Mercurial > repos > iuc > roary
changeset 9:91887494eb97 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 40335305f3461201b017380c60c4c96c7e07322f"
| author | iuc |
|---|---|
| date | Wed, 24 Nov 2021 21:06:31 +0000 |
| parents | e88a7de55d6e |
| children | 9b2b122d0415 |
| files | roary.xml |
| diffstat | 1 files changed, 8 insertions(+), 7 deletions(-) [+] |
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--- a/roary.xml Thu Sep 23 13:08:51 2021 +0000 +++ b/roary.xml Wed Nov 24 21:06:31 2021 +0000 @@ -1,12 +1,12 @@ <tool id="roary" name="Roary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description> + <macros> + <token name="@TOOL_VERSION@">3.13.0</token> + <token name="@VERSION_SUFFIX@">2</token> + </macros> <xrefs> <xref type="bio.tools">roary</xref> </xrefs> - <macros> - <token name="@TOOL_VERSION@">3.13.0</token> - <token name="@VERSION_SUFFIX@">1</token> - </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">roary</requirement> </requirements> @@ -14,10 +14,11 @@ <command detect_errors="exit_code"><![CDATA[ #import re #set $filenames = list() + ## Roary resolves symbolic links and breaks if there is whitespace in the path. + ## Copying and renaming the files resolves that issue. #for $gff in $gff_input.gffs - #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($gff.element_identifier)) - ln -s '$gff' '${escaped_element_identifier}.gff' && - #set $filename = str($escaped_element_identifier) + '.gff' + #set $filename = '%s.gff' % re.sub('[^\w_-]', '_', str($gff.element_identifier)) + cp '$gff' $filename && $filenames.append(str($filename)) #end for