Mercurial > repos > iuc > spades_biosyntheticspades

changeset 1:8a9a9350ffaf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
author iuc
date Mon, 24 Jan 2022 18:47:05 +0000
parents 42a39792aaae
children 1bb12736175c
files macros.xml
diffstat 1 files changed, 18 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Sun Jan 23 21:35:21 2022 +0000
+++ b/macros.xml	Mon Jan 24 18:47:05 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.15.3</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
@@ -54,7 +54,7 @@
         #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
         #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
         #set $file_path = 'reads1/' + $fname
-        ln -s '$input_file' $file_path &&
+        ln -s '$input_file' '$file_path' &&
         $file_paths1.append($file_path)
     #end for
 #else if $singlePaired.sPaired == "paired"
@@ -64,7 +64,7 @@
         #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
         #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
         #set $file_path = 'paired_reads1/' + str($fname)
-        ln -s '$input_file' $file_path &&
+        ln -s '$input_file' '$file_path' &&
         $fw_reads1.append($file_path)
     #end for
     #set rv_reads1 = []
@@ -72,7 +72,7 @@
         #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
         #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
         #set $file_path = 'paired_reads1/' + str($fname)
-        ln -s '$input_file' $file_path &&
+        ln -s '$input_file' '$file_path' &&
         $rv_reads1.append($file_path)
     #end for
     #silent $fw_reads1.sort()
@@ -84,10 +84,10 @@
     #for $i, $input_file in enumerate($singlePaired.input)
         #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq')
         #set $file_path = 'paired_reads1/fw' + str($i) + '.' + $ext
-        ln -s '$input_file.forward' $file_path &&
+        ln -s '$input_file.forward' '$file_path' &&
         $fw_reads1.append($file_path)
         #set $file_path = 'paired_reads1/rv' + str($i) + '.' + $ext
-        ln -s '$input_file.reverse' $file_path &&
+        ln -s '$input_file.reverse' '$file_path' &&
         $rv_reads1.append($file_path)
     #end for
 #end if
@@ -101,7 +101,7 @@
         #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
         #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
         #set $file_path = 'reads2/' + $fname
-        ln -s '$input_file' $file_path &&
+        ln -s '$input_file' '$file_path' &&
         $file_paths2.append($file_path)
     #end for
 #else if $additional_reads.singlePaired.sPaired == "paired"
@@ -111,7 +111,7 @@
         #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
         #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
         #set $file_path = 'paired_reads2/' + str($fname)
-        ln -s '$input_file' $file_path &&
+        ln -s '$input_file' '$file_path' &&
         $fw_reads2.append($file_path)
     #end for
     #set rv_reads2 = []
@@ -119,7 +119,7 @@
         #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
         #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
         #set $file_path = 'paired_reads2/' + str($fname)
-        ln -s '$input_file' $file_path &&
+        ln -s '$input_file' '$file_path' &&
         $rv_reads2.append($file_path)
     #end for
     #silent $fw_reads2.sort()
@@ -131,10 +131,10 @@
     #for $i, $input_file in enumerate($additional_reads.singlePaired.input)
         #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq')
         #set $file_path = 'paired_reads2/fw' + str($i) + '.' + $ext
-        ln -s '$input_file.forward' $file_path &&
+        ln -s '$input_file.forward' '$file_path' &&
         $fw_reads2.append($file_path)
         #set $file_path = 'paired_reads2/rv' + str($i) + '.' + $ext
-        ln -s '$input_file.reverse' $file_path &&
+        ln -s '$input_file.reverse' '$file_path' &&
         $rv_reads2.append($file_path)
     #end for
 #end if
@@ -235,7 +235,7 @@
         #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
         #set $fname = 'file' + str($i) + '.' + $ext
         #set $file_path = 'trusted_contigs/' + $fname
-        ln -s '$input_file' $file_path &&
+        ln -s '$input_file' '$file_path' &&
         $trusted_contigs.append($file_path)
     #end for
 #end if
@@ -246,7 +246,7 @@
         #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
         #set $fname = 'file' + str($i) + '.' + $ext
         #set $file_path = 'untrusted_contigs/' + $fname
-        ln -s '$input_file' $file_path &&
+        ln -s '$input_file' '$file_path' &&
         $untrusted_contigs.append($file_path)
     #end for
 #end if
@@ -260,7 +260,7 @@
         #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
         #set $fname = 'file' + str($i) + '.' + $ext
         #set $file_path = 'nanopore_reads/' + $fname
-        ln -s '$input_file' $file_path &&
+        ln -s '$input_file' '$file_path' &&
         $nanopore_reads.append($file_path)
     #end for
 #end if
@@ -271,7 +271,7 @@
         #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
         #set $fname = 'file' + str($i) + '.' + $ext
         #set $file_path = 'pacbio_reads/' + $fname
-        ln -s '$input_file' $file_path &&
+        ln -s '$input_file' '$file_path' &&
         $pacbio_reads.append($file_path)
     #end for
 #end if
@@ -285,7 +285,7 @@
             #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
             #set $fname = 'file' + str($i) + '.' + $ext
             #set $file_path = 'sanger_reads/' + $fname
-            ln -s '$input_file' $file_path &&
+            ln -s '$input_file' '$file_path' &&
             $sanger_reads.append($file_path)
         #end for
     #end if
@@ -299,7 +299,7 @@
             #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
             #set $fname = 'file' + str($i) + '.' + $ext
             #set $file_path = 'flrna_reads/' + $fname
-            ln -s '$input_file' $file_path &&
+            ln -s '$input_file' '$file_path' &&
             $flrna_reads.append($file_path)
         #end for
     #end if
@@ -313,7 +313,7 @@
             #set $ext = $input_file.ext.replace('gfa1', 'gfa')
             #set $fname = 'file' + str($i) + '.' + $ext
             #set $file_path = 'assembly_graphs/' + $fname
-            ln -s '$input_file' $file_path &&
+            ln -s '$input_file' '$file_path' &&
             $assembly_graphs.append($file_path)
         #end for
     #end if