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annotate maxbin2.xml @ 5:8a0473eb465e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
author iuc
date Fri, 17 Jun 2022 17:27:40 +0000
parents 4ef88f9a195d
children 2bc40bfbcfb4
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8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
iuc
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1 <tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy3">
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2 <description>clusters metagenomic contigs into bins</description>
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3 <xrefs>
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4 <xref type="bio.tools">masigpro</xref>
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5 </xrefs>
2
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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6 <macros>
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7 <token name="@MAXBIN_VERSION@">2.2.7</token>
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8 <xml name="contig">
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9 <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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10 </xml>
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11 <xml name="input_type">
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12 <param name="type" type="select" label="Input type">
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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13 <option value="reads" selected="true">Sequencing Reads</option>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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14 <option value="abund">Abundances</option>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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15 </param>
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16 </xml>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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17 <xml name="reads_extra_params">
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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18 <param name="output_abundances" type="boolean" checked="false" label="Output abundances" help="" />
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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19 <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="Reassembly" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." />
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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20 </xml>
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21 </macros>
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22 <requirements>
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23 <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement>
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35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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24 </requirements>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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25 <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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26 <command detect_errors="exit_code"><![CDATA[
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27 ## generate read or abundance files
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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28 #if $assembly.inputs.type == 'reads'
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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29 #if $assembly.type == 'individual'
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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30 echo '$assembly.inputs.reads' >> reads_list &&
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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31 #else
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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32 #for $r in $assembly.inputs.reads
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35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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33 #if $r
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34 echo '$r' >> reads_list &&
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35 #end if
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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36 #end for
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8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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37 #end if
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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38 #else if $assembly.inputs.type == 'abund'
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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39 #if $assembly.type == 'individual'
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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40 echo '$assembly.inputs.abund' >> abund_list &&
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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41 #else
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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42 #for $a in $assembly.inputs.abund
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43 #if $a
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44 echo '$a' >> abund_list &&
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35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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45 #end if
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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46 #end for
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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47 #end if
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8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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48 #end if
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49
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50 ## in case of reassembly the IBDA out and err is appended
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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51 ## to differentiate this a header is added also befor the
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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52 ## MaxBin2 outputs
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53 #if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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54 echo "==== MaxBin2 stdout ====" &&
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55 echo "==== MaxBin2 stderr ====" 1>&2 &&
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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56 #end if
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57
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58 run_MaxBin.pl
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59 -contig '$contig'
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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60 -out out
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61 #if $assembly.inputs.type == 'reads':
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62 -reads_list reads_list
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63 $assembly.inputs.reassembly
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64 #else if $assembly.inputs.type == 'abund':
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65 -abund_list abund_list
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66 #end if
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67 -min_contig_length $adv.min_contig_length
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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68 -max_iteration $adv.max_iteration
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69 -prob_threshold $adv.prob_threshold
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70 $output.plotmarker
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71 -markerset $output.markerset
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72 -thread \${GALAXY_SLOTS:-1}
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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73
5
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74 && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -
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75
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76 ## redirect the idba out and err file content to stdout and err
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77 ## since this is also wanted in case the error case ';' is used here to
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78 ## separate commands
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79 #if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
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80 ; echo "==== IDBA stdout ===="
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81 && if [[ -f out.idba.out ]]; then cat out.idba.out; fi
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82 && echo "==== IDBA stderr ====" 1>&2
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83 && if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi
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84 #end if
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35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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85 ]]></command>
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86 <inputs>
5
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87 <expand macro="contig"/>
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88 <conditional name="assembly">
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89 <param name="type" type="select" label="Assembly type used to generate contig(s)">
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90 <option value="individual">Assembly of sample(s) one by one (individual assembly)</option>
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91 <option value="coassembly">Assembly of different samples together (co-assembly)</option>
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92 </param>
5
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93 <when value="individual">
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94 <conditional name="inputs">
