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annotate maxbin2.xml @ 0:35aa0df55a62 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
author mbernt
date Thu, 28 Jun 2018 08:49:29 -0400
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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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1 <tool id="maxbin2" name="MaxBin2" version="2.2.4">
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2 <requirements>
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3 <requirement type="package" version="2.2.4">maxbin2</requirement>
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4 </requirements>
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5 <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
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6 <command detect_errors="exit_code"><![CDATA[
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7 ## generate read or abundance files
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8 #if $intype_cond.intype_select == 'rds':
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9 #for $r in $intype_cond.reads
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10 #if $r
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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11 echo '$r' >> reads_list &&
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12 #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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13 #end for
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14 #else if $intype_cond.intype_select == 'abdc':
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15 #for $a in $intype_cond.abund
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16 #if $a
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17 echo '$a' >> abund_list &&
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18 #end if
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19 #end for
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20 #end if
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21
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22 ## in case of reassembly the IBDA out and err is appended
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23 ## to differentiate this a header is added also befor the
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24 ## MaxBin2 outputs
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25 #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
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26 echo "==== MaxBin2 stdout ====" &&
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27 echo "==== MaxBin2 stderr ====" 1>&2 &&
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28 #end if
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29
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
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30 run_MaxBin.pl
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31 -contig '$contig'
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32 -out out
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33 #if $intype_cond.intype_select == 'rds':
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34 -reads_list reads_list
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35 $intype_cond.reassembly
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36 #else if $intype_cond.intype_select == 'abdc':
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37 -abund_list abund_list
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38 #end if
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39 #if $adv_cond.adv_select == 'yes':
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40 -min_contig_length $adv_cond.min_contig_length
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41 -max_iteration $adv_cond.max_iteration
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42 -prob_threshold $adv_cond.prob_threshold
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43 $adv_cond.plotmarker
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44 -markerset $adv_cond.markerset
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45 #end if
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46 -thread \${GALAXY_SLOTS:-1}
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47
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48 && tar -xf out.marker_of_each_bin.tar.gz
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49
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50 ## redirect the idba out and err file content to stdout and err
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51 #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
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52 && echo "==== IDBA stdout ===="
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53 && cat out.idba.out
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54 && echo "==== IDBA stderr ====" 1>&2
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55 && cat out.idba.err 1>&2
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56 #end if
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57 ]]></command>
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58 <inputs>
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59 <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
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60 <conditional name="intype_cond">
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61 <param name="intype_select" type="select" label="Input type">
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62 <option value="rds" selected="true">Sequencing Reads</option>
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63 <option value="abdc">Abundances</option>
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64 </param>
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65 <when value="rds">
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66 <param name="reads" argument="-read/-read2/..." type="data" format="fasta,fastq" multiple="true" label="Reads file(s)"/>
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67 <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file if you were to use this option." />
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68 </when>
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69 <when value="abdc">
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70 <param name="abund" argument="-abund/-abund2/..." type="data" format="tabular" multiple="true" label="Abundance file(s)"/>
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71 </when>
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72 </conditional>
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73 <conditional name="adv_cond">
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74 <param name="adv_select" type="select" label="Advanced options">
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75 <option value="yes">Yes</option>
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76 <option value="no" selected="true">No</option>
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77 </param>
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78 <when value="no"/>
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79 <when value="yes">
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80 <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" />
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81 <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" />
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82 <param argument="-prob_threshold" type="float" min="0" max="1.0" value="0.9" label="Probability threshold for EM final classification" />
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83 <param name="plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" />
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84 <param argument="-markerset" type="select" label="Marker gene set">
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85 <option value="107" selected="true">107 marker genes present in >95% of bacteria</option>
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86 <option value="40">40 marker gene sets that are universal among bacteria and archaea</option>
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87 </param>
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88 </when>
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89 </conditional>
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90 </inputs>
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91 <outputs>
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92 <collection name="bins" type="list" label="${tool.name} on ${on_string} (bins)">
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93 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
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94 </collection>
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95 <data name="summary" format="tabular" label="${tool.name} on ${on_string} (summary)" from_work_dir="out.summary"/>
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96 <data name="log" format="txt" label="${tool.name} on ${on_string} (log)" from_work_dir="out.log"/>
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97 <data name="abundout" format="tabular" label="${tool.name} on ${on_string} (abundances)" from_work_dir="out.abund1">
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98 <filter>intype_cond['intype_select']=='rds'</filter>
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99 </data>
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100 <data name="marker" format="tabular" label="${tool.name} on ${on_string} (marker gene presence)" from_work_dir="out.marker"/>
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101 <data name="plot" format="pdf" label="${tool.name} on ${on_string} (marker gene presence plot)" from_work_dir="out.marker.pdf">
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102 <filter>adv_cond['adv_select']=='yes' and adv_cond['plotmarker']</filter>
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103 </data>
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104 <data name="noclass" format="fasta" label="${tool.name} on ${on_string} (unclassified sequences)" from_work_dir="out.noclass"/>
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105 <data name="toshort" format="fasta" label="${tool.name} on ${on_string} (to short sequences)" from_work_dir="out.tooshort"/>
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106 <collection name="markers" type="list" label="${tool.name} on ${on_string} (markers prediced for bins)">
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107 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" />
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108 </collection>
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109 <!-- additional output in case of reassembly -->
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110 <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string} (reassembly bins)">
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111 <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
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112 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
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113 </collection>
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114 <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string} (reassembly reads)">
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115 <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" />
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116 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
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117 </collection>
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118 <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string} (reassembly unclassified sequences)" from_work_dir="out.reassem/out.reads.noclass">
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119 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
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120 </data>
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121 <data name="reassembly_n50" format="text" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt">
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122 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
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123 </data>
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124 </outputs>
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125 <tests>
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126 <test><!-- test w contigs and reads as input -->
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127 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
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128 <conditional name="intype_cond">
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129 <param name="intype_select" value="rds"/>
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130 <param name="reads" value="interleavedPE_unