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annotate maxbin2.xml @ 6:2bc40bfbcfb4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
author iuc
date Mon, 16 Oct 2023 07:46:13 +0000
parents 8a0473eb465e
children 28a0b1446d2b
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6
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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1 <tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy4">
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6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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2 <description>clusters metagenomic contigs into bins</description>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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3 <macros>
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4 <token name="@MAXBIN_VERSION@">2.2.7</token>
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5 <xml name="contig">
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6 <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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7 </xml>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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8 <xml name="input_type">
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9 <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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10 <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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11 <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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12 </param>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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13 </xml>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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14 <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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15 <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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16 <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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17 </xml>
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18 </macros>
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19 <xrefs>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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20 <xref type="bio.tools">maxbin</xref>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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21 </xrefs>
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22 <requirements>
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6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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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
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2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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28 #import re
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29 #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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30 #if $assembly.type == 'individual'
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2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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31 ## uncompress .gz reads files if necessary
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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32 #set $e = $assembly.inputs.reads
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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33 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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34 #if $e.ext.endswith(".gz")
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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35 gunzip -c '$e' > '$identifier' &&
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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36 echo '$identifier' >> reads_list &&
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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37 #else
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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38 ln -s '$e' '$identifier' &&
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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39 echo '$identifier' >> reads_list &&
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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40 #end if
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41 #else
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42 #for $i, $r in enumerate($assembly.inputs.reads)
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43 #if $r
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2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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44 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($r.element_identifier))
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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45 #set $newid = $identifier + '_' + str($i)
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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46 #if $r.ext.endswith(".gz")
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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47 gunzip -c '$r' > '$newid' &&
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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48 echo '$newid' >> reads_list &&
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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49 #else
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50 ln -s '$r' '$newid' &&
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51 echo '$newid' >> reads_list &&
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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52 #end if
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53 #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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54 #end for
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55 #end if
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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56 #else if $assembly.inputs.type == 'abund'
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57 #if $assembly.type == 'individual'
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58 echo '$assembly.inputs.abund' >> abund_list &&
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59 #else
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60 #for $a in $assembly.inputs.abund
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61 #if $a
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62 echo '$a' >> abund_list &&
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63 #end if
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64 #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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65 #end if
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66 #end if
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67
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68 ## in case of reassembly the IBDA out and err is appended
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69 ## to differentiate this a header is added also befor the
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70 ## MaxBin2 outputs
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71 #if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
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72 echo "==== MaxBin2 stdout ====" &&
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73 echo "==== MaxBin2 stderr ====" 1>&2 &&
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74 #end if
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75
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76 run_MaxBin.pl
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77 -contig '$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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78 -out out
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79 #if $assembly.inputs.type == 'reads':
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80 -reads_list reads_list
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81 $assembly.inputs.reassembly
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82 #else if $assembly.inputs.type == 'abund':
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83 -abund_list abund_list
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84 #end if
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85 -min_contig_length $adv.min_contig_length
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86 -max_iteration $adv.max_iteration
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87 -prob_threshold $adv.prob_threshold
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88 $output.plotmarker
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89 -markerset $output.markerset
0
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90 -thread \${GALAXY_SLOTS:-1}
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91
5
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92 && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -
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93
5
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94 ## redirect the idba out and err file content to stdout and err
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95 ## since this is also wanted in case the error case ';' is used here to
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96 ## separate commands
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97 #if $assembly.inputs.type == 'reads' and $assembly.inputs.reassembly != ""
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98 ; echo "==== IDBA stdout ===="
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99 && if [[ -f out.idba.out ]]; then cat out.idba.out; fi
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100 && echo "==== IDBA stderr ====" 1>&2
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101 && if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi
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102 #end if
0
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103 ]]></command>
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104 <inputs>
5
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105 <expand macro="contig"/>
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106 <conditional name="assembly">
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107 <param name="type" type="select" label="Assembly type used to generate contig(s)">
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108 <option value="individual">Assembly of sample(s) one by one (individual assembly)</option>
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109 <option value="coassembly">Assembly of different samples together (co-assembly)</option>
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110 </param>
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111 <when value="individual">
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112 <conditional name="inputs">
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113 <expand macro="input_type"/>
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114 <when value="reads">
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115 <param argument="-reads" type="data" format="fasta,fastq,fastq.gz,fasta.gz" label="Reads file"/>
5
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116 <expand macro="reads_extra_params"/>
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117 </when>
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118 <when value="abund">
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119 <param argument="-abund" type="data" format="tabular" label="Abundance file"/>
