s seq_info.fsize -A) useful with mRNA/EST/protein mappings &lt;br&gt;
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230 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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231 "seq-name" "seq-length" "seq-description" &lt;br&gt;
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232 </help>
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233 </param>
0
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234 -->
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235
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236 <!-- merging -->
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237 <conditional name="merging">
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238 <param name="merge_sel" type="select" label="Transcript merging" help="">
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239 <option value="none">none</option>
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240 <option value="merge">merge: cluster the input transcripts into loci, collapsing matching transcripts (--merge)</option>
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241 <option value="cluster">cluster-only: merge but without collapsing matching transcripts (--cluster-only)</option>
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242 </param>
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243 <when value="none"/>
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244 <when value="merge">
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245 <param name="merge_cmd" type="hidden" value="--merge"/>
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246 <expand macro="merge_opt_sel" />
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247 </when>
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248 <when value="cluster">
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249 <param name="merge_cmd" type="hidden" value="--cluster-only"/>
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250 <expand macro="cluster_opt_sel" />
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251 </when>
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252 </conditional>
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253 <!-- reference sequence file -->
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254 <!-- Error: -g option is required for options -w, -x, -y, -V, -N, -M -->
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255 <conditional name="reference_genome">
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256 <param name="source" type="select" label="Reference Genome" help="NOTE: Required for fasta outputs">
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257 <option value="none">none</option>
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258 <option value="cached">Cached reference data</option>
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259 <option value="history">From your history</option>
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260 </param>
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261 <when value="none"/>
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262 <when value="cached">
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263 <param argument="-g" name="fasta_indexes" type="select" label="Source FASTA Sequence">
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264 <options from_data_table="all_fasta"/>
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265 </param>
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266 <expand macro="ref_filtering_select" />
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267 <expand macro="fasta_output_select" />
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268 </when>
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269 <when value="history">
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270 <param argument="-g" name="genome_fasta" type="data" format="fasta" label="Genome Reference Fasta"/>
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271 <expand macro="ref_filtering_select" />
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272 <expand macro="fasta_output_select" />
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273 </when>
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274 </conditional>
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275
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276 <!-- outputs -->
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277 <conditional name="gffs">
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278 <param name="gff_fmt" type="select" label="Feature File Output" help="(-o output.gff3|output.gtf)">
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279 <option value="none">none</option>
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280 <option value="gff">GFF</option>
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281 <option value="gtf">GTF</option>
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282 <option value="bed">BED</option>
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283 </param>
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284 <when value="none"/>
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285 <when value="gff">
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286 <param argument="-L" name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help=""/>
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287 <expand macro="trackname" />
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288 </when>
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289 <when value="gtf">
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290 <expand macro="trackname" />
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291 </when>
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292 <when value="bed"/>
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293 </conditional>
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294
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295 <param argument="-F" name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false"
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296 label="full GFF attribute preservation (all attributes are shown)" help=""/>
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297 <param argument="-D" name="decode_url" type="boolean" truevalue="-D" falsevalue="" checked="false"
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298 label="decode url encoded characters within attributes" help=""/>
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299 <param argument="-E" name="expose" type="boolean" truevalue="-E" falsevalue="" checked="false"
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300 label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help=""/>
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301
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302 </inputs>
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303 <outputs>
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304 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff">
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305 <!-- output gff also if the user deselected all outputs: none is selected and all .fa outputs are disabled -->
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306 <filter>gffs['gff_fmt'] == 'gff' or (gffs['gff_fmt'] == 'none' and ('fa_outputs' not in reference_genome or '.fa' not in str(reference_genome['fa_outputs'])))</filter>
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307 </data>
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308 <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf">
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309 <filter>gffs['gff_fmt'] == 'gtf'</filter>
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310 </data>
