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annotate gffread.xml @ 4:0cf496c45054 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
author iuc
date Fri, 01 Nov 2019 12:54:23 -0400
parents 29769f789b8f
children f312cff50fda
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0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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1 <tool id="gffread" name="gffread" version="@VERSION@.1">
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2 <description>Filters and/or converts GFF3/GTF2 records</description>
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3 <macros>
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0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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4 <token name="@VERSION@">0.11.4</token>
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5 <xml name="fasta_output_select">
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6 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">
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7 <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w exons.fa)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 <option value="-x cds.fa">fasta file with spliced CDS for each GFF transcript (-x cds.fa)</option>
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9 <option value="-y pep.fa">protein fasta file with the translation of CDS for each record (-y pep.fa)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 <option value="-W">for each fasta: record the exon coordinates projected onto the spliced sequence (-W)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 </xml>
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13 <xml name="ref_filtering_select">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 <param name="ref_filtering" type="select" display="checkboxes" multiple="true" label="reference based filters">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 <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>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 <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>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 <option value="-V">discard any mRNAs with CDS having in-frame stop codons (-V)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 <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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19 <!-- gffread bug: B not in missing from param to the arg parser
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20 <option value="-B">single-exon transcripts are also checked on the opposite strand (-B with -V)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 -->
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22 </param>
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23 </xml>
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24 <xml name="trackname">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 <param name="tname" type="text" value="" optional="true" label="Trackname to use in the second column of each GFF output line" help="(-t track_name}">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 <validator type="regex">\w+</validator>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 </xml>
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29 <xml name="merge_opts">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30 <option value="-K">also collapse shorter, fully contained transcripts with fewer introns than the container (-K)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 <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>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 <option value="-d dupinfo">output collapsing info (-d dupinfo)</option>
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33 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 <xml name="cluster_opts">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35 <option value="--force-exons"> make sure that the lowest level GFF features are printed as 'exon' features (--force-exons)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36 <option value="-Z">merge close exons into a single exon (for intron size &lt; 4) (-Z)</option>
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37 </xml>
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38 <xml name="merge_opt_sel">
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39 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Merge options">
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40 <expand macro="cluster_opts" />
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41 <expand macro="merge_opts" />
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42 </param>
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43 </xml>
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44 <xml name="cluster_opt_sel">
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45 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options">
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46 <expand macro="cluster_opts" />
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47 </param>
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48 </xml>
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49 </macros>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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50 <requirements>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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51 <requirement type="package" version="@VERSION@">gffread</requirement>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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52 </requirements>
2
6562753c6bdc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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53 <command detect_errors="aggressive">
0
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54 <![CDATA[
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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55 #if $reference_genome.source == 'history':
1
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56 ln -s '$reference_genome.genome_fasta' genomeref.fa &&
0
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57 #end if
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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58 gffread '$input'
0
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59 #if $reference_genome.source == 'cached':
1
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60 -g '${reference_genome.fasta_indexes.fields.path}'
0
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61 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
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62 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
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63 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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64 #elif $reference_genome.source == 'history':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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65 -g genomeref.fa
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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66 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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67 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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68 #end if
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69 #end if
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70 #if $filtering and str($filtering) != '':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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71 #echo " "
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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72 #echo ' '.join(str($filtering).split(','))
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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73 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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74 #if $maxintron and $maxintron > 0:
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75 -i $maxintron
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76 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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77 #if $region.region_filter == 'filter':
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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78 -r '$region.range' $region.discard_partial
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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79 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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80 #if $merging.merge_sel != 'none':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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81 $merging.merge_cmd
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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82 #if $merging.merge_options:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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83 #echo ' '.join(str($merging.merge_options).split(','))
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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84 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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85 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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86 #if $chr_replace:
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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87 -m '$chr_replace'
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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88 #end if
3
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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89
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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90 $full_gff_attribute_preservation
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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91 $decode_url
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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92 $expose
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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93
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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94 ##
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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95 ## Although documented, does not appear to be used in the gffread code
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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96 ## #if $seq_info:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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97 ## -A -s "$seq_info"
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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98 ## #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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99 ##
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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100 ## outputs
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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101 #if $reference_genome.source != 'none':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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102 #if $reference_genome.fa_outputs and str($reference_genome.fa_outputs) != '':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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103 #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(','))
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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104 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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105 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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106 #if $gffs.gff_fmt != 'none':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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107 #if $gffs.tname:
1
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108 -t '$gffs.tname'
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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109 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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110 #if $gffs.gff_fmt == 'gff':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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111 #if $input.datatype.file_ext == 'gft':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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112 $gffs.ensembl
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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113 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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114 $gffs.output_cmd
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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115 #elif $gffs.gff_fmt == 'gtf':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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116 $gffs.output_cmd
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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117 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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118 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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119 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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120 </command>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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121 <inputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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122 <param name="input" type="data" format="gff3,gtf" label="Input GFF3 or GTF feature file"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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123 <!-- filtering -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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124 <param name="filtering" type="select" display="checkboxes" multiple="true" label="filters">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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125 <option value="-U">discard single-exon transcripts (-U)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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126 <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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127 <option value="-G">only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) (-G)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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128 <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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129 <!-- The no-pseudo option is broken in 0.11.4 of gffread.