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120 </when>
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121 </conditional>
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122 </when>
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123 <when value="coassembly">
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124 <conditional name="inputs">
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125 <expand macro="input_type"/>
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126 <when value="reads">
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127 <param argument="-reads" type="data" multiple="true" format="fasta,fastq" label="Reads file(s)"/>
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128 <expand macro="reads_extra_params"/>
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129 </when>
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130 <when value="abund">
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131 <param argument="-abund" type="data" format="tabular" multiple="true" label="Abundance file(s)"/>
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132 </when>
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133 </conditional>
0
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134 </when>
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135 </conditional>
5
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136 <section name="adv" title="Advanced options">
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137 <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" />
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138 <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" />
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139 <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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140 </section>
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141 <section name="output" title="Outputs">
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142 <param argument="-plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" />
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143 <param name="marker" type="boolean" checked="false" label="Output marker gene presence for bins table" />
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144 <param name="markers" type="boolean" checked="false" label="Output marker genes for each bin as fasta" />
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145 <param name="log" type="boolean" checked="false" label="Output log" />
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146 <param argument="-markerset" type="select" label="Marker gene set">
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147 <option value="107" selected="true">107 marker genes present in >95% of bacteria</option>
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148 <option value="40">40 marker gene sets that are universal among bacteria and archaea</option>
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149 </param>
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150 </section>
0
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151 </inputs>
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152 <outputs>
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153 <!-- default outputs -->
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154 <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
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155 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
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156 </collection>
5
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157 <data name="noclass" format="fasta" label="${tool.name} on ${on_string}: Unclassified sequences" from_work_dir="out.noclass"/>
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158 <data name="toshort" format="fasta" label="${tool.name} on ${on_string}: Too short sequences" from_work_dir="out.tooshort"/>
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159 <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" from_work_dir="out.summary"/>
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160 <!-- optional outputs -->
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161 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="out.log">
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162 <filter>output['log']</filter>
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163 </data>
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164 <data name="marker" format="tabular" label="${tool.name} on ${on_string}: Marker gene presence" from_work_dir="out.marker">
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165 <filter>output['marker']</filter>
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166 </data>
5
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167 <data name="abundout" format="tabular" label="${tool.name} on ${on_string}: Abundances" from_work_dir="out.abund1">
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168 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['output_abundances']</filter>
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169 </data>
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170 <data name="plot" format="pdf" label="${tool.name} on ${on_string}: Marker gene presence plot" from_work_dir="out.marker.pdf">
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171 <filter>output['plotmarker']</filter>
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172 </data>
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173 <collection name="markers" type="list" label="${tool.name} on ${on_string}: Markers prediced for bins">
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174 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" />
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175 <filter>output['markers']</filter>
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176 </collection>
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177 <!-- additional output in case of reassembly -->
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178 <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string}: Reassembly bins">
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179 <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
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180 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
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181 </collection>
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182 <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string}: Reassembly reads">
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183 <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" />
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184 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
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185 </collection>
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186 <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string}: Reassembly unclassified sequences" from_work_dir="out.reassem/out.reads.noclass">
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187 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
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188 </data>
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189 <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string}: Reassembly N50" from_work_dir="out.reassem/N50.txt">
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190 <filter>assembly['inputs']['type']=='reads' and assembly['inputs']['reassembly']</filter>
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191 </data>
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192 </outputs>
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193 <tests>
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194 <!-- test w contigs and reads as input -->
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195 <test expect_num_outputs="4">
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196 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
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197 <conditional name="assembly">
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198 <param name="type" value="individual"/>
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199 <conditional name="inputs">
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200 <param name="type" value="reads"/>
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201 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
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202 <param name="output_abundances" value="false"/>
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203 <param name="reassembly" value=""/>
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204 </conditional>
0
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205 </conditional>
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206 <section name="adv">
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207 <param name="min_contig_length" value="1000"/>
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208 <param name="max_iteration" value="50"/>
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209 <param name="prob_threshold" value="0.5"/>
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210 </section>
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211 <section name="output">
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212 <param name="plotmarker" value=""/>
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213 <param name="marker" value="false"/>
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214 <param name="markers" value="false" />
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215 <param name="log" value="false"/>
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216 <param name="markerset" value="107"/>
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217 </section>
0
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218 <output_collection name="bins" type="list" count="2">
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219 <element name="001" file="1/out.001.fasta" ftype="fasta"/>
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220 <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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221 </output_collection>
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222 <output name="summary" file="1/out.summary" ftype="tabular" />
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223 <output name="noclass" file="1/out.noclass" ftype="fasta" />
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224 <output name="toshort" file="1/out.tooshort" ftype="fasta" />
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225 </test>
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226 <!-- test w co-assembled contigs and multiple reads and optional outputs -->
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227 <test expect_num_outputs="9">
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228 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
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229 <conditional name="assembly">
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230 <param name="type" value="coassembly"/>
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231 <conditional name="inputs">
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232 <param name="type" value="reads"/>
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233 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta,interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
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234 <param name="output_abundances" value="true"/>
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235 <param name="reassembly" value=""/>
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236 </conditional>
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237 </conditional>
