Mercurial > repos > iuc > nanocompore_sampcomp

changeset 4:c0fb573c1e8d 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 17:29:34 +0000
parents b833eff63b10
children
files macros.xml sampcomp.xml
diffstat 2 files changed, 11 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Jul 09 02:38:37 2020 -0400
+++ b/macros.xml	Thu Jun 23 17:29:34 2022 +0000
@@ -2,6 +2,11 @@
 <macros>
     <token name="@TOOL_VERSION@">1.0.0rc3.post2</token>
     <token name="@DESCRIPTION@"></token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">Nanocompore</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">nanocompore</requirement>
--- a/sampcomp.xml	Thu Jul 09 02:38:37 2020 -0400
+++ b/sampcomp.xml	Thu Jun 23 17:29:34 2022 +0000
@@ -1,6 +1,7 @@
 <?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>
         <import>macros.xml</import>
     </macros>
@@ -20,6 +21,9 @@
             ln -s '$current.index' 'sample_2_${i}.tsv.idx' &&
         #end for
 
+        ## symlink fasta file because a .fai file is created
+        ln -s '$fasta' reference.fa &&
+
         ## run
         nanocompore sampcomp
         ## required
@@ -29,7 +33,7 @@
         --label2 '$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'