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comparison mapsembler2.xml @ 0:c90f5219b67a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
author iuc
date Fri, 20 Oct 2017 03:12:16 -0400
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-1:000000000000 0:c90f5219b67a
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool profile="16.04" id="mapsembler2" name="Mapsembler2" version="2.2.4">
3 <description>is a targeted assembly software</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <requirements>
8 <requirement type="package" version="2.2.4">mapsembler2</requirement>
9 </requirements>
10 <command><![CDATA[
11
12 #set $starter_filename = str($s) + "." + $s.ext
13 ln -sf '${s}' '${starter_filename}' &&
14
15 #set $samples = []
16 #for $read in $r
17 #set $filename = str($read) + "." + $read.ext
18 ln -sf '${read}' '${filename}' &&
19 #silent $samples.append($filename)
20 #end for
21
22 run_mapsembler2_pipeline.sh
23 -s '${starter_filename}'
24 -r "${ ' '.join(['%s' % read for read in $samples]) }"
25 -t ${t}
26 -k ${k}
27 -c ${c}
28 -d ${d}
29 -g ${g}
30 -f ${f}
31 -x ${x}
32 -y ${y}
33 ]]></command>
34
35 <inputs>
36 <!-- Input data files -->
37 <param argument="-s" type="data" format="fasta" label="Starters" help="Set of input sequences" />
38 <param argument="-r" type="data" multiple="true" format="fasta,fastq" label="List of reads" />
39 <param argument="-t" type="select" label="Select your output extension type">
40 <option value="1">a strict sequence</option>
41 <option value="2">a consensus sequence</option>
42 </param>
43 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Set the length of used kmers. Must fit the compiled value. Only uneven number" />
44 <param argument="-c" type="integer" label="Minimal coverage" value="5" help="Set the minimal coverage: Used by Phaser (don't use kmers with lower coverage) "/>
45 <param argument="-d" type="integer" label="Number of authorized substitutions" value="1" help="Set the number of authorized substitutions used while mapping reads on finding SNPs"/>
46 <param argument="-g" type="integer" label="Estimated genome size" value="10000000" help="Used only to control memory usage. e.g.3 billion (3000000000) uses 4Gb of RAM." />
47 <param argument="-f" type="select" label="Process of search" help="Set the process of search in the graph" >
48 <option value="1">Breadth</option>
49 <option value="2">Depth</option>
50 </param>
51 <param argument="-x" type="integer" label="Max length of nodes" value="40" help="Set the maximal length of nodes"/>
52 <param argument="-y" type="integer" label="Max depth of nodes" value="10000" help="Set the maximal depth of the graph"/>
53 </inputs>
54
55 <outputs>
56 <data name="fasta" from_work_dir="res_k_*.fasta" format="fasta" label="Assembly with ${tool.name} on $on_string"/>
57 <data name="coherent" from_work_dir="res_coherent_*.fasta" format="fasta" label="Coherent with ${tool.name} on $on_string" hidden="true"/>
58 <data name="uncoherent" from_work_dir="res_uncoherent_*.fasta" format="fasta" label="Uncoherent with ${tool.name} on $on_string" hidden="true"/>
59 <data name="extremities" from_work_dir="starter_extremities.fa" format="fasta" label="Starter extremities with ${tool.name} on $on_string" hidden="true"/>
60 </outputs>
61
62 <tests>
63 <test>
64 <param name="s" value="mapsembler2/starter.fa" />
65 <param name="r" value="mapsembler2/reads1,mapsembler2/reads2" />
66 <param name="t" value="2"/>
67 <output name="fasta" file="mapsembler2/assembly.fa"/>
68 </test>
69 <test>
70 <param name="s" value="mapsembler2/starter.fa" />
71 <param name="r" value="mapsembler2/reads2,mapsembler2/reads1" />
72 <param name="t" value="1"/>
73 <output name="fasta" file="mapsembler2/assembly_2.fa"/>
74 <output name="coherent" file="mapsembler2/coherent.fa"/>
75 <output name="extremities" file="mapsembler2/starter_extremities.fa"/>
76 </test>
77 </tests>
78
79 <help><![CDATA[
80
81 **Description**
82
83 Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
84 Mapsembler2 may be used for (not limited to):
85
86 · Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced.
87
88 · Checks if a gene (input as starter) has an homolog in a set of reads.
89
90 · Checks if a known enzyme is present in a metagenomic NGS read set.
91
92 · Enrich unmappable reads by extending them, possibly making them mappable.
93
94 · Checks what happens at the extremities of a contig.
95
96 · Remove contaminants or symbiont reads from a read set
97
98 -------
99
100 **Web site**
101
102 http://colibread.inria.fr/mapsembler2/
103
104
105 ]]></help>
106 <expand macro="citations">
107 <citation type="doi">10.1186/1471-2105-13-48</citation>
108 </expand>
109
110 </tool>