Mercurial > repos > devteam > gffread
comparison gffread.xml @ 3:29769f789b8f draft
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
| author | devteam |
|---|---|
| date | Tue, 01 Oct 2019 12:19:52 -0400 |
| parents | 6562753c6bdc |
| children | 0cf496c45054 |
comparison
equal
deleted
inserted
replaced
| 2:6562753c6bdc | 3:29769f789b8f |
|---|---|
| 1 <tool id="gffread" name="gffread" version="@VERSION@.1"> | 1 <tool id="gffread" name="gffread" version="@VERSION@.2"> |
| 2 <description>Filters and/or converts GFF3/GTF2 records</description> | 2 <description>Filters and/or converts GFF3/GTF2 records</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>cuff_macros.xml</import> | 4 <import>cuff_macros.xml</import> |
| 5 <xml name="fasta_output_select"> | 5 <xml name="fasta_output_select"> |
| 6 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs"> | 6 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs"> |
| 82 #end if | 82 #end if |
| 83 #end if | 83 #end if |
| 84 #if $chr_replace: | 84 #if $chr_replace: |
| 85 -m '$chr_replace' | 85 -m '$chr_replace' |
| 86 #end if | 86 #end if |
| 87 | |
| 88 $full_gff_attribute_preservation | |
| 89 $decode_url | |
| 90 $expose | |
| 91 | |
| 87 ## | 92 ## |
| 88 ## Although documented, does not appear to be used in the gffread code | 93 ## Although documented, does not appear to be used in the gffread code |
| 89 ## #if $seq_info: | 94 ## #if $seq_info: |
| 90 ## -A -s "$seq_info" | 95 ## -A -s "$seq_info" |
| 91 ## #end if | 96 ## #end if |
| 257 <tests> | 262 <tests> |
| 258 <test> | 263 <test> |
| 259 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 264 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
| 260 <param name="gff_fmt" value="gff"/> | 265 <param name="gff_fmt" value="gff"/> |
| 261 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" /> | 266 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" /> |
| 267 </test> | |
| 268 | |
| 269 <test> | |
| 270 <param name="input" ftype="gtf" value="ecoli-k12.gff3"/> | |
| 271 <param name="gff_fmt" value="gff"/> | |
| 272 <param name="full_gff_attribute_preservation" value="-F"/> | |
| 273 <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" /> | |
| 262 </test> | 274 </test> |
| 263 | 275 |
| 264 <test> | 276 <test> |
| 265 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 277 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
| 266 <param name="filtering" value="--no-pseudo"/> | 278 <param name="filtering" value="--no-pseudo"/> |