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311 <data name="output_bed" format="bed" metadata_source="input" label="${tool.name} on ${on_string}: bed" from_work_dir="output.bed">
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312 <filter>gffs['gff_fmt'] == 'bed'</filter>
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313 </data>
0
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314 <data name="output_exons" format="fasta" label="${tool.name} on ${on_string}: exons.fa" from_work_dir="exons.fa">
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315 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('exons.fa') > 0 </filter>
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316 </data>
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317 <data name="output_cds" format="fasta" label="${tool.name} on ${on_string}: cds.fa" from_work_dir="cds.fa">
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318 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('cds.fa') > 0</filter>
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319 </data>
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320 <data name="output_pep" format="fasta" label="${tool.name} on ${on_string}: pep.fa" from_work_dir="pep.fa">
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321 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('pep.fa') > 0</filter>
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322 </data>
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323 <data name="output_dupinfo" format="txt" label="${tool.name} on ${on_string}: dupinfo" from_work_dir="dupinfo">
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324 <filter>'merge_options' in merging and merging['merge_options'].find('dupinfo') > 0</filter>
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325 </data>
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326 </outputs>
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327 <tests>
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328 <test expect_num_outputs="1">
0
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329 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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330 <param name="gff_fmt" value="gff"/>
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331 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" />
9
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332 <assert_stdout>
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333 <has_n_lines n="0"/>
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334 </assert_stdout>
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335 </test>
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336 <!-- mapping -->
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337 <test expect_num_outputs="1">
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338 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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339 <param name="gff_fmt" value="gff"/>
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340 <param name="chr_replace" ftype="tabular" value="chr_replace"/>
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341 <output name="output_gff" ftype="gff3">
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342 <assert_contents>
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343 <has_n_lines n="314"/>
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344 <has_line_matching expression="^chr.*"/>
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345 <has_line_matching expression="^1.*" negate="true"/>
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346 </assert_contents>
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347 </output>
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348 <assert_stdout>
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349 <has_n_lines n="0"/>
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350 </assert_stdout>
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351 </test>
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352 <!-- none output and all .fa outputs deselected .. gff is produced anyway, since we need one output -->
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353 <test expect_num_outputs="1">
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354 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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355 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" />
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356 <assert_stdout>
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357 <has_n_lines n="0"/>
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358 </assert_stdout>
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359 </test>
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360 <!-- test ensemble gtf to gff conversion -->
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361 <test expect_num_outputs="1">
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362 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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363 <conditional name="gffs">
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364 <param name="gff_fmt" value="gff"/>
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365 <param name="ensembl" value="true"/>
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366 <param name="tname" value="track name"/>
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367 </conditional>
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368 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71_ensemble.gff3" ftype="gff3" lines_diff="4" />
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369 <assert_command>
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370 <has_text text="-L"/>
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371 <has_text text="-t &#39;track name&#39;"/>
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372 </assert_command>
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373 <assert_stdout>
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374 <has_n_lines n="0"/>
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375 </assert_stdout>
0
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376 </test>
8
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377 <test expect_num_outputs="1">
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378 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
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379 <param name="gff_fmt" value="gff"/>
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380 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" />
9
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381 <assert_stdout>
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382 <has_n_lines n="0"/>
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383 </assert_stdout>
8
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384 </test>
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385 <test expect_num_outputs="1">
5
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386 <param name="input" ftype="gtf" value="ecoli-k12.gff3"/>
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387 <param name="gff_fmt" value="gff"/>
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388 <param name="full_gff_attribute_preservation" value="-F"/>
8
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389 <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="4" />
9
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390 <assert_stdout>
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391 <has_n_lines n="0"/>
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392 </assert_stdout>
5
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393 </test>
8
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394 <!-- bed output -->