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130 See https://github.com/gpertea/gffread/issues/43 -->
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
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131 <!-- <option value="\-\-no-pseudo">filter out records matching the 'pseudo' keyword (\-\-no-pseudo)</option> -->
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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132 </param>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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133 <conditional name="region">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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134 <param name="region_filter" type="select" label="Filter by genome region">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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135 <option value="none">No</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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136 <option value="filter">Yes</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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137 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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138 <when value="none"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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139 <when value="filter">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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140 <param name="range" type="text" value="" label="Only show transcripts overlapping coordinate range">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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141 <help><![CDATA[
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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142 (-r [['strand']'chr':]'start'..'end') <br>
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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diff changeset
143 examples: <br>
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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144 1000..500000 <br>
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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145 chr1:1000..500000 <br>
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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146 +chr1:1000..500000 <br>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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147 -chr1:1000..500000
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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148 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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149 </help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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150 <validator type="regex">(([+-])?(\w+:))?\d+\.\.\d+</validator>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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151 </param>
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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152 <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" checked="false"
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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153 label="Discard all transcripts that are not fully contained within the given range" help="(-R)"/>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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154 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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155 </conditional>
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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156 <param name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns"
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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157 help="If set, discard transcripts having an intron larger (-i max_intron)"/>
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158 <param name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names" >
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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159 <help><![CDATA[(-m chr_replace) <br>
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160 chr_replace is a reference sequence replacement table consisting of 2 columns: "original_ref_ID" "new_ref_ID"<br>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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161 It is useful for switching between Ensembl and UCSC naming conventions <br>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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162 NOTE: GFF records on reference sequences that are not found among the "original_ref_ID" entries in this file will be filtered out
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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163 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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164 </help>
1
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165 </param>
0
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166
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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167 <!-- Although documented, does not appear to be used in the gffread code
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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168 <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">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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169 <help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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170 (-s seq_info.fsize -A) useful with mRNA/EST/protein mappings &lt;br&gt;
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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171 seq_info input file is a 3 column tab-delimited file providing this info for each of the mapped sequences: &lt;br&gt;
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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172 "seq-name" "seq-length" "seq-description" &lt;br&gt;
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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173 </help>
1
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174 </param>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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175 -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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176
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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177 <!-- merging -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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178 <conditional name="merging">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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179 <param name="merge_sel" type="select" label="Transcript merging" help="(-M/--merge or --cluster-only)">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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180 <option value="none">none</option>
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181 <option value="merge">merge: cluster the input transcripts into loci, collapsing matching transcripts</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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182 <option value="cluster">cluster-only: merge but without collapsing matching transcripts</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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183 </param>
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184 <when value="none"/>
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185 <when value="merge">
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186 <param name="merge_cmd" type="hidden" value="--merge"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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187 <expand macro="merge_opt_sel" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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188 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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189 <when value="cluster">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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190 <param name="merge_cmd" type="hidden" value="--cluster-only"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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191 <expand macro="cluster_opt_sel" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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192 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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193 </conditional>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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194 <!-- reference sequence file -->
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195 <!-- Error: -g option is required for options -w, -x, -y, -V, -N, -M -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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196 <conditional name="reference_genome">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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197 <param name="source" type="select" label="Reference Genome" help="(-g genome.fasta) NOTE: Required for fasta outputs">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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198 <option value="none">none</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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199 <option value="cached"></option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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200 <option value="history">From your history</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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201 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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202 <when value="none">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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203 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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204 <when value="cached">
