Mercurial > repos > iuc > colibread_mapsembler2

comparison mapsembler2.xml @ 5:71d60a931e2f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
author iuc
date Thu, 06 May 2021 12:42:40 +0000
parents 9216689fe94b
children e8a8cb93878a
comparison
equal deleted inserted replaced
4:21f081b808ff 5:71d60a931e2f
1 <?xml version='1.0' encoding='utf-8'?> 1 <tool id="mapsembler2" name="Mapsembler2" version="2.2.4+galaxy0" profile="@PROFILE@">
2 <tool profile="16.04" id="mapsembler2" name="Mapsembler2" version="2.2.4">
3 <description>is a targeted assembly software</description> 2 <description>is a targeted assembly software</description>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
7 <requirements> 6 <requirements>
8 <requirement type="package" version="2.2.4">mapsembler2</requirement> 7 <requirement type="package" version="2.2.4">mapsembler2</requirement>
9 </requirements> 8 </requirements>
10 <command><![CDATA[ 9 <command><![CDATA[
11 10 #import re
12 #set $starter_filename = os.path.basename(str($s)) + "." + $s.ext 11 #set $starter_filename = re.sub('[^\w_]', '_', $s.element_identifier) + ".fasta"
13 ln -sf '${s}' '${starter_filename}' && 12 #if $s.ext.endswith('.gz'):
14 13 gunzip -c '${s}' > '${starter_filename}' &&
14 #else:
15 ln -sf '${s}' '${starter_filename}' &&
16 #end if
15 #set $samples = [] 17 #set $samples = []
16 #for $read in $r 18 #for $input in $r
17 #set $filename = os.path.basename(str($read)) + "." + $read.ext 19 #set $base_filename = re.sub('[^\w_]', '_', $input.element_identifier)
18 ln -sf '${read}' '${filename}' && 20 @single_reads@
19 #silent $samples.append($filename) 21 #silent $samples.append($filename)
20 #end for 22 #end for
21
22 run_mapsembler2_pipeline.sh 23 run_mapsembler2_pipeline.sh
23 -s '${starter_filename}' 24 -s '${starter_filename}'
24 -r "${ ' '.join(['%s' % read for read in $samples]) }" 25 -r "${ ' '.join(['%s' % read for read in $samples]) }"
25 -t ${t} 26 -t ${t}
26 -k ${k} 27 -k ${k}
29 -g ${g} 30 -g ${g}
30 -f ${f} 31 -f ${f}
31 -x ${x} 32 -x ${x}
32 -y ${y} 33 -y ${y}
33 ]]></command> 34 ]]></command>
34
35 <inputs> 35 <inputs>
36 <!-- Input data files --> 36 <!-- Input data files -->
37 <param argument="-s" type="data" format="fasta" label="Starters" help="Set of input sequences" /> 37 <param argument="-s" type="data" format="fasta,fasta.gz" label="Starters" help="Set of input sequences" />
38 <param argument="-r" type="data" multiple="true" format="fasta,fastq" label="List of reads" /> 38 <param argument="-r" type="data" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" label="List of reads" />
39 <param argument="-t" type="select" label="Select your output extension type"> 39 <param argument="-t" type="select" label="Select your output extension type">
40 <option value="1">a strict sequence</option> 40 <option value="1">a strict sequence</option>
41 <option value="2">a consensus sequence</option> 41 <option value="2">a consensus sequence</option>
42 </param> 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" /> 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" />
49 <option value="2">Depth</option> 49 <option value="2">Depth</option>
50 </param> 50 </param>
51 <param argument="-x" type="integer" label="Max length of nodes" value="40" help="Set the maximal length of nodes"/> 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"/> 52 <param argument="-y" type="integer" label="Max depth of nodes" value="10000" help="Set the maximal depth of the graph"/>
53 </inputs> 53 </inputs>
54
55 <outputs> 54 <outputs>
56 <data name="fasta" from_work_dir="res_k_*.fasta" format="fasta" label="Assembly with ${tool.name} on $on_string"/> 55 <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"/> 56 <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"/> 57 <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"/> 58 <data name="extremities" from_work_dir="starter_extremities.fa" format="fasta" label="Starter extremities with ${tool.name} on $on_string" hidden="true"/>
60 </outputs> 59 </outputs>
61
62 <tests> 60 <tests>
63 <test> 61 <test>
64 <param name="s" value="mapsembler2/starter.fa" /> 62 <param name="s" value="mapsembler2/starter.fa.gz" ftype="fasta.gz"/>
65 <param name="r" value="mapsembler2/reads1,mapsembler2/reads2" /> 63 <param name="r" value="mapsembler2/reads1.gz,mapsembler2/reads2.gz" ftype="fasta.gz"/>
66 <param name="t" value="2"/> 64 <param name="t" value="2"/>
67 <output name="fasta" file="mapsembler2/assembly.fa"/> 65 <output name="fasta" file="mapsembler2/assembly.fa"/>
68 </test> 66 </test>
69 <test> 67 <test>
70 <param name="s" value="mapsembler2/starter.fa" /> 68 <param name="s" value="mapsembler2/starter.fa.gz" ftype="fasta.gz"/>
71 <param name="r" value="mapsembler2/reads2,mapsembler2/reads1" /> 69 <param name="r" value="mapsembler2/reads2.gz,mapsembler2/reads1.gz" ftype="fasta.gz"/>
72 <param name="t" value="1"/> 70 <param name="t" value="1"/>
73 <output name="fasta" file="mapsembler2/assembly_2.fa"/> 71 <output name="fasta" file="mapsembler2/assembly_2.fa"/>
74 <output name="coherent" file="mapsembler2/coherent.fa"/> 72 <output name="coherent" file="mapsembler2/coherent.fa"/>
75 <output name="extremities" file="mapsembler2/starter_extremities.fa"/> 73 <output name="extremities" file="mapsembler2/starter_extremities.fa"/>
76 </test> 74 </test>
77 </tests> 75 </tests>
78
79 <help><![CDATA[ 76 <help><![CDATA[
80 77
81 **Description** 78 **Description**
82 79
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. 80 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.