Mercurial > repos > iuc > maker

changeset 4:5e96efe6e6c6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b"
author iuc
date Thu, 10 Oct 2019 02:56:46 -0400
parents 96ac930d84fa
children 5201ec38c01f
files maker.xml
diffstat 1 files changed, 8 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/maker.xml	Mon May 06 10:06:04 2019 -0400
+++ b/maker.xml	Thu Oct 10 02:56:46 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="maker" name="Maker" profile="16.04" version="@VERSION@">
+<tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy1">
     <description>genome annotation pipeline</description>
     <macros>
         <import>macros.xml</import>
@@ -125,7 +125,11 @@
 
 #else if $repeat_masking.repeat_source.source_type == 'library'
 model_org= # select a model organism for RepBase masking in RepeatMasker
-rmlib=${repeat_masking.repeat_source.repeatmasker.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker
+#if $repeat_masking.repeat_source.rmlib
+rmlib=${repeat_masking.repeat_source.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker
+#else
+rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
+#end if
 
 #if $repeat_masking.repeat_source.repeat_protein
 repeat_protein=${repeat_masking.repeat_source.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner
@@ -432,8 +436,9 @@
                 <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
               </when>
               <when value="library">
+                <param name="rmlib" type="data" format="fasta" label="Transposable element sequences for RepeatRunner" optional="True" />
                 <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" />
-                <param name="rm_gff" type="data" format="fasta" label="Pre-identified repeat elements from an external GFF file" optional="True" />
+                <param name="rm_gff" type="data" format="gff" label="Pre-identified repeat elements from an external GFF file" optional="True" />
                 <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
               </when>
               <when value="no"/>