| Previous changeset 7:78608ec02d62 (2021-02-13) Next changeset 9:91887494eb97 (2021-11-24) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit fde1985c9d6860f9a03ddfd38378a5c3f5e31fcb" |
|
modified:
roary.xml |
| b |
| diff -r 78608ec02d62 -r e88a7de55d6e roary.xml --- a/roary.xml Sat Feb 13 11:59:15 2021 +0000 +++ b/roary.xml Thu Sep 23 13:08:51 2021 +0000 |
| [ |
| @@ -1,5 +1,8 @@ <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> + <xrefs> + <xref type="bio.tools">roary</xref> + </xrefs> <macros> <token name="@TOOL_VERSION@">3.13.0</token> <token name="@VERSION_SUFFIX@">1</token> @@ -9,10 +12,12 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ + #import re #set $filenames = list() #for $gff in $gff_input.gffs - cp '$gff' '${gff.element_identifier}.gff' && - #set $filename = str($gff.element_identifier) + '.gff' + #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' $filenames.append(str($filename)) #end for |