Mercurial > repos > iuc > unicycler
changeset 10:d10bdad2fd17 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
| author | iuc |
|---|---|
| date | Fri, 21 Oct 2022 16:02:46 +0000 |
| parents | 6e26c9afd301 |
| children | 8f9f06995f98 |
| files | unicycler.xml |
| diffstat | 1 files changed, 21 insertions(+), 18 deletions(-) [+] |
line wrap: on
line diff
--- a/unicycler.xml Sat Sep 24 21:14:02 2022 +0000 +++ b/unicycler.xml Fri Oct 21 16:02:46 2022 +0000 @@ -1,7 +1,8 @@ <tool id="unicycler" name="Create assemblies with Unicycler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> +<description>pipeline for bacterial genomes</description> <macros> <token name="@TOOL_VERSION@">0.5.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <xrefs> <xref type="bio.tools">unicycler</xref> @@ -18,44 +19,46 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ ## Preparing files +#set $uncompressed = ('fastqsanger','fastq') +#set $compressed = ('fastqsanger.gz','fastq.gz') #if str( $paired_unpaired.fastq_input_selector ) == "paired" - #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger') + #if $paired_unpaired.fastq_input1.file_ext in $uncompressed #set fq1 = "fq1.fastq" - #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz') + #elif $paired_unpaired.fastq_input1.file_ext in $compressed #set fq1 = "fq1.fastq.gz" #end if - #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger') + #if $paired_unpaired.fastq_input2.file_ext in $uncompressed #set fq2 = "fq2.fastq" - #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz') + #elif $paired_unpaired.fastq_input2.file_ext in $compressed #set fq2 = "fq2.fastq.gz" #end if ln -s '${paired_unpaired.fastq_input1}' $fq1 && ln -s '${paired_unpaired.fastq_input2}' $fq2 && #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" - #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger') + #if $paired_unpaired.fastq_input1.forward.file_ext in $uncompressed #set fq1 = "fq1.fastq" - #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz') + #elif $paired_unpaired.fastq_input1.forward.file_ext in $compressed #set fq1 = "fq1.fastq.gz" #end if - #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger') + #if $paired_unpaired.fastq_input1.reverse.file_ext in $uncompressed #set fq2 = "fq2.fastq" - #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz') + #elif $paired_unpaired.fastq_input1.reverse.file_ext in $compressed #set fq2 = "fq2.fastq.gz" #end if ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 && ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 && #elif str( $paired_unpaired.fastq_input_selector ) == "single" - #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger') + #if $paired_unpaired.fastq_input1.file_ext in $uncompressed #set fq = "fq.fastq" - #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz') + #elif $paired_unpaired.fastq_input1.file_ext in $compressed #set fq = "fq.fastq.gz" #end if ln -s '${paired_unpaired.fastq_input1}' '$fq' && #end if #if $long - #if $long.is_of_type('fastqsanger') + #if $long.file_ext in $uncompressed #set lr = "lr.fastq" - #elif $long.is_of_type('fastqsanger.gz') + #elif $long.file_ext in $compressed #set lr = "lr.fastq.gz" #elif $long.is_of_type('fasta') #set lr = "lr.fasta" @@ -138,22 +141,22 @@ <option value="none">None</option> </param> <when value="paired"> - <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz" + <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> - <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz" + <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> </when> <when value="paired_collection"> - <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" /> + <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" type="data_collection" collection_type="paired" label="Select a paired collection" /> </when> <when value="single"> - <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" + <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/> </when> <when value="none"> </when> </conditional> - <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/> + <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta,fastq,fastq.gz" label="Select long reads. If there are no long reads, leave this empty"/> <param argument="--mode" type="select" label="Select Bridging mode"> <option value="conservative">Conservative (smaller contigs, lower misassembly)</option> <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>