Mercurial > repos > iuc > colibread_mapsembler2

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
author iuc
date Sat, 05 Oct 2024 19:52:52 +0000
parents 71d60a931e2f
children
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1 <tool id="mapsembler2" name="Mapsembler2" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>is a targeted assembly software</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.2.4</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">mapsembler2</requirement>
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9 </requirements>
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10 <command><![CDATA[
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11 #import re
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12 #set $starter_filename = re.sub('[^\w_]', '_', $s.element_identifier) + ".fasta"
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13 #if $s.ext.endswith('.gz'):
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14 gunzip -c '${s}' > '${starter_filename}' &&
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15 #else:
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16 ln -sf '${s}' '${starter_filename}' &&
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17 #end if
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18 #set $samples = []
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19 #for $input in $r
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20 #set $base_filename = re.sub('[^\w_]', '_', $input.element_identifier)
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21 @single_reads@
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22 #silent $samples.append($filename)
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23 #end for
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24 run_mapsembler2_pipeline.sh
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25 -s '${starter_filename}'
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26 -r "${ ' '.join(['%s' % read for read in $samples]) }"
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27 -t ${t}
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28 -k ${k}
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29 -c ${c}
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30 -d ${d}
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31 -g ${g}
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32 -f ${f}
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33 -x ${x}
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34 -y ${y}
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35 ]]></command>
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36 <inputs>
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37 <!-- Input data files -->
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38 <param argument="-s" type="data" format="fasta,fasta.gz" label="Starters" help="Set of input sequences" />
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39 <param argument="-r" type="data" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" label="List of reads" />
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40 <param argument="-t" type="select" label="Select your output extension type">
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41 <option value="1">a strict sequence</option>
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42 <option value="2">a consensus sequence</option>
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43 </param>
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44 <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" />
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45 <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) "/>
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46 <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"/>
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47 <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." />
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48 <param argument="-f" type="select" label="Process of search" help="Set the process of search in the graph" >
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49 <option value="1">Breadth</option>
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50 <option value="2">Depth</option>
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51 </param>
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52 <param argument="-x" type="integer" label="Max length of nodes" value="40" help="Set the maximal length of nodes"/>
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53 <param argument="-y" type="integer" label="Max depth of nodes" value="10000" help="Set the maximal depth of the graph"/>
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54 </inputs>
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55 <outputs>
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56 <data name="fasta" from_work_dir="res_k_*.fasta" format="fasta" label="${tool.name} on ${on_string}: Assembly"/>
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57 <data name="coherent" from_work_dir="res_coherent_*.fasta" format="fasta" label="${tool.name} on ${on_string}: Coherent" hidden="true"/>
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58 <data name="uncoherent" from_work_dir="res_uncoherent_*.fasta" format="fasta" label="${tool.name} on ${on_string}: Uncoherent" hidden="true"/>
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59 <data name="extremities" from_work_dir="starter_extremities.fa" format="fasta" label="${tool.name} on ${on_string}: Starter extremities" hidden="true"/>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="s" value="mapsembler2/starter.fa.gz" ftype="fasta.gz"/>
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64 <param name="r" value="mapsembler2/reads1.gz,mapsembler2/reads2.gz" ftype="fasta.gz"/>
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65 <param name="t" value="2"/>
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66 <output name="fasta" file="mapsembler2/assembly.fa"/>
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67 </test>
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68 <test>
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69 <param name="s" value="mapsembler2/starter.fa.gz" ftype="fasta.gz"/>
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70 <param name="r" value="mapsembler2/reads2.gz,mapsembler2/reads1.gz" ftype="fasta.gz"/>
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71 <param name="t" value="1"/>
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72 <output name="fasta" file="mapsembler2/assembly_2.fa"/>
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73 <output name="coherent" file="mapsembler2/coherent.fa"/>
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74 <output name="extremities" file="mapsembler2/starter_extremities.fa"/>
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78
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79 **Description**
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80
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81 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.
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82 Mapsembler2 may be used for (not limited to):
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83
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84 · Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced.
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85
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86 · Checks if a gene (input as starter) has an homolog in a set of reads.
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87
c90f5219b67a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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88 · Checks if a known enzyme is present in a metagenomic NGS read set.
c90f5219b67a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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89
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90 · Enrich unmappable reads by extending them, possibly making them mappable.
c90f5219b67a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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91
c90f5219b67a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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92 · Checks what happens at the extremities of a contig.
c90f5219b67a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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93
c90f5219b67a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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94 · Remove contaminants or symbiont reads from a read set
c90f5219b67a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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95
c90f5219b67a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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96 -------
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97
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98 **Web site**
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99
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100 http://colibread.inria.fr/mapsembler2/
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101
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102
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103 ]]></help>
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104 <expand macro="citations">
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105 <citation type="doi">10.1186/1471-2105-13-48</citation>
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106 </expand>
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107
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108 </tool>