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annotate maxbin2.xml @ 4:4ef88f9a195d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 0711faee9590029e6cf99c263ed97c0bb756d9a4"
author iuc
date Wed, 18 Nov 2020 10:42:37 +0000
parents cfd50144a871
children 8a0473eb465e
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cfd50144a871 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit fe30b00aa09587876f4c8be2a1494ca5ef6b8bac"
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1 <tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy2">
2
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>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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5 </macros>
0
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6 <requirements>
2
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7 <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement>
0
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8 </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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9 <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ## generate read or abundance files
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12 #if $intype_cond.intype_select == 'rds':
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13 #for $r in $intype_cond.reads
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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14 #if $r
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15 echo '$r' >> reads_list &&
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16 #end if
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17 #end for
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18 #else if $intype_cond.intype_select == 'abdc':
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19 #for $a in $intype_cond.abund
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20 #if $a
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21 echo '$a' >> abund_list &&
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22 #end if
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23 #end for
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24 #end if
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25
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 ## in case of reassembly the IBDA out and err is appended
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27 ## to differentiate this a header is added also befor 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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28 ## MaxBin2 outputs
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29 #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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30 echo "==== MaxBin2 stdout ====" &&
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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31 echo "==== MaxBin2 stderr ====" 1>&2 &&
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32 #end if
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33
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34 run_MaxBin.pl
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35 -contig '$contig'
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36 -out out
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37 #if $intype_cond.intype_select == 'rds':
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38 -reads_list reads_list
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39 $intype_cond.reassembly
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40 #else if $intype_cond.intype_select == 'abdc':
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41 -abund_list abund_list
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42 #end if
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43 #if $adv_cond.adv_select == 'yes':
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44 -min_contig_length $adv_cond.min_contig_length
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45 -max_iteration $adv_cond.max_iteration
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46 -prob_threshold $adv_cond.prob_threshold
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47 $adv_cond.plotmarker
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48 -markerset $adv_cond.markerset
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49 #end if
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50 -thread \${GALAXY_SLOTS:-1}
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51
3
cfd50144a871 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit fe30b00aa09587876f4c8be2a1494ca5ef6b8bac"
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52 && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -
0
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53
3
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54 ## redirect the idba out and err file content to stdout and err
cfd50144a871 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit fe30b00aa09587876f4c8be2a1494ca5ef6b8bac"
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55 ## since this is also wanted in case the error case ';' is used here to
cfd50144a871 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit fe30b00aa09587876f4c8be2a1494ca5ef6b8bac"
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56 ## separate commands
0
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57 #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
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58 ; echo "==== IDBA stdout ===="
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59 && if [[ -f out.idba.out ]]; then cat out.idba.out; fi
0
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60 && echo "==== IDBA stderr ====" 1>&2
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61 && if [[ -f out.idba.err ]]; then cat out.idba.err 1>&2; fi
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62 #end if
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63 ]]></command>
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64 <inputs>
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65 <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
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66 <conditional name="intype_cond">
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67 <param name="intype_select" type="select" label="Input type">
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68 <option value="rds" selected="true">Sequencing Reads</option>
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69 <option value="abdc">Abundances</option>
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70 </param>
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71 <when value="rds">
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72 <param name="reads" type="data" format="fasta,fastq" multiple="true" label="Reads file(s)" help="(-read/-read2/...)"/>
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73 <param name="output_abundances" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output abundances" help="" />
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74 <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." />
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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75 </when>
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76 <when value="abdc">
2
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77 <param name="abund" type="data" format="tabular" multiple="true" label="Abundance file(s)" help="(-abund/-abund2/...)" />
0
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78 </when>
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79 </conditional>
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80 <conditional name="adv_cond">
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81 <param name="adv_select" type="select" label="Advanced options">
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82 <option value="yes">Yes</option>
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83 <option value="no" selected="true">No</option>
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84 </param>
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85 <when value="no"/>
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86 <when value="yes">
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87 <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" />
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88 <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" />
2
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89 <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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90 <param argument="-plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" />
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91 <param name="output_marker" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output marker gene presence for bins table" />
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92 <param name="output_markers" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output marker genes for each bin as fasta" />
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93 <param name="output_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log" />
0
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94 <param argument="-markerset" type="select" label="Marker gene set">
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95 <option value="107" selected="true">107 marker genes present in >95% of bacteria</option>
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96 <option value="40">40 marker gene sets that are universal among bacteria and archaea</option>
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97 </param>
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98 </when>
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99 </conditional>
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100 </inputs>
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101 <outputs>
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102 <!-- default outputs -->
0
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103 <collection name="bins" type="list" label="${tool.name} on ${on_string} (bins)">
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104 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
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105 </collection>
2
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106 <data name="noclass" format="fasta" label="${tool.name} on ${on_string} (unclassified sequences)" from_work_dir="out.noclass"/>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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107 <data name="toshort" format="fasta" label="${tool.name} on ${on_string} (to short sequences)" from_work_dir="out.tooshort"/>
0
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108 <data name="summary" format="tabular" label="${tool.name} on ${on_string} (summary)" from_work_dir="out.summary"/>