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395 <test expect_num_outputs="1">
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396 <param name="input" ftype="gff3" value="Homo_sapiens.GRCh37_19.71.gff3"/>
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397 <param name="gff_fmt" value="bed"/>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
398 <output name="output_bed" ftype="bed">
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
399 <assert_contents>
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
400 <has_n_lines n="42"/>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
401 <has_n_columns n="13"/>
3
9f243677c4c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 2
diff changeset
402 </assert_contents>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
403 </output>
9
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
404 <assert_stdout>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
405 <has_n_lines n="0"/>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
406 </assert_stdout>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
407 </test>
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
408 <!-- bed input and test tname -->
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
409 <test expect_num_outputs="1">
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
410 <param name="input" ftype="bed" value="Homo_sapiens.GRCh37_19.71.bed"/>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
411 <param name="gff_fmt" value="gff"/>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
412 <param name="tname" value="track name"/>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
413 <output name="output_bed" ftype="gff3">
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
414 <assert_contents>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
415 <has_n_lines n="388"/>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
416 <!-- this will work with https://github.com/galaxyproject/galaxy/pull/12528 -->
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
417 <!-- <has_n_columns n="9" comment="#"/> -->
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
418 <has_text text="track name"/>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
419 </assert_contents>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
420 </output>
9
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
421 <assert_stdout>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
422 <has_n_lines n="0"/>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
423 </assert_stdout>
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
424 </test>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
425 <test expect_num_outputs="1">
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
426 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
427 <param name="region_filter" value="filter"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
428 <param name="range" value="19:496500..504965"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
429 <param name="gff_fmt" value="gtf"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
430 <output name="output_gtf">
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
431 <assert_contents>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
432 <has_text text="ENST00000587541" />
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
433 <has_text text="ENST00000382683" />
3
9f243677c4c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 2
diff changeset
434 </assert_contents>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
435 </output>
9
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
436 <assert_stdout>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
437 <has_n_lines n="0"/>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
438 </assert_stdout>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
439 </test>
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
440 <test expect_num_outputs="1">
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
441 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
442 <param name="region_filter" value="filter"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
443 <param name="range" value="19:496500..504965"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
444 <param name="discard_partial" value="true"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
445 <param name="gff_fmt" value="gtf"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
446 <output name="output_gtf">
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
447 <assert_contents>
3
9f243677c4c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 2
diff changeset
448 <not_has_text text="ENST00000587541" />
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
449 <has_text text="ENST00000382683" />
3
9f243677c4c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 2
diff changeset
450 </assert_contents>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
451 </output>
9
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
452 <assert_stdout>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
453 <has_n_lines n="0"/>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
454 </assert_stdout>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
455 </test>
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
456 <test expect_num_outputs="1">
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
457 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
458 <param name="filtering" value="-C"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
459 <param name="region_filter" value="filter"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
460 <param name="range" value="19:496500..504965"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
461 <param name="gff_fmt" value="gtf"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
462 <output name="output_gtf">
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
463 <assert_contents>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
464 <not_has_text text="ENST00000587541" />
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
465 <has_text text="ENST00000382683" />
3
9f243677c4c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 2
diff changeset
466 </assert_contents>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
467 </output>
9
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
468 <assert_stdout>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
469 <has_n_lines n="0"/>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
470 </assert_stdout>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
471 </test>
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
472 <test expect_num_outputs="4">
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
473 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
474 <param name="source" value="history"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
475 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
3
9f243677c4c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 2
diff changeset
476 <param name="fa_outputs" value="-w exons.fa,-x cds.fa,-y pep.fa"/>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
477 <param name="region_filter" value="filter"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
478 <param name="range" value="19:496500..504965"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
479 <param name="gff_fmt" value="gtf"/>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
480 <output name="output_gtf">
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
481 <assert_contents>
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
482 <has_text text="ENST00000587541" />
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
483 <has_text text="ENST00000382683" />
3
9f243677c4c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 2
diff changeset
484 </assert_contents>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
485 </output>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
486 <output name="output_exons">
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
487 <assert_contents>
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
488 <has_text text="ENST00000346144 CDS=47-934" />
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
489 <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" />
3
9f243677c4c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 2
diff changeset
490 </assert_contents>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
491 </output>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
492 <output name="output_cds">
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
493 <assert_contents>
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
494 <has_text text="ENST00000346144" />
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
495 <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" />
3
9f243677c4c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 2
diff changeset
496 </assert_contents>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
497 </output>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
498 <output name="output_pep">
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
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499 <assert_contents>
6
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500 <has_text text="ENST00000346144" />
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
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501 <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" />
3
9f243677c4c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
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diff changeset
502 </assert_contents>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
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503 </output>
9
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
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diff changeset
504 <assert_stdout>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
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diff changeset
505 <has_n_lines n="0"/>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
parents: 8
diff changeset
506 </assert_stdout>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
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diff changeset
507 </test>
8
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diff changeset
508 <test expect_num_outputs="1">
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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diff changeset
509 <param name="input" ftype="gtf" value="stop_codons.gtf"/>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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diff changeset
510 <param name="source" value="history"/>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
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diff changeset
511 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
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diff changeset
512 <param name="fa_outputs" value="-y pep.fa,-S"/>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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diff changeset
513 <output name="output_pep">
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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diff changeset
514 <assert_contents>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
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diff changeset
515 <has_text text="ENST00000269812" />
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
516 <has_text text="PLRGLHPRV*LQTPLERCPCWPPAGGTGGCPHCLLHLRLLQSPTPTALSEGGGAGTEAQPVTDVDPGRG*" />
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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diff changeset
517 </assert_contents>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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diff changeset
518 </output>
9
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
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parents: 8
diff changeset
519 <assert_stdout>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
iuc
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diff changeset
520 <has_n_lines n="0"/>
3e436657dcd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
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parents: 8
diff changeset
521 </assert_stdout>
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
522 </test>
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
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diff changeset
523 </tests>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
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diff changeset
524 <help>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
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diff changeset
525 <![CDATA[
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
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526 **gffread Filters and/or converts GFF3/GTF2 records**
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
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diff changeset
527
6
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diff changeset
528 The gffread command is documented with the stringtie_ package.
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
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diff changeset
529
6
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iuc
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diff changeset
530 .. _stringtie: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
2
12aeae6d8587 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 3bc5271145f939d85bb709fc95197be66b348328
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parents: 1
diff changeset
531
8
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diff changeset
532 gffread v0.12.7. Usage: ::
0
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533
8
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diff changeset
534 gffread [-g <genomic_seqs_fasta> | <dir>] [-s <seq_info.fsize>]
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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535 [-o <outfile>] [-t <trackname>] [-r [<strand>]<chr>:<start>-<end> [-R]]
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diff changeset
536 [--jmatch <chr>:<start>-<end>] [--no-pseudo]
6
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diff changeset
537 [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]
8
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diff changeset
538 [-j ][--ids <IDs.lst> | --nids <IDs.lst>] [--attrs <attr-list>] [-i <maxintron>]
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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diff changeset
539 [--stream] [--bed | --gtf | --tlf] [--table <attrlist>] [--sort-by <ref.lst>]
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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diff changeset
540 [<input_gff>]
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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diff changeset
541
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
542 Filter, convert or cluster GFF/GTF/BED records, extract the sequence of
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
543 transcripts (exon or CDS) and more.
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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diff changeset
544 By default (i.e. without -O) only transcripts are processed, discarding any
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
545 other non-transcript features. Default output is a simplified GFF3 with only
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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diff changeset
546 the basic attributes.
