Mercurial > repos > iuc > colibread_mapsembler2
comparison mapsembler2.xml @ 5:c5371f68db91 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
author | iuc |
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date | Thu, 06 May 2021 12:46:55 +0000 |
parents | 00fd0b4274fd |
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4:e7c5b81b3c22 | 5:c5371f68db91 |
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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. |