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95 <expand macro="input_type"/>
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96 <when value="reads">
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97 <param argument="-reads" type="data" format="fasta,fastq" label="Reads file"/>
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98 <expand macro="reads_extra_params"/>
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99 </when>
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100 <when value="abund">
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101 <param argument="-abund" type="data" format="tabular" label="Abundance file"/>
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102 </when>
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103 </conditional>
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104 </when>
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105 <when value="coassembly">
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106 <conditional name="inputs">
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107 <expand macro="input_type"/>
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108 <when value="reads">
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109 <param argument="-reads" type="data" multiple="true" format="fasta,fastq" label="Reads file(s)"/>
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110 <expand macro="reads_extra_params"/>
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111 </when>
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112 <when value="abund">
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113 <param argument="-abund" type="data" format="tabular" multiple="true" label="Abundance file(s)"/>
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114 </when>
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115 </conditional>
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116 </when>
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117 </conditional>
5
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118 <section name="adv" title="Advanced options">
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119 <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" />
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120 <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" />
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121 <param argument="-prob_threshold" type="float" min="0" max="1.0" value="0.5" label="Probability threshold for EM final classification" />
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122 </section>
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123 <section name="output" title="Outputs">
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124 <param argument="-plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" />
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125 <param name="marker" type="boolean" checked="false" label="Output marker gene presence for bins table" />
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126 <param name="markers" type="boolean" checked="false" label="Output marker genes for each bin as fasta" />
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127 <param name="log" type="boolean" checked="false" label="Output log" />
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128 <param argument="-markerset" type="select" label="Marker gene set">
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129 <option value="107" selected="true">107 marker genes present in >95% of bacteria</option>
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130 <option value="40">40 marker gene sets that are universal among bacteria and archaea</option>
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131 </param>
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132 </section>
0
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133 </inputs>
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134 <outputs>
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135 <!-- default outputs -->
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136 <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
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137 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
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138 </collection>
5
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139 <data name="noclass" format="fasta" label="${tool.name} on ${on_string}: Unclassified sequences" from_work_dir="out.noclass"/>
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140 <data name="toshort" format="fasta" label="${tool.name} on ${on_string}: Too short sequences" from_work_dir="out.tooshort"/>
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141 <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" from_work_dir="out.summary"/>
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142 <!-- optional outputs -->
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143 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="out.log">
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144 <filter>output['log']</filter>
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145 </data>
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146 <data name="marker" format="tabular" label="${tool.name} on ${on_string}: Marker gene presence" from_work_dir="out.marker">
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147 <filter>output['marker']</filter>
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148 </data>
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149 <data name="abundout" format="tabular" label="${tool.name} on ${on_string}: Abundances" from_work_dir="out.abund1">
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150 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['output_abundances']</filter>
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151 </data>
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152 <data name="plot" format="pdf" label="${tool.name} on ${on_string}: Marker gene presence plot" from_work_dir="out.marker.pdf">
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153 <filter>output['plotmarker']</filter>
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154 </data>
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155 <collection name="markers" type="list" label="${tool.name} on ${on_string}: Markers prediced for bins">
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156 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" />
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157 <filter>output['markers']</filter>
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158 </collection>
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159 <!-- additional output in case of reassembly -->
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160 <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string}: Reassembly bins">
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161 <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
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162 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
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163 </collection>
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164 <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string}: Reassembly reads">
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165 <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" />
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166 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
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167 </collection>
5
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168 <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string}: Reassembly unclassified sequences" from_work_dir="out.reassem/out.reads.noclass">
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169 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
0
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170 </data>
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171 <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string}: Reassembly N50" from_work_dir="out.reassem/N50.txt">
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172 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
0
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173 </data>
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174 </outputs>
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175 <tests>
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176 <!-- test w contigs and reads as input -->
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177 <test expect_num_outputs="4">
0
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178 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
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179 <conditional name="assembly">
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180 <param name="type" value="individual"/>
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181 <conditional name="inputs">
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182 <param name="type" value="reads"/>
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183 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
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184 <param name="output_abundances" value="false"/>
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185 <param name="reassembly" value=""/>
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186 </conditional>
0
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187 </conditional>
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188 <section name="adv">
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189 <param name="min_contig_length" value="1000"/>
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190 <param name="max_iteration" value="50"/>
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191 <param name="prob_threshold" value="0.5"/>
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192 </section>
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193 <section name="output">
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194 <param name="plotmarker" value=""/>
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195 <param name="marker" value="false"/>
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196 <param name="markers" value="false" />
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197 <param name="log" value="false"/>
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198 <param name="markerset" value="107"/>
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199 </section>
0