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205 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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206 <options from_data_table="all_fasta"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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207 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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208 <expand macro="ref_filtering_select" />
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209 <expand macro="fasta_output_select" />
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210 </when>
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211 <when value="history">
1
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212 <param name="genome_fasta" type="data" format="fasta" label="Genome Reference Fasta"/>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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213 <expand macro="ref_filtering_select" />
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214 <expand macro="fasta_output_select" />
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215 </when>
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216 </conditional>
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217
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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218 <!-- outputs -->
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219 <conditional name="gffs">
1
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220 <param name="gff_fmt" type="select" label="Feature File Output" help="(-o output.gff3|output.gtf)">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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221 <option value="none">none</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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222 <option value="gff">GFF</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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223 <option value="gtf">GTF</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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224 </param>
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225 <when value="none">
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226 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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227 <when value="gff">
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228 <param name="output_cmd" type="hidden" value="-o output.gff3"/>
1
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229 <param name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help="(-L)"/>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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230 <expand macro="trackname" />
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231 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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232 <when value="gtf">
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233 <param name="output_cmd" type="hidden" value="-T -o output.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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234 <expand macro="trackname" />
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235 </when>
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236 </conditional>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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237
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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238 <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false"
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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239 label="full GFF attribute preservation (all attributes are shown)" help="(-F)"/>
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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240 <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" checked="false"
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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241 label="decode url encoded characters within attributes" help="(-D)"/>
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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diff changeset
242 <param name="expose" type="boolean" truevalue="-E" falsevalue="" checked="false"
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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243 label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help="(-E)"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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244
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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245 </inputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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246 <outputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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247 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff3">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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248 <filter>gffs['gff_fmt'] == 'gff'</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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249 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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250 <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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251 <filter>gffs['gff_fmt'] == 'gtf'</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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252 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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253 <data name="output_exons" format="fasta" label="${tool.name} on ${on_string}: exons.fa" from_work_dir="exons.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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254 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('exons.fa') > 0 </filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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255 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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256 <data name="output_cds" format="fasta" label="${tool.name} on ${on_string}: cds.fa" from_work_dir="cds.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
257 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('cds.fa') > 0</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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258 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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259 <data name="output_pep" format="fasta" label="${tool.name} on ${on_string}: pep.fa" from_work_dir="pep.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
260 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('pep.fa') > 0</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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261 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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262 <data name="output_dupinfo" format="txt" label="${tool.name} on ${on_string}: dupinfo" from_work_dir="dupinfo">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
263 <filter>'merge_options' in merging and merging['merge_options'].find('dupinfo') > 0</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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264 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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265 </outputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
266 <tests>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
267 <test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
268 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
269 <param name="gff_fmt" value="gff"/>
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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270 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" />
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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271 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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272
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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273 <test>
3
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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274 <param name="input" ftype="gtf" value="ecoli-k12.gff3"/>
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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275 <param name="gff_fmt" value="gff"/>
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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276 <param name="full_gff_attribute_preservation" value="-F"/>
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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277 <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" />
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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278 </test>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
279
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
280 <!-- The no-pseudo option is broken in 0.11.4 of gffread.
