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comparison unicycler.xml @ 10:d10bdad2fd17 draft

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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
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9:6e26c9afd301 10:d10bdad2fd17
1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> 1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
2 <description>pipeline for bacterial genomes</description>
2 <macros> 3 <macros>
3 <token name="@TOOL_VERSION@">0.5.0</token> 4 <token name="@TOOL_VERSION@">0.5.0</token>
4 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
5 </macros> 6 </macros>
6 <xrefs> 7 <xrefs>
7 <xref type="bio.tools">unicycler</xref> 8 <xref type="bio.tools">unicycler</xref>
8 </xrefs> 9 </xrefs>
9 <edam_topics> 10 <edam_topics>
16 <requirement type="package" version="@TOOL_VERSION@">unicycler</requirement> 17 <requirement type="package" version="@TOOL_VERSION@">unicycler</requirement>
17 <requirement type="package" version="1.15.1">samtools</requirement> 18 <requirement type="package" version="1.15.1">samtools</requirement>
18 </requirements> 19 </requirements>
19 <command detect_errors="exit_code"><![CDATA[ 20 <command detect_errors="exit_code"><![CDATA[
20 ## Preparing files 21 ## Preparing files
22 #set $uncompressed = ('fastqsanger','fastq')
23 #set $compressed = ('fastqsanger.gz','fastq.gz')
21 #if str( $paired_unpaired.fastq_input_selector ) == "paired" 24 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
22 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger') 25 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed
23 #set fq1 = "fq1.fastq" 26 #set fq1 = "fq1.fastq"
24 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz') 27 #elif $paired_unpaired.fastq_input1.file_ext in $compressed
25 #set fq1 = "fq1.fastq.gz" 28 #set fq1 = "fq1.fastq.gz"
26 #end if 29 #end if
27 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger') 30 #if $paired_unpaired.fastq_input2.file_ext in $uncompressed
28 #set fq2 = "fq2.fastq" 31 #set fq2 = "fq2.fastq"
29 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz') 32 #elif $paired_unpaired.fastq_input2.file_ext in $compressed
30 #set fq2 = "fq2.fastq.gz" 33 #set fq2 = "fq2.fastq.gz"
31 #end if 34 #end if
32 ln -s '${paired_unpaired.fastq_input1}' $fq1 && 35 ln -s '${paired_unpaired.fastq_input1}' $fq1 &&
33 ln -s '${paired_unpaired.fastq_input2}' $fq2 && 36 ln -s '${paired_unpaired.fastq_input2}' $fq2 &&
34 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" 37 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
35 #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger') 38 #if $paired_unpaired.fastq_input1.forward.file_ext in $uncompressed
36 #set fq1 = "fq1.fastq" 39 #set fq1 = "fq1.fastq"
37 #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz') 40 #elif $paired_unpaired.fastq_input1.forward.file_ext in $compressed
38 #set fq1 = "fq1.fastq.gz" 41 #set fq1 = "fq1.fastq.gz"
39 #end if 42 #end if
40 #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger') 43 #if $paired_unpaired.fastq_input1.reverse.file_ext in $uncompressed
41 #set fq2 = "fq2.fastq" 44 #set fq2 = "fq2.fastq"
42 #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz') 45 #elif $paired_unpaired.fastq_input1.reverse.file_ext in $compressed
43 #set fq2 = "fq2.fastq.gz" 46 #set fq2 = "fq2.fastq.gz"
44 #end if 47 #end if
45 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 && 48 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 &&
46 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 && 49 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 &&
47 #elif str( $paired_unpaired.fastq_input_selector ) == "single" 50 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
48 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger') 51 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed
49 #set fq = "fq.fastq" 52 #set fq = "fq.fastq"
50 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz') 53 #elif $paired_unpaired.fastq_input1.file_ext in $compressed
51 #set fq = "fq.fastq.gz" 54 #set fq = "fq.fastq.gz"
52 #end if 55 #end if
53 ln -s '${paired_unpaired.fastq_input1}' '$fq' && 56 ln -s '${paired_unpaired.fastq_input1}' '$fq' &&
54 #end if 57 #end if
55 #if $long 58 #if $long
56 #if $long.is_of_type('fastqsanger') 59 #if $long.file_ext in $uncompressed
57 #set lr = "lr.fastq" 60 #set lr = "lr.fastq"
58 #elif $long.is_of_type('fastqsanger.gz') 61 #elif $long.file_ext in $compressed
59 #set lr = "lr.fastq.gz" 62 #set lr = "lr.fastq.gz"
60 #elif $long.is_of_type('fasta') 63 #elif $long.is_of_type('fasta')
61 #set lr = "lr.fasta" 64 #set lr = "lr.fasta"
62 #end if 65 #end if
63 ln -s '${long}' '$lr' && 66 ln -s '${long}' '$lr' &&
136 <option value="paired_collection">Paired Collection</option> 139 <option value="paired_collection">Paired Collection</option>
137 <option value="single">Single</option> 140 <option value="single">Single</option>
138 <option value="none">None</option> 141 <option value="none">None</option>
139 </param> 142 </param>
140 <when value="paired"> 143 <when value="paired">
141 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz" 144 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
142 label="Select first set of reads" help="Specify dataset with forward reads"/> 145 label="Select first set of reads" help="Specify dataset with forward reads"/>
143 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz" 146 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
144 label="Select second set of reads" help="Specify dataset with reverse reads"/> 147 label="Select second set of reads" help="Specify dataset with reverse reads"/>
145 </when> 148 </when>
146 <when value="paired_collection"> 149 <when value="paired_collection">
147 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" /> 150 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
148 </when> 151 </when>
149 <when value="single"> 152 <when value="single">
150 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" 153 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
151 label="Select unpaired reads" help="Specify dataset with unpaired reads"/> 154 label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
152 </when> 155 </when>
153 <when value="none"> 156 <when value="none">
154 </when> 157 </when>
155 </conditional> 158 </conditional>
156 <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"/> 159 <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"/>
157 <param argument="--mode" type="select" label="Select Bridging mode"> 160 <param argument="--mode" type="select" label="Select Bridging mode">
158 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option> 161 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option>
159 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option> 162 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>
160 <option value="bold">Bold (longest contigs, higher misassembly rate)</option> 163 <option value="bold">Bold (longest contigs, higher misassembly rate)</option>
161 </param> 164 </param>