| Previous changeset 0:42a39792aaae (2022-01-23) Next changeset 2:1bb12736175c (2022-01-25) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77" |
|
modified:
macros.xml |
| b |
| diff -r 42a39792aaae -r 8a9a9350ffaf macros.xml --- 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 |