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200 <output_collection name="bins" type="list" count="2">
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201 <element name="001" file="1/out.001.fasta" ftype="fasta"/>
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202 <element name="002" file="1/out.002.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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203 </output_collection>
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204 <output name="summary" file="1/out.summary" ftype="tabular" />
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205 <output name="noclass" file="1/out.noclass" ftype="fasta" />
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206 <output name="toshort" file="1/out.tooshort" ftype="fasta" />
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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207 </test>
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208 <!-- test w co-assembled contigs and multiple reads and optional outputs -->
2
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209 <test expect_num_outputs="9">
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210 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
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211 <conditional name="assembly">
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212 <param name="type" value="coassembly"/>
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213 <conditional name="inputs">
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214 <param name="type" value="reads"/>
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215 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta,interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
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216 <param name="output_abundances" value="true"/>
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217 <param name="reassembly" value=""/>
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218 </conditional>
2
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219 </conditional>
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220 <section name="adv">
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221 <param name="min_contig_length" value="1000"/>
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222 <param name="max_iteration" value="50"/>
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223 <param name="prob_threshold" value="0.5"/>
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224 </section>
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225 <section name="output">
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226 <param name="plotmarker" value="true"/>
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227 <param name="marker" value="true"/>
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228 <param name="markers" value="true" />
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229 <param name="log" value="true"/>
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230 <param name="markerset" value="107"/>
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231 </section>
2
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232 <output_collection name="bins" type="list" count="2">
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233 <element name="001" file="1/out.001.fasta" ftype="fasta"/>
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234 <element name="002" file="1/out.002.fasta" ftype="fasta"/>
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235 </output_collection>
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236 <output name="summary" ftype="tabular">
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237 <assert_contents>
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238 <has_text text="Completeness"/>
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239 <has_text text="out.001.fasta"/>
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240 </assert_contents>
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241 </output>
2
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242 <output name="noclass" file="1/out.noclass" ftype="fasta" />
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243 <output name="toshort" file="1/out.tooshort" ftype="fasta" />
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244 <output name="log" ftype="txt" >
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245 <assert_contents>
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246 <has_text text="Input contig"/>
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247 <has_text text="Elapsed time"/>
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248 <has_text text="Yielded 2 bins for contig (scaffold) file"/>
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249 </assert_contents>
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250 </output>
0
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251 <output name="abundout" file="1/out.abund1" ftype="tabular" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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252 <output name="marker" file="1/out.marker" ftype="tabular" />
2
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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253 <output name="plot" file="1/out.marker.pdf" ftype="pdf" compare="sim_size" />
0
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254 <output_collection name="markers" type="list" count="1">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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255 <element name="001" file="1/out.001.marker.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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256 </output_collection>
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257 </test>
2
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258 <!--test w contigs and abundances as input + advanced options -->
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259 <test expect_num_outputs="5">
0
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260 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
5
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261 <conditional name="assembly">
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262 <param name="type" value="individual"/>
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263 <conditional name="inputs">
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264 <param name="type" value="abund"/>
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265 <param name="abund" value="abundances.tsv" ftype="tabular"/>
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266 </conditional>
0
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267 </conditional>
5
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268 <section name="adv">
0
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269 <param name="min_contig_length" value="500"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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270 <param name="max_iteration" value="10"/>
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271 <param name="prob_threshold" value="0.95"/>
5
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272 </section>
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273 <section name="output">
0
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274 <param name="plotmarker" value="-plotmarker"/>
5
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275 <param name="marker" value="false"/>
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276 <param name="markers" value="false" />
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277 <param name="log" value="false"/>
0
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278 <param name="markerset" value="107"/>
5
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279 </section>
0
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280 <output_collection name="bins" type="list" count="2">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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281 <element name="001" file="2/out.001.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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282 <element name="002" file="2/out.002.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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283 </output_collection>
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284 <output name="summary" file="2/out.summary" ftype="tabular" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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285 <output name="noclass" file="2/out.noclass" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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286 <output name="toshort" file="2/out.tooshort" ftype="fasta" />
2
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
iuc
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287 <output name="plot" file="2/out.marker.pdf" ftype="pdf" compare="sim_size" />
0
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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288 </test>
2
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iuc
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289 <!-- test w contigs and reads as input + reassembly-->
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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290 <test expect_num_outputs="8">
0
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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291 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
5
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292 <conditional name="assembly">
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293 <param name="type" value="individual"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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294 <conditional name="inputs">
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295 <param name="type" value="reads"/>
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296 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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297 <param name="output_abundances" value="false"/>
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298 <param name="reassembly" value="-reassembly"/>
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299 </conditional>
0
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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300 </conditional>
5
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301 <section name="adv">