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238 <section name="adv">
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239 <param name="min_contig_length" value="1000"/>
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240 <param name="max_iteration" value="50"/>
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241 <param name="prob_threshold" value="0.5"/>
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242 </section>
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243 <section name="output">
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244 <param name="plotmarker" value="true"/>
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245 <param name="marker" value="true"/>
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246 <param name="markers" value="true" />
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247 <param name="log" value="true"/>
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248 <param name="markerset" value="107"/>
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249 </section>
2
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250 <output_collection name="bins" type="list" count="2">
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251 <element name="001" file="1/out.001.fasta" ftype="fasta"/>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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252 <element name="002" file="1/out.002.fasta" ftype="fasta"/>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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253 </output_collection>
5
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254 <output name="summary" ftype="tabular">
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255 <assert_contents>
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256 <has_text text="Completeness"/>
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257 <has_text text="out.001.fasta"/>
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258 </assert_contents>
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259 </output>
2
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260 <output name="noclass" file="1/out.noclass" ftype="fasta" />
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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261 <output name="toshort" file="1/out.tooshort" ftype="fasta" />
5
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262 <output name="log" ftype="txt" >
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263 <assert_contents>
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264 <has_text text="Input contig"/>
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265 <has_text text="Elapsed time"/>
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266 <has_text text="Yielded 2 bins for contig (scaffold) file"/>
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267 </assert_contents>
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268 </output>
0
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269 <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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270 <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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271 <output name="plot" file="1/out.marker.pdf" ftype="pdf" compare="sim_size" />
0
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272 <output_collection name="markers" type="list" count="1">
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273 <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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274 </output_collection>
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275 </test>
2
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276 <!--test w contigs and abundances as input + advanced options -->
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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277 <test expect_num_outputs="5">
0
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278 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
5
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279 <conditional name="assembly">
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280 <param name="type" value="individual"/>
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281 <conditional name="inputs">
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282 <param name="type" value="abund"/>
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283 <param name="abund" value="abundances.tsv" ftype="tabular"/>
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284 </conditional>
0
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285 </conditional>
5
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286 <section name="adv">
0
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287 <param name="min_contig_length" value="500"/>
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288 <param name="max_iteration" value="10"/>
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289 <param name="prob_threshold" value="0.95"/>
5
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290 </section>
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291 <section name="output">
0
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292 <param name="plotmarker" value="-plotmarker"/>
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293 <param name="marker" value="false"/>
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294 <param name="markers" value="false" />
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295 <param name="log" value="false"/>
0
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296 <param name="markerset" value="107"/>
5
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297 </section>
0
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298 <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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299 <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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300 <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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301 </output_collection>
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302 <output name="summary" file="2/out.summary" ftype="tabular" />
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303 <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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304 <output name="toshort" file="2/out.tooshort" ftype="fasta" />
2
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305 <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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306 </test>
2
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307 <!-- 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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308 <test expect_num_outputs="8">
0
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309 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
5
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310 <conditional name="assembly">
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311 <param name="type" value="individual"/>
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312 <conditional name="inputs">
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313 <param name="type" value="reads"/>
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314 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
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315 <param name="output_abundances" value="false"/>
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316 <param name="reassembly" value="-reassembly"/>
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317 </conditional>
0
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318 </conditional>
5
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319 <section name="adv">
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320 <param name="min_contig_length" value="1000"/>
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321 <param name="max_iteration" value="50"/>
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322 <param name="prob_threshold" value="0.5"/>
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323 </section>
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324 <section name="output">
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325 <param name="plotmarker" value=""/>
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326 <param name="marker" value="false"/>
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327 <param name="markers" value="false" />
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328 <param name="log" value="false"/>
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329 <param name="markerset" value="107"/>
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330 </section>
0
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331 <output_collection name="bins" type="list" count="2">
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332 <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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333 <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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334 </output_collection>
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335 <output name="summary" file="3/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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336 <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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337 <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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338 <output_collection name="reassembly_bins" type="list" count="2">
5
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339 <element name="001" ftype="fasta">
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340 <assert_contents>
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341 <has_text text=">scaffold_0"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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342 <has_text text=">scaffold_523"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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343 </assert_contents>
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344 </element>
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345 <element name="002" ftype="fasta">
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346 <assert_contents>
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iuc
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347 <has_text text=">scaffold_0"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
iuc
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348 <has_text text=">scaffold_523"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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349 </assert_contents>
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350 </element>
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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351 </output_collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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352 <output_collection name="reassembly_reads" 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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353 <element name="001" file="3/out.reassem/out.reads.001" 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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354 <element name="002" file="3/out.reassem/out.reads.002" 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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355 </output_collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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356 <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />
5
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357 <output name="reassembly_n50" ftype="txt">