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
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281 See https://github.com/gpertea/gffread/issues/43 -->
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
282 <!--
3
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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283 <test>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
284 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
285 <param name="filtering" value="/-/-no-pseudo"/> # Fix dashes when uncommenting
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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286 <param name="gff_fmt" value="gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
287 <output name="output_gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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288 <assert_contents>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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289 <not_has_text text="pseudo" />
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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290 </assert_contents>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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291 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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292 </test>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
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293 -->
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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294
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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295 <test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
296 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
297 <param name="region_filter" value="filter"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
298 <param name="range" value="19:496500..504965"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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299 <param name="gff_fmt" value="gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
300 <output name="output_gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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301 <assert_contents>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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302 <has_text text="ENST00000587541" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
303 <has_text text="ENST00000382683" />
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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304 </assert_contents>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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305 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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306 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
307
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
308 <test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
309 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
310 <param name="region_filter" value="filter"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
311 <param name="range" value="19:496500..504965"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
312 <param name="discard_partial" value="true"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
313 <param name="gff_fmt" value="gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
314 <output name="output_gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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315 <assert_contents>
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
316 <not_has_text text="ENST00000587541" />
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
317 <has_text text="ENST00000382683" />
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
318 </assert_contents>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
319 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
320 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
321
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
322 <test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
323 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
324 <param name="filtering" value="-C"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
325 <param name="region_filter" value="filter"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
326 <param name="range" value="19:496500..504965"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
327 <param name="gff_fmt" value="gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
328 <output name="output_gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
329 <assert_contents>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
330 <not_has_text text="ENST00000587541" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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331 <has_text text="ENST00000382683" />
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
332 </assert_contents>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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333 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
334 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
335
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
336 <test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
337 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
338 <param name="source" value="history"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
339 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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parents: 0
diff changeset
340 <param name="fa_outputs" value="-w exons.fa,-x cds.fa,-y pep.fa"/>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
341 <param name="region_filter" value="filter"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
342 <param name="range" value="19:496500..504965"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
343 <param name="gff_fmt" value="gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
344 <output name="output_gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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345 <assert_contents>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
346 <has_text text="ENST00000587541" />
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
347 <has_text text="ENST00000382683" />
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
348 </assert_contents>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
349 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
350 <output name="output_exons">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
351 <assert_contents>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
352 <has_text text="ENST00000346144 CDS=47-934" />
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
353 <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" />
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
354 </assert_contents>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
355 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
356 <output name="output_cds">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
357 <assert_contents>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
358 <has_text text="ENST00000346144" />
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
359 <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" />
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
360 </assert_contents>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
361 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
362 <output name="output_pep">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
363 <assert_contents>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
364 <has_text text="ENST00000346144" />
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
365 <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" />
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
366 </assert_contents>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
367 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
368 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
369
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
370 </tests>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
371 <help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
372 <![CDATA[
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
373 **gffread Filters and/or converts GFF3/GTF2 records**
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
374
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
375 The gffread command is documented with the stringtie_ package.
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
376
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
377 .. _stringtie: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
378
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
379
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
380 gffread v0.11.4. Usage: ::
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
381
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
382 gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>]
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
383 [-o <outfile>] [-t <trackname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
384 [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
385 [-i <maxintron>] [--bed] [--table <attrlist>] [--sort-by <refseq_list.txt>]
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
386
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
387 Filter, convert or cluster GFF/GTF/BED records, extract the sequence of
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
388 transcripts (exon or CDS) and more.
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
389 By default (i.e. without -O) only transcripts are processed, discarding any
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
390 other non-transcript features. Default output is a simplified GFF3 with only
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
391 the basic attributes.
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
392
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
393 <input_gff> is a GFF file, use '-' for stdin
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
394
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
395 Options:
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
396
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
397 -i discard transcripts having an intron larger than <maxintron>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
398 -l discard transcripts shorter than <minlen> bases
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
399 -r only show transcripts overlapping coordinate range <start>..<end>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
400 (on chromosome/contig <chr>, strand <strand> if provided)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
401 -R for -r option, discard all transcripts that are not fully
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
402 contained within the given range
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
403 -U discard single-exon transcripts
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
404 -C coding only: discard mRNAs that have no CDS features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
405 --nc non-coding only: discard mRNAs that have CDS features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
406 --ignore-locus : discard locus features and attributes found in the input
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
