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comparison roary.xml @ 3:38d47369d021 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 9c9db9f5e815e6a9b55c4adf378c7aa6a76a58da"
author iuc
date Wed, 21 Aug 2019 11:10:38 -0400
parents 9d36f948b56c
children fc19ad96e9bb
comparison
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2:9d36f948b56c 3:38d47369d021
1 <tool id="roary" name="Roary" version="3.10.2"> 1 <tool id="roary" name="Roary" version="3.12.0+galaxy0">
2 <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description> 2 <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.10.2">roary</requirement> 5 <requirement type="package" version="3.12.0">roary</requirement>
6 </requirements> 6 </requirements>
7 7
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 9
10 #for $counter, $gff in enumerate($gff_input.gffs) 10 #for $gff in $gff_input.gffs
11 cp $gff temp${counter}.gff && 11 cp $gff '${gff.element_identifier}'.gff &&
12 #end for 12 #end for
13 13
14 roary 14 roary
15 -f out 15 -f out
16 -p \${GALAXY_SLOTS:-1} 16 -p \${GALAXY_SLOTS:-1}
17 -e 17 -e
18 -n 18 -n
19 -i '$percent_ident' 19 -i '$percent_ident'
20 -cd '$core_diff' 20 -cd '$core_diff'
21 -g '$advanced.maxclust' 21 -g '$advanced.maxclust'
22 $advanced.split_para 22 $advanced.split_para
23 -t '$advanced.trans_tab' 23 -t '$advanced.trans_tab'
24 -iv '$advanced.mcl' 24 -iv '$advanced.mcl'
25 25
26 temp*.gff 26 *.gff
27 27
28 ]]></command> 28 ]]></command>
29 29
30 <inputs> 30 <inputs>
31 <conditional name="gff_input"> 31 <conditional name="gff_input">
32 <param name="gff_input_selector" type="select" label="Individual gff files or a dataset collection" help="Select between individual gff files or a collection of gff files"> 32 <param name="gff_input_selector" type="select" label="Individual gff files or a dataset collection" help="Select between individual gff files or a collection of gff files">
33 <option value="individual">Individual</option> 33 <option value="individual">Individual</option>
34 <option value="collection">Collection</option> 34 <option value="collection">Collection</option>
35 </param> 35 </param>
36 <when value="individual"> 36 <when value="individual">
37 <param name="gffs" type="data" multiple="true" format="gff3" label="select gff inputs to Roary" help="Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file." /> 37 <param name="gffs" type="data" multiple="true" format="gff,gff3" label="select gff inputs to Roary" help="Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file." />
38 </when> 38 </when>
39 <when value='collection'> 39 <when value='collection'>
40 <param name="gffs" type="data_collection" collection_type="list" format="gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." /> 40 <param name="gffs" type="data_collection" collection_type="list" format="gff,gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." />
41 </when> 41 </when>
42 </conditional> 42 </conditional>
43 <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/> 43 <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/>
44 <param name="core_diff" type="float" label="percentage of isolates a gene must be in to be core" help="The total percentage of the isolates that must have the gene for it to be considered a core gene." value="99.0"/> 44 <param name="core_diff" type="float" label="percentage of isolates a gene must be in to be core" help="The total percentage of the isolates that must have the gene for it to be considered a core gene." value="99.0"/>
45 45
169 For further info see: http://sanger-pathogens.github.io/Roary/ 169 For further info see: http://sanger-pathogens.github.io/Roary/
170 170
171 ]]></help> 171 ]]></help>
172 172
173 <citations> 173 <citations>
174 <citation type="doi">http://doi.org/10.1093/bioinformatics/btv421</citation> 174 <citation type="doi">10.1093/bioinformatics/btv421</citation>
175 </citations> 175 </citations>
176 176
177 </tool> 177 </tool>