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109
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110 <!-- optional outputs -->
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111 <data name="log" format="txt" label="${tool.name} on ${on_string} (log)" from_work_dir="out.log">
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112 <filter>adv_cond['adv_select']=='yes' and adv_cond['output_log']</filter>
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113 </data>
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114 <data name="marker" format="tabular" label="${tool.name} on ${on_string} (marker gene presence)" from_work_dir="out.marker">
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115 <filter>adv_cond['adv_select']=='yes' and adv_cond['output_marker']</filter>
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116 </data>
0
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117 <data name="abundout" format="tabular" label="${tool.name} on ${on_string} (abundances)" from_work_dir="out.abund1">
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118 <filter>intype_cond['intype_select']=='rds' and intype_cond['output_abundances']</filter>
0
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119 </data>
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120 <data name="plot" format="pdf" label="${tool.name} on ${on_string} (marker gene presence plot)" from_work_dir="out.marker.pdf">
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121 <filter>adv_cond['adv_select']=='yes' and adv_cond['plotmarker']</filter>
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122 </data>
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123 <collection name="markers" type="list" label="${tool.name} on ${on_string} (markers prediced for bins)">
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124 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" />
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125 <filter>adv_cond['adv_select']=='yes' and adv_cond['output_markers']</filter>
0
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126 </collection>
2
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127
0
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128 <!-- additional output in case of reassembly -->
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129 <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string} (reassembly bins)">
0
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130 <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
1
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131 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
0
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132 </collection>
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133 <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string} (reassembly reads)">
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134 <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" />
1
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135 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
0
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136 </collection>
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137 <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string} (reassembly unclassified sequences)" from_work_dir="out.reassem/out.reads.noclass">
1
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138 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
0
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139 </data>
1
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140 <data name="reassembly_n50" format="txt" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt">
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141 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter>
0
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142 </data>
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143 </outputs>
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144 <tests>
3
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145 <!-- test w contigs and reads as input -->
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146 <test expect_num_outputs="4">
0
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147 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
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148 <conditional name="intype_cond">
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149 <param name="intype_select" value="rds"/>
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150 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
0
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151 </conditional>
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152 <conditional name="adv_cond">
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153 <param name="adv_select" value="no"/>
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154 </conditional>
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155 <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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156 <element name="001" file="1/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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157 <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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158 </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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159 <output name="summary" file="1/out.summary" ftype="tabular" />
2
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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160 <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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161 <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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162 </test>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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163 <!-- test w contigs and reads as input test for optional outputs -->
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
iuc
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164 <test expect_num_outputs="9">
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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165 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
iuc
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166 <conditional name="intype_cond">
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
iuc
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167 <param name="intype_select" value="rds"/>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
iuc
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168 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
iuc
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169 <param name="output_abundances" value="true" />
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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170 </conditional>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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171 <conditional name="adv_cond">
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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172 <param name="adv_select" value="yes"/>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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173 <param name="plotmarker" value="true" />
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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174 <param name="output_marker" value="true" />
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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175 <param name="output_markers" value="true" />
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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176 <param name="output_log" value="true" />
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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177 </conditional>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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178 <output_collection name="bins" type="list" count="2">
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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179 <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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180 <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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181 </output_collection>
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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182 <output name="summary" file="1/out.summary" ftype="tabular" />
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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183 <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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184 <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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185 <output name="log" file="1/out.log" ftype="txt" compare="diff" lines_diff="21" />
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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186 <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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187 <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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188 <output name="plot" file="1/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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189 <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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190 <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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191 </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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192 </test>
2
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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193 <!--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"
iuc
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194 <test expect_num_outputs="5">