407 -A use the description field from <seq_info.fsize> and add it
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
408 as the value for a 'descr' attribute to the GFF record
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
409 -s <seq_info.fsize> is a tab-delimited file providing this info
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
410 for each of the mapped sequences:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
411 <seq-name> <seq-length> <seq-description>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
412 (useful for -A option with mRNA/EST/protein mappings)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
413
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
414 Sorting: (by default, chromosomes are kept in the order they were found)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
415 --sort-alpha : chromosomes (reference sequences) are sorted alphabetically
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
416 --sort-by : sort the reference sequences by the order in which their
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
417 names are given in the <refseq.lst> file
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
418
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
419 Misc options:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
420 -F preserve all GFF attributes (for non-exon features)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
421 --keep-exon-attrs : for -F option, do not attempt to reduce redundant
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
422 exon/CDS attributes
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
423 -G do not keep exon attributes, move them to the transcript feature
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
424 (for GFF3 output)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
425 --keep-genes : in transcript-only mode (default), also preserve gene records
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
426 --keep-comments: for GFF3 input/output, try to preserve comments
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
427 -O process other non-transcript GFF records (by default non-transcript
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
428 records are ignored)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
429 -V discard any mRNAs with CDS having in-frame stop codons (requires -g)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
430 -H for -V option, check and adjust the starting CDS phase
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
431 if the original phase leads to a translation with an
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
432 in-frame stop codon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
433 -B for -V option, single-exon transcripts are also checked on the
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
434 opposite strand (requires -g)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
435 -P add transcript level GFF attributes about the coding status of each
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
436 transcript, including partialness or in-frame stop codons (requires -g)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
437 --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
438 that have CDS features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
439 --adj-stop stop codon adjustment: enables -P and performs automatic
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
440 adjustment of the CDS stop coordinate if premature or downstream
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
441 -N discard multi-exon mRNAs that have any intron with a non-canonical
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
442 splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
443 -J discard any mRNAs that either lack initial START codon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
444 or the terminal STOP codon, or have an in-frame stop codon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
445 (i.e. only print mRNAs with a complete CDS)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
446 --no-pseudo: filter out records matching the 'pseudo' keyword
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
447 --in-bed: input should be parsed as BED format (automatic if the input
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
448 filename ends with .bed*)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
449 --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
450 features (see --tlf option below); automatic if the input
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
451 filename ends with .tlf)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
452
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
453 Clustering:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
454 -M/--merge : cluster the input transcripts into loci, discarding
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
455 "duplicated" transcripts (those with the same exact introns
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
456 and fully contained or equal boundaries)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
457 -d <dupinfo> : for -M option, write duplication info to file <dupinfo>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
458 --cluster-only: same as -M/--merge but without discarding any of the
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
459 "duplicate" transcripts, only create "locus" features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
460 -K for -M option: also discard as redundant the shorter, fully contained
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
461 transcripts (intron chains matching a part of the container)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
462 -Q for -M option, no longer require boundary containment when assessing
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
463 redundancy (can be combined with -K); only introns have to match for
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
464 multi-exon transcripts, and >=80% overlap for single-exon transcripts
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
465 -Y for -M option, enforce -Q but also discard overlapping single-exon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
466 transcripts, even on the opposite strand (can be combined with -K)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
467
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
468 Output options:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
469 --force-exons: make sure that the lowest level GFF features are considered
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
470 "exon" features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
471 --gene2exon: for single-line genes not parenting any transcripts, add an
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
472 exon feature spanning the entire gene (treat it as a transcript)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
473 --t-adopt: try to find a parent gene overlapping/containing a transcript
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
474 that does not have any explicit gene Parent
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
475 -D decode url encoded characters within attributes
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
476 -Z merge very close exons into a single exon (when intron size<4)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
477 -g full path to a multi-fasta file with the genomic sequences
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
478 for all input mappings, OR a directory with single-fasta files
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
479 (one per genomic sequence, with file names matching sequence names)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
480 -w write a fasta file with spliced exons for each GFF transcript
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
481 -x write a fasta file with spliced CDS for each GFF transcript
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
482 -y write a protein fasta file with the translation of CDS for each record
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
483 -W for -w and -x options, write in the FASTA defline the exon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
484 coordinates projected onto the spliced sequence;
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
485 for -y option, write transcript attributes in the FASTA defline
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
486 -S for -y option, use '*' instead of '.' as stop codon translation
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
487 -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
488 -m <chr_replace> is a name mapping table for converting reference
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
489 sequence names, having this 2-column format:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
490 <original_ref_ID> <new_ref_ID>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
491 WARNING: all GFF records on reference sequences whose original IDs
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
492 are not found in the 1st column of this table will be discarded!
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
493 -t use <trackname> in the 2nd column of each GFF/GTF output line
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
494 -o write the records into <outfile> instead of stdout
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
495 -T main output will be GTF instead of GFF3
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
496 --bed output records in BED format instead of default GFF3
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
497 --tlf output "transcript line format" which is like GFF
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
498 but exons, CDS features and related data are stored as GFF
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
499 attributes in the transcript feature line, like this:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
500 exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
501 <exons> is a comma-delimited list of exon_start-exon_end coordinates;
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
502 <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
503 --table output a simple tab delimited format instead of GFF, with columns
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
504 having the values of GFF attributes given in <attrlist>; special
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
505 pseudo-attributes (prefixed by @) are recognized:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
506 @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
507 -v,-E expose (warn about) duplicate transcript IDs and other potential
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
508 problems with the given GFF/GTF records
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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509 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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510 </help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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511 <citations>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
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512 <citation type="doi">10.1038/nbt.1621</citation>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
513 </citations>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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514 </tool>