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
547
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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parents: 5
diff changeset
548 Options:
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
549 --ids discard records/transcripts if their IDs are not listed in <IDs.lst>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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diff changeset
550 --nids discard records/transcripts if their IDs are listed in <IDs.lst>
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
551 -i discard transcripts having an intron larger than <maxintron>
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
552 -l discard transcripts shorter than <minlen> bases
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
553 -r only show transcripts overlapping coordinate range <start>..<end>
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
554 (on chromosome/contig <chr>, strand <strand> if provided)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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parents: 5
diff changeset
555 -R for -r option, discard all transcripts that are not fully
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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parents: 5
diff changeset
556 contained within the given range
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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parents: 7
diff changeset
557 --jmatch only output transcripts matching the given junction
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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parents: 5
diff changeset
558 -U discard single-exon transcripts
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
559 -C coding only: discard mRNAs that have no CDS features
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
560 --nc non-coding only: discard mRNAs that have CDS features
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
561 --ignore-locus : discard locus features and attributes found in the input
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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parents: 5
diff changeset
562 -A use the description field from <seq_info.fsize> and add it
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
563 as the value for a 'descr' attribute to the GFF record
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
564 -s <seq_info.fsize> is a tab-delimited file providing this info
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
565 for each of the mapped sequences:
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
566 <seq-name> <seq-length> <seq-description>
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
567 (useful for -A option with mRNA/EST/protein mappings)
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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parents: 7
diff changeset
568 Sorting: (by default, chromosomes are kept in the order they were found)
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
569 --sort-alpha : chromosomes (reference sequences) are sorted alphabetically
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
570 --sort-by : sort the reference sequences by the order in which their
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
571 names are given in the <refseq.lst> file
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
572 Misc options:
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
573 -F keep all GFF attributes (for non-exon features)
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
574 --keep-exon-attrs : for -F option, do not attempt to reduce redundant
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
575 exon/CDS attributes
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
576 -G do not keep exon attributes, move them to the transcript feature
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
577 (for GFF3 output)
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
578 --attrs <attr-list> only output the GTF/GFF attributes listed in <attr-list>
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
579 which is a comma delimited list of attribute names to
6
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iuc
parents: 5
diff changeset
580 --keep-genes : in transcript-only mode (default), also preserve gene records
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
581 --keep-comments: for GFF3 input/output, try to preserve comments
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
582 -O process other non-transcript GFF records (by default non-transcript
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
583 records are ignored)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
584 -V discard any mRNAs with CDS having in-frame stop codons (requires -g)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
585 -H for -V option, check and adjust the starting CDS phase
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
586 if the original phase leads to a translation with an
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
587 in-frame stop codon
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
588 -B for -V option, single-exon transcripts are also checked on the
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
589 opposite strand (requires -g)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
590 -P add transcript level GFF attributes about the coding status of each
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
591 transcript, including partialness or in-frame stop codons (requires -g)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
592 --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
593 that have CDS features
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
594 --adj-stop stop codon adjustment: enables -P and performs automatic
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
595 adjustment of the CDS stop coordinate if premature or downstream
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
596 -N discard multi-exon mRNAs that have any intron with a non-canonical
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
597 splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
598 -J discard any mRNAs that either lack initial START codon
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
599 or the terminal STOP codon, or have an in-frame stop codon
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
600 (i.e. only print mRNAs with a complete CDS)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
601 --no-pseudo: filter out records matching the 'pseudo' keyword
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
602 --in-bed: input should be parsed as BED format (automatic if the input
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
603 filename ends with .bed*)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
604 --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
605 features (see --tlf option below); automatic if the input
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
606 filename ends with .tlf)
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
607 --stream: fast processing of input GFF/BED transcripts as they are received
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
608 ((no sorting, exons must be grouped by transcript in the input data)
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
609 Clustering:
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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diff changeset
610 -M/--merge : cluster the input transcripts into loci, discarding
8
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iuc
parents: 7
diff changeset
611 "redundant" transcripts (those with the same exact introns
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
