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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071 |
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modified:
macros.xml ragtag.xml |
| b |
| diff -r a04e64efa43a -r d110a4141898 macros.xml --- a/macros.xml Wed Nov 10 23:33:13 2021 +0000 +++ b/macros.xml Thu Jun 23 17:28:50 2022 +0000 |
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| @@ -67,8 +67,8 @@ </conditional> </xml> <token name="@INPUTS@"><![CDATA[ - $mode_conditional.reference - $mode_conditional.query + reference.fa + query.fa ]]></token> <token name="@COMMON_PARAMETERS@"><![CDATA[ --aligner $mode_conditional.advanced_options.mapping_conditional.mapping_option |
| b |
| diff -r a04e64efa43a -r d110a4141898 ragtag.xml --- a/ragtag.xml Wed Nov 10 23:33:13 2021 +0000 +++ b/ragtag.xml Thu Jun 23 17:28:50 2022 +0000 |
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| @@ -23,6 +23,15 @@ #end for #set $merge_files = " ".join($input_files) #end if + + ## symlink reference because a .fai file is created + #if $mode_conditional.mode_option in ['correct', 'scaffold', 'patch'] + ln -s '$mode_conditional.reference' reference.fa && + ln -s '$mode_conditional.query' query.fa && + #else + ln -s '$assembly_fasta' assembly.fa && + #end if + ragtag.py $mode_conditional.mode_option -u #if $mode_conditional.mode_option == 'correct' @INPUTS@ @@ -72,7 +81,7 @@ $mode_conditional.advanced_options.patching_mode #end if #else - $assembly_fasta + assembly.fa #if $mode_conditional.scaffold_files $merge_files #end if |