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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358 <assert_contents>
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iuc
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359 <has_text text="N50 before reassem"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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360 <has_text text="out.002.fasta"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
iuc
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361 <has_text text="2878"/>
8a0473eb465e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26
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362 </assert_contents>
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363 </output>
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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364 </test>
6
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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365 <!-- test w contigs and reads in fastqsanger format as input -->
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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366 <test expect_num_outputs="4">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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367 <param name="contig" value="test4_contigs.fasta" ftype="fasta" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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368 <conditional name="assembly">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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369 <param name="type" value="individual"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
370 <conditional name="inputs">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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371 <param name="type" value="reads"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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372 <param name="reads" value="test4_reads.fastqsanger" ftype="fastqsanger"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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373 <param name="output_abundances" value="false"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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374 <param name="reassembly" value=""/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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375 </conditional>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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376 </conditional>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
377 <section name="adv">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
378 <param name="min_contig_length" value="1000"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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379 <param name="max_iteration" value="50"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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diff changeset
380 <param name="prob_threshold" value="0.5"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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381 </section>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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diff changeset
382 <section name="output">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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diff changeset
383 <param name="plotmarker" value=""/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents: 5
diff changeset
384 <param name="marker" value="false"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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diff changeset
385 <param name="markers" value="false" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
386 <param name="log" value="false"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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387 <param name="markerset" value="107"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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388 </section>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
389 <output_collection name="bins" type="list" count="2">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
390 <element name="001" file="4/out.001.fasta" ftype="fasta"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
391 <element name="002" file="4/out.002.fasta" ftype="fasta"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
392 </output_collection>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
393 <output name="summary" file="4/out.summary" ftype="tabular" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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394 <output name="noclass" file="4/out.noclass" ftype="fasta" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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395 <output name="toshort" file="4/out.tooshort" ftype="fasta" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
396 </test>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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397 <!-- test w contigs and reads in fastqsanger.gz format as input -->
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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398 <test expect_num_outputs="4">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
399 <param name="contig" value="test4_contigs.fasta" ftype="fasta" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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diff changeset
400 <conditional name="assembly">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
parents: 5
diff changeset
401 <param name="type" value="individual"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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diff changeset
402 <conditional name="inputs">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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diff changeset
403 <param name="type" value="reads"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
404 <param name="reads" value="test4_reads.fastqsanger.gz" ftype="fastqsanger.gz"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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diff changeset
405 <param name="output_abundances" value="false"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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406 <param name="reassembly" value=""/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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407 </conditional>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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408 </conditional>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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diff changeset
409 <section name="adv">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
410 <param name="min_contig_length" value="1000"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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411 <param name="max_iteration" value="50"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
412 <param name="prob_threshold" value="0.5"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
413 </section>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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diff changeset
414 <section name="output">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
iuc
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diff changeset
415 <param name="plotmarker" value=""/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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416 <param name="marker" value="false"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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417 <param name="markers" value="false" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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418 <param name="log" value="false"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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419 <param name="markerset" value="107"/>
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420 </section>
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421 <output_collection name="bins" type="list" count="2">
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422 <element name="001" file="4/out.001.fasta" ftype="fasta"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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423 <element name="002" file="4/out.002.fasta" ftype="fasta"/>
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424 </output_collection>
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425 <output name="summary" file="4/out.summary" ftype="tabular" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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426 <output name="noclass" file="4/out.noclass" ftype="fasta" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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427 <output name="toshort" file="4/out.tooshort" ftype="fasta" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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428 </test>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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429 <!-- test w co-assembled contigs and multiple reads as .gz and optional outputs -->
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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430 <test expect_num_outputs="9">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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431 <param name="contig" value="test4_contigs.fasta" ftype="fasta" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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432 <conditional name="assembly">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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433 <param name="type" value="coassembly"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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434 <conditional name="inputs">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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435 <param name="type" value="reads"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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436 <param name="reads" value="test4_reads.fastqsanger.gz,test4_reads.fastqsanger.gz" ftype="fasta"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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437 <param name="output_abundances" value="true"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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438 <param name="reassembly" value=""/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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439 </conditional>
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440 </conditional>
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441 <section name="adv">
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442 <param name="min_contig_length" value="1000"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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443 <param name="max_iteration" value="50"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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444 <param name="prob_threshold" value="0.5"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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445 </section>