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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195 <param name="contig" value="Bin_Sample3_contigs.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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196 <conditional name="intype_cond">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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197 <param name="intype_select" value="abdc"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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198 <param name="abund" value="abundances.tsv" 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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199 </conditional>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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200 <conditional name="adv_cond">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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201 <param name="adv_select" value="yes"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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202 <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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203 <param name="max_iteration" value="10"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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204 <param name="prob_threshold" value="0.95"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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205 <param name="plotmarker" value="-plotmarker"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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206 <param name="markerset" value="107"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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207 </conditional>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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208 <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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209 <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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210 <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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211 </output_collection>
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212 <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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213 <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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214 <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"
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215 <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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216 </test>
2
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
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217 <!-- 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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218 <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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219 <param name="contig" value="Bin_Sample3_contigs.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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220 <conditional name="intype_cond">
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 <param name="intype_select" value="rds"/>
2
6a638de7915c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
iuc
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222 <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>
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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223 <param name="reassembly" value="-reassembly"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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224 </conditional>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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225 <conditional name="adv_cond">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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226 <param name="adv_select" value="no"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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227 </conditional>
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228 <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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229 <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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230 <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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231 </output_collection>
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232 <output name="summary" file="3/out.summary" ftype="tabular" />
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233 <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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234 <output name="toshort" file="3/out.tooshort" ftype="fasta" />
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235 <output_collection name="reassembly_bins" type="list" count="2">
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236 <element name="001" file="3/out.reassem/out.001.fasta" ftype="fasta"/>
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237 <element name="002" file="3/out.reassem/out.002.fasta" ftype="fasta"/>
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238 </output_collection>
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239 <output_collection name="reassembly_reads" type="list" count="2">
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240 <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/>
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241 <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/>
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242 </output_collection>
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243 <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />
1
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244 <output name="reassembly_n50" file="3/out.reassem/N50.txt" ftype="txt" />
0
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245 </test>
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246 </tests>
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247 <help><![CDATA[
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248 MaxBin is a software that clusters metagenomic contigs into different bins,
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249 each consists (hopefully) of contigs from one species. MaxBin uses the
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250 nucleotide composition information and contig abundance information to do
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251 achieve binning through an Expectation-Maximization algorithm.
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252
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253 **Input**:
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254
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255 MaxBin need the contigs and contig abundance information. The contig abundance
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256 information can be provided in two ways: the user can choose to provide
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257
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258 - the abundance file or
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259 - the sequencing reads in fasta format (and MaxBin will use Bowtie2 to map the
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260 sequencing reads against the contigs and generate the abundance information)
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261
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262 The abundance information can be provided as tabular file:
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263
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264 For example, assume I have three contigs named A0001, A0002, and A0003, then my abundance file will look like
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265
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266 A0001 30.89
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267 A0002 20.02
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268 A0003 78.93
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269
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270 Reads/Abundundance files can be given in multiple files.
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271
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272 By default MaxBin will look for 107 marker genes present in >95% of bacteria.
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273 Alternatively you can also choose 40 marker gene sets that are universal among
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274 bacteria and archaea (Wu et al., PLoS ONE 2013). This option may be better
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275 suited for environment dominated by archaea; however it tend to split genomes
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276 into more bins. You can choose between different marker gene sets and see which
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277 one works better.
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278
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279 **Outputs**
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280
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281 - bins: binned sequences
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282 - summary: a summary file describing which contigs are being classified into which bin.
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283 - log: a log file recording the core steps of MaxBin algorithm
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284 - abundances (only if reads are used as input): a summary file describing which contigs are being classified into which bin
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285 - 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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286 - 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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287 - unclassified sequences: this file stores all sequences that pass the minimum length threshold but are not classified successfully.
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288 - to short sequences: this file stores all sequences that do not meet the minimum length threshold.
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289 - markers prediced for bins: these data sets store all markers predicted from the individual bins.
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290
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291 **Reassembly**
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292
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293 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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294
2
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295
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296 ** More information **
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297
4
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298 https://web.archive.org/web/20190417100740/https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html
2
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299
0
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300 ]]></help>
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301 <citations>
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302 <citation type="doi">10.1093/bioinformatics/btv638</citation>
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303 </citations>
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304 </tool>