Mercurial > repos > iuc > nanocompore_sampcomp

changeset 4:89b4ed4145b3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 51078f4c0eab9cc41a0cb2190000e428322631a4
author iuc
date Thu, 23 Jun 2022 17:27:25 +0000
parents e7d7d87dc1a3
children
files sampcomp.xml
diffstat 1 files changed, 5 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/sampcomp.xml	Wed Sep 01 07:46:51 2021 +0000
+++ b/sampcomp.xml	Thu Jun 23 17:27:25 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+galaxy0">
+<tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+galaxy1">
     <description>to compare Nanopolished datasets</description>
     <expand macro="bio_tools"/>
     <macros>
@@ -21,6 +21,9 @@
             ln -s '$current.index' 'sample_2_${i}.tsv.idx' &&
         #end for
 
+        ## symlink fasta file because a .fai file is created
+        ln -s '$fasta' reference.fa &&
+
         ## run
         nanocompore sampcomp
         ## required
@@ -30,7 +33,7 @@
         --label2 '$label2'
         #set files2 = ','.join(['sample_2_' + str(item) + '.tsv' for item in range(len($file2_rep))])
         --file_list2 '$files2'
-        --fasta '$fasta'
+        --fasta reference.fa
         ## optional
         #if $ap.bed
             --bed '$ap.bed'