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comparison masurca_simple.xml @ 0:0a33488ca043 draft

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author dnbenso
date Sun, 23 Jan 2022 22:08:50 +0000
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1 <tool id="masurca_simple" name="MaSuRCA simple" version="@TOOL_VERSION@+galaxy0">
2 <description>The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit without config</description>
3 <macros>
4 <token name="@TOOL_VERSION@">4.0.6</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">masurca</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 #set $long = 'false'
11 #if $nanopore_input.np_input == "Yes":
12 #if $pacbio_input.pb_input == "Yes":
13 cat '$nanopore_input.nano' '$pacbio_input.pacbio' > long.fastq.gz &&
14 #else:
15 ln -s '$nanopore_input.nano' long.fastq.gz &&
16 #end if
17 #set $long = 'true'
18 #elif $pacbio_input.pb_input == "Yes":
19 ln -s '$pacbio_input.pacbio' long.fastq.gz &&
20 #set $long = 'true'
21 #end if
22 masurca -t \${GALAXY_SLOTS:-8} -i
23 #if str( $illumina_input.input_type ) == "single"
24 '$illumina_input.fastq_input1'
25 #elif str( $illumina_input.input_type ) == "paired"
26 '$illumina_input.fastq_input1','$illumina_input.fastq_input2'
27 #elif str( $illumina_input.input_type ) == "paired_collection"
28 '$illumina_input.fastq_input1','$illumina_input.fastq_input2'
29 #end if
30 #if $long == "true":
31 -r long.fastq.gz
32 #end if
33 ]]></command>
34 <inputs>
35 <conditional name="illumina_input">
36 <param name="input_type" type="select" label="Paired-end reads" help="Select between paired and paired collection">
37 <option value="single">Single</option>
38 <option value="paired">Paired</option>
39 <option value="paired_collection">Paired Collection</option>
40 </param>
41 <when value="single">
42 <param type="data" name="fastq_input1" format="fastqsanger,fastqsanger.gz"
43 label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
44 </when>
45 <when value="paired">
46 <param type="data" name="fastq_input1" format="fastqsanger,fastqsanger.gz"
47 label="Select first set of reads" help="Specify dataset with forward reads"/>
48 <param type="data" name="fastq_input2" format="fastqsanger,fastqsanger.gz"
49 label="Select second set of reads" help="Specify dataset with reverse reads"/>
50 </when>
51 <when value="paired_collection">
52 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
53 </when>
54 </conditional>
55 <conditional name="nanopore_input">
56 <param name="np_input" type="select" label="Use Nanopore long reads" help="Optional Nanopore reads must be in a single fasta or fastq file">
57 <option value="No" selected="true">No</option>
58 <option value="Yes">Yes</option>
59 </param>
60 <when value="No"/>
61 <when value="Yes">
62 <param type="data" name="nano" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="nanopore reads" />
63 </when>
64 </conditional>
65 <conditional name="pacbio_input">
66 <param name="pb_input" type="select" label="Use Pacbio long reads" help="Optional Pacbio reads must be in a single fasta or fastq file">
67 <option value="No" selected="true">No</option>
68 <option value="Yes">Yes</option>
69 </param>
70 <when value="No"/>
71 <when value="Yes">
72 <param type="data" name="pacbio" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="pacbio reads" />
73 </when>
74 </conditional>
75 </inputs>
76 <outputs>
77 <data name="superReads" format="fasta" from_work_dir="work1/superReadSequences.fasta" label="${tool.name} on ${on_string}: superReads" />
78 <data name="scaffold_prm" format="fasta" from_work_dir="CA.mr.*/primary.genome.scf.fasta" label="${tool.name} on ${on_string}: primary_genome" />
79 <data name="scaffold_alt" format="fasta" from_work_dir="CA.mr.*/alternative.genome.scf.fasta" label="${tool.name} on ${on_string}: alternative_genome" />
80 </outputs>
81 <tests>
82 <test>
83 <conditional name="illumina_input">
84 <param name="input_type" value="paired" />
85 <param name="fastq_input1" value="phix_f.fq.gz"/>
86 <param name="fastq_input2" value="phix_r.fq.gz"/>
87 </conditional>
88 <conditional name="nanopore_input">
89 <param name="np_input" value="Yes" />
90 <param name="nano" value="onp.fa"/>
91 </conditional>
92 <conditional name="pacbio_input">
93 <param name="pb_input" value="No" />
94 </conditional>
95 <output name="superReads" ftype="fasta" />
96 </test>
97 </tests>
98 <help><![CDATA[
99
100 This implementation of MaSuRCA is for small projects that only have PE
101 Illumina reads (mandatory) and long reads from PACBIO or Oxford
102 Nanopore or both. For larger projects and if you want to change the
103 default options, you will need to run masurca_complex
104
105 ]]></help>
106 <citations>
107 <citation type="doi">10.1093/bioinformatics/btt476</citation>
108 </citations>
109 </tool>