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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit bc948510a50635ce98123c9e09ae09b39f1e5cee
author iuc
date Sun, 07 Jul 2024 19:46:39 +0000
parents 8f9f06995f98
children
comparison
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11:8f9f06995f98 12:3e44ef016b45
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 <description>pipeline for bacterial genomes</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.5.0</token> 4 <token name="@TOOL_VERSION@">0.5.0</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 6 </macros>
7 <edam_topics> 7 <edam_topics>
8 <edam_topic>topic_0196</edam_topic> 8 <edam_topic>topic_0196</edam_topic>
9 </edam_topics> 9 </edam_topics>
10 <edam_operations> 10 <edam_operations>
21 #for r in $reuse 21 #for r in $reuse
22 ln -s $r.reuse_file ${r.reuse_step}.gfa && 22 ln -s $r.reuse_file ${r.reuse_step}.gfa &&
23 #end for 23 #end for
24 24
25 ## Preparing files 25 ## Preparing files
26 #set $uncompressed = ('fastqsanger','fastq')
27 #set $compressed = ('fastqsanger.gz','fastq.gz')
28 #if str( $paired_unpaired.fastq_input_selector ) == "paired" 26 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
29 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed 27 #if $paired_unpaired.fastq_input1.is_of_type("fastq.gz"):
28 #set fq1 = "fq1.fastq.gz"
29 #else
30 #set fq1 = "fq1.fastq" 30 #set fq1 = "fq1.fastq"
31 #elif $paired_unpaired.fastq_input1.file_ext in $compressed
32 #set fq1 = "fq1.fastq.gz"
33 #end if 31 #end if
34 #if $paired_unpaired.fastq_input2.file_ext in $uncompressed 32 #if $paired_unpaired.fastq_input2.is_of_type("fastq.gz"):
33 #set fq2 = "fq2.fastq.gz"
34 #else
35 #set fq2 = "fq2.fastq" 35 #set fq2 = "fq2.fastq"
36 #elif $paired_unpaired.fastq_input2.file_ext in $compressed
37 #set fq2 = "fq2.fastq.gz"
38 #end if 36 #end if
39 ln -s '${paired_unpaired.fastq_input1}' $fq1 && 37 ln -s '${paired_unpaired.fastq_input1}' $fq1 &&
40 ln -s '${paired_unpaired.fastq_input2}' $fq2 && 38 ln -s '${paired_unpaired.fastq_input2}' $fq2 &&
41 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" 39 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
42 #if $paired_unpaired.fastq_input1.forward.file_ext in $uncompressed 40 #if $paired_unpaired.fastq_input1.forward.is_of_type("fastq.gz"):
41 #set fq1 = "fq1.fastq.gz"
42 #else
43 #set fq1 = "fq1.fastq" 43 #set fq1 = "fq1.fastq"
44 #elif $paired_unpaired.fastq_input1.forward.file_ext in $compressed
45 #set fq1 = "fq1.fastq.gz"
46 #end if 44 #end if
47 #if $paired_unpaired.fastq_input1.reverse.file_ext in $uncompressed 45 #if $paired_unpaired.fastq_input1.reverse.is_of_type("fastq.gz"):
46 #set fq2 = "fq2.fastq.gz"
47 #else
48 #set fq2 = "fq2.fastq" 48 #set fq2 = "fq2.fastq"
49 #elif $paired_unpaired.fastq_input1.reverse.file_ext in $compressed
50 #set fq2 = "fq2.fastq.gz"
51 #end if 49 #end if
52 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 && 50 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 &&
53 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 && 51 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 &&
54 #elif str( $paired_unpaired.fastq_input_selector ) == "single" 52 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
55 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed 53 #if $paired_unpaired.fastq_input1.is_of_type("fastqsanger.gz"):
54 #set fq = "fq.fastq.gz"
55 #else
56 #set fq = "fq.fastq" 56 #set fq = "fq.fastq"
57 #elif $paired_unpaired.fastq_input1.file_ext in $compressed
58 #set fq = "fq.fastq.gz"
59 #end if 57 #end if
60 ln -s '${paired_unpaired.fastq_input1}' '$fq' && 58 ln -s '${paired_unpaired.fastq_input1}' '$fq' &&
61 #end if 59 #end if
62 #if $long 60 #if $long
63 #if $long.file_ext in $uncompressed 61 #if $long.is_of_type("fastq"):
64 #set lr = "lr.fastq" 62 #set lr = "lr.fastq"
65 #elif $long.file_ext in $compressed 63 #elif $long.is_of_type("fastq.gz"):
66 #set lr = "lr.fastq.gz" 64 #set lr = "lr.fastq.gz"
67 #elif $long.is_of_type('fasta') 65 #elif $long.is_of_type("fasta")
68 #set lr = "lr.fasta" 66 #set lr = "lr.fasta"
69 #end if 67 #end if
70 ln -s '${long}' '$lr' && 68 ln -s '${long}' '$lr' &&
71 #end if 69 #end if
72 ## Running Unicycler 70 ## Running Unicycler