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302 <param name="min_contig_length" value="1000"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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303 <param name="max_iteration" value="50"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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304 <param name="prob_threshold" value="0.5"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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305 </section>
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306 <section name="output">
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307 <param name="plotmarker" value=""/>
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308 <param name="marker" value="false"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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309 <param name="markers" value="false" />
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310 <param name="log" value="false"/>
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311 <param name="markerset" value="107"/>
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312 </section>
0
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313 <output_collection name="bins" type="list" count="2">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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314 <element name="001" file="3/out.001.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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315 <element name="002" file="3/out.002.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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316 </output_collection>
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317 <output name="summary" file="3/out.summary" ftype="tabular" />
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318 <output name="noclass" file="3/out.noclass" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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319 <output name="toshort" file="3/out.tooshort" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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320 <output_collection name="reassembly_bins" type="list" count="2">
5
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321 <element name="001" ftype="fasta">
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322 <assert_contents>
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323 <has_text text=">scaffold_0"/>
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324 <has_text text=">scaffold_523"/>
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325 </assert_contents>
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326 </element>
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327 <element name="002" ftype="fasta">
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328 <assert_contents>
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329 <has_text text=">scaffold_0"/>
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330 <has_text text=">scaffold_523"/>
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331 </assert_contents>
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332 </element>
0
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333 </output_collection>
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334 <output_collection name="reassembly_reads" type="list" count="2">
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335 <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/>
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336 <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/>
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337 </output_collection>
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338 <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />
5
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339 <output name="reassembly_n50" ftype="txt">
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340 <assert_contents>
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341 <has_text text="N50 before reassem"/>
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342 <has_text text="out.002.fasta"/>
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343 <has_text text="2878"/>
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344 </assert_contents>
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345 </output>
0
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346 </test>
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347 </tests>
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348 <help><![CDATA[
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349 MaxBin is a software that clusters metagenomic contigs into different bins,
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350 each consists (hopefully) of contigs from one species. MaxBin uses the
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351 nucleotide composition information and contig abundance information to do
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352 achieve binning through an Expectation-Maximization algorithm.
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353
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354 **Input**:
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355
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356 MaxBin need the contigs and contig abundance information. The contig abundance
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357 information can be provided in two ways: the user can choose to provide
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358
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359 - the abundance file or
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360 - the sequencing reads in fasta format (and MaxBin will use Bowtie2 to map the
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361 sequencing reads against the contigs and generate the abundance information)
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362
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363 The abundance information can be provided as tabular file:
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364
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365 For example, assume I have three contigs named A0001, A0002, and A0003, then my abundance file will look like
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366
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367 A0001 30.89
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368 A0002 20.02
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369 A0003 78.93
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370
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371 Reads/Abundundance files can be given in multiple files.
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372
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373 By default MaxBin will look for 107 marker genes present in >95% of bacteria.
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374 Alternatively you can also choose 40 marker gene sets that are universal among
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375 bacteria and archaea (Wu et al., PLoS ONE 2013). This option may be better
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376 suited for environment dominated by archaea; however it tend to split genomes
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377 into more bins. You can choose between different marker gene sets and see which
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378 one works better.
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379
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380 **Outputs**
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381
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382 - bins: binned sequences
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383 - summary: a summary file describing which contigs are being classified into which bin.
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384 - log: a log file recording the core steps of MaxBin algorithm
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385 - abundances (only if reads are used as input): a summary file describing which contigs are being classified into which bin
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386 - marker: marker gene presence numbers for each bin. This table is ready to be plotted by R or other 3rd-party software.
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387 - marker plot (anly present if selected in the advanced options): visualization of the marker gene presence numbers using R. Will only appear if -plotmarker is specified.
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388 - unclassified sequences: this file stores all sequences that pass the minimum length threshold but are not classified successfully.
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389 - to short sequences: this file stores all sequences that do not meet the minimum length threshold.
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390 - markers prediced for bins: these data sets store all markers predicted from the individual bins.
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391
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392 **Reassembly**
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393
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394 This is an experimental feature of MaxBin. It calls for each read bin IDBA_UD with the pre_correction parameter. Of course this IDBA_UD call can be done also with the corresponding Galaxy tool
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395
2
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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396
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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397 ** More information **
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398
4
4ef88f9a195d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 0711faee9590029e6cf99c263ed97c0bb756d9a4"
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399 https://web.archive.org/web/20190417100740/https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html
2
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400
0
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401 ]]></help>
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402 <citations>
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403 <citation type="doi">10.1093/bioinformatics/btv638</citation>
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404 </citations>
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405 </tool>