612 and fully contained or equal boundaries)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
613 -d <dupinfo> : for -M option, write duplication info to file <dupinfo>
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
614 --cluster-only: same as -M/--merge but without discarding any of the
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
615 "duplicate" transcripts, only create "locus" features
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
616 -K for -M option: also discard as redundant the shorter, fully contained
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
617 transcripts (intron chains matching a part of the container)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
618 -Q for -M option, no longer require boundary containment when assessing
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
619 redundancy (can be combined with -K); only introns have to match for
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
620 multi-exon transcripts, and >=80% overlap for single-exon transcripts
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
621 -Y for -M option, enforce -Q but also discard overlapping single-exon
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
622 transcripts, even on the opposite strand (can be combined with -K)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
623 Output options:
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
624 --force-exons: make sure that the lowest level GFF features are considered
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
625 "exon" features
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
626 --gene2exon: for single-line genes not parenting any transcripts, add an
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
627 exon feature spanning the entire gene (treat it as a transcript)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
628 --t-adopt: try to find a parent gene overlapping/containing a transcript
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
629 that does not have any explicit gene Parent
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
630 -D decode url encoded characters within attributes
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
631 -Z merge very close exons into a single exon (when intron size<4)
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
632 -g full path to a multi-fasta file with the genomic sequences
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
633 for all input mappings, OR a directory with single-fasta files
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
634 (one per genomic sequence, with file names matching sequence names)
8
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parents: 7
diff changeset
635 -j output the junctions and the corresponding transcripts
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
636 -w write a fasta file with spliced exons for each transcript
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
637 --w-add <N> for the -w option, extract additional <N> bases
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
638 both upstream and downstream of the transcript boundaries
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
639 --w-nocds for -w, disable the output of CDS info in the FASTA file
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
640 -x write a fasta file with spliced CDS for each GFF transcript
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
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diff changeset
641 -y write a protein fasta file with the translation of CDS for each record
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
642 -W for -w, -x and -y options, write in the FASTA defline all the exon
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
643 coordinates projected onto the spliced sequence;
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
644 -S for -y option, use '*' instead of '.' as stop codon translation
8
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iuc
parents: 7
diff changeset
645 -L Ensembl GTF to GFF3 conversion, adds version to IDs
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
646 -m <chr_replace> is a name mapping table for converting reference
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
647 sequence names, having this 2-column format:
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
648 <original_ref_ID> <new_ref_ID>
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
649 -t use <trackname> in the 2nd column of each GFF/GTF output line
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
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parents: 7
diff changeset
650 -o write the output records into <outfile> instead of stdout
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
651 -T main output will be GTF instead of GFF3
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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652 --bed output records in BED format instead of default GFF3
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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parents: 5
diff changeset
653 --tlf output "transcript line format" which is like GFF
8
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
654 but with exons and CDS related features stored as GFF
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
655 attributes in the transcript feature line, like this:
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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parents: 5
diff changeset
656 exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords>
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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parents: 5
diff changeset
657 <exons> is a comma-delimited list of exon_start-exon_end coordinates;
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
658 <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
659 --table output a simple tab delimited format instead of GFF, with columns
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
660 having the values of GFF attributes given in <attrlist>; special
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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parents: 5
diff changeset
661 pseudo-attributes (prefixed by @) are recognized:
8
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parents: 7
diff changeset
662 @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons,
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
663 @cds, @covlen, @cdslen
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
664 If any of -w/-y/-x FASTA output files are enabled, the same fields
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
665 (excluding @id) are appended to the definition line of corresponding
154d00cbbf2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 7
diff changeset
666 FASTA records
6
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 5
diff changeset
667 -v,-E expose (warn about) duplicate transcript IDs and other potential
6ea09f60dee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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parents: 5
diff changeset
668 problems with the given GFF/GTF records
8
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iuc
parents: 7
diff changeset
669
0
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
670 ]]>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
671 </help>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
672 <citations>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
diff changeset
673 <citation type="doi">10.1038/nbt.1621</citation>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
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674 </citations>
5f6e6582c01d planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c
devteam
parents:
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675 </tool>