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comparison gffread.xml @ 5:69e0806b63a4 draft

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"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 12:20:13 -0400
parents 0232f19d300f
children 6ea09f60dee9
comparison
equal deleted inserted replaced
4:0232f19d300f 5:69e0806b63a4
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"/>