Mercurial > repos > iuc > roary
changeset 3:15ca041134a9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 9c9db9f5e815e6a9b55c4adf378c7aa6a76a58da"
| author | iuc |
|---|---|
| date | Wed, 21 Aug 2019 11:11:15 -0400 |
| parents | f1ccc8a6eb05 |
| children | 809e42326fc2 |
| files | roary.xml |
| diffstat | 1 files changed, 12 insertions(+), 12 deletions(-) [+] |
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--- a/roary.xml Fri Oct 20 04:30:53 2017 -0400 +++ b/roary.xml Wed Aug 21 11:11:15 2019 -0400 @@ -1,18 +1,18 @@ -<tool id="roary" name="Roary" version="3.10.2"> +<tool id="roary" name="Roary" version="3.12.0+galaxy0"> <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description> <requirements> - <requirement type="package" version="3.10.2">roary</requirement> + <requirement type="package" version="3.12.0">roary</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - #for $counter, $gff in enumerate($gff_input.gffs) - cp $gff temp${counter}.gff && + #for $gff in $gff_input.gffs + cp $gff '${gff.element_identifier}'.gff && #end for - + roary - -f out + -f out -p \${GALAXY_SLOTS:-1} -e -n @@ -22,8 +22,8 @@ $advanced.split_para -t '$advanced.trans_tab' -iv '$advanced.mcl' - - temp*.gff + + *.gff ]]></command> @@ -34,10 +34,10 @@ <option value="collection">Collection</option> </param> <when value="individual"> - <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." /> + <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." /> </when> <when value='collection'> - <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." /> + <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." /> </when> </conditional> <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/> @@ -171,7 +171,7 @@ ]]></help> <citations> - <citation type="doi">http://doi.org/10.1093/bioinformatics/btv421</citation> + <citation type="doi">10.1093/bioinformatics/btv421</citation> </citations> -</tool> \ No newline at end of file +</tool>