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446 <section name="output">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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447 <param name="plotmarker" value="true"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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448 <param name="marker" value="true"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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449 <param name="markers" value="true" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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450 <param name="log" value="true"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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451 <param name="markerset" value="107"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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452 </section>
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453 <output_collection name="bins" type="list" count="2">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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454 <element name="001" file="4/out.001.fasta" ftype="fasta"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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455 <element name="002" file="4/out.002.fasta" ftype="fasta"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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456 </output_collection>
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457 <output name="summary" ftype="tabular">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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458 <assert_contents>
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459 <has_text text="Completeness"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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460 <has_text text="out.001.fasta"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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461 </assert_contents>
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462 </output>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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463 <output name="noclass" file="4/out.noclass" ftype="fasta" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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464 <output name="toshort" file="4/out.tooshort" ftype="fasta" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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465 <output name="log" ftype="txt" >
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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466 <assert_contents>
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467 <has_text text="Input contig"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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468 <has_text text="Elapsed time"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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469 <has_text text="Yielded 2 bins for contig (scaffold) file"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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470 </assert_contents>
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471 </output>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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472 <output name="abundout" file="4/out.abund1" ftype="tabular" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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473 <output name="marker" file="4/out.marker" ftype="tabular" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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474 <output name="plot" file="4/out.marker.pdf" ftype="pdf" compare="sim_size" />
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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475 <output_collection name="markers" type="list" count="2">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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476 <element name="001" ftype="fasta">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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477 <assert_contents>
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478 <has_text text=">out.001.Methyltransf_5"/>
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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479 </assert_contents>
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480 </element>
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481 <element name="002" ftype="fasta">
2bc40bfbcfb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78
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482 <assert_contents>
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483 <has_text text=">out.002.Methyltransf_5"/>
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484 </assert_contents>
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485 </element>
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486 </output_collection>
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487 </test>
0
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488 </tests>
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489 <help><![CDATA[
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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490 MaxBin is a software that clusters metagenomic contigs into different bins,
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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491 each consists (hopefully) of contigs from one species. MaxBin uses the
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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492 nucleotide composition information and contig abundance information to do
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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493 achieve binning through an Expectation-Maximization algorithm.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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494
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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495 **Input**:
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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496
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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497 MaxBin need the contigs and contig abundance information. The contig abundance
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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498 information can be provided in two ways: the user can choose to provide
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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499
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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500 - the abundance file or
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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501 - the sequencing reads in fasta format (and MaxBin will use Bowtie2 to map the
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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502 sequencing reads against the contigs and generate the abundance information)
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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503
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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504 The abundance information can be provided as tabular file:
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505
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506 For example, assume I have three contigs named A0001, A0002, and A0003, then my abundance file will look like
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507
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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508 A0001 30.89
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509 A0002 20.02
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510 A0003 78.93
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511
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512 Reads/Abundundance files can be given in multiple files.
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513
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514 By default MaxBin will look for 107 marker genes present in >95% of bacteria.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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515 Alternatively you can also choose 40 marker gene sets that are universal among
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516 bacteria and archaea (Wu et al., PLoS ONE 2013). This option may be better
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517 suited for environment dominated by archaea; however it tend to split genomes
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518 into more bins. You can choose between different marker gene sets and see which
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519 one works better.
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520
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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521 **Outputs**
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522
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523 - bins: binned sequences
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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524 - summary: a summary file describing which contigs are being classified into which bin.
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525 - log: a log file recording the core steps of MaxBin algorithm
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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526 - abundances (only if reads are used as input): a summary file describing which contigs are being classified into which bin
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527 - 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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528 - 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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529 - unclassified sequences: this file stores all sequences that pass the minimum length threshold but are not classified successfully.
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530 - to short sequences: this file stores all sequences that do not meet the minimum length threshold.
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531 - markers prediced for bins: these data sets store all markers predicted from the individual bins.
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532
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533 **Reassembly**
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534
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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535 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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536
2
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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537
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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538 ** More information **
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539
4
4ef88f9a195d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 0711faee9590029e6cf99c263ed97c0bb756d9a4"
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540 https://web.archive.org/web/20190417100740/https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html
2
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541
0
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542 ]]></help>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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543 <citations>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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544 <citation type="doi">10.1093/bioinformatics/btv638</citation>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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545 </citations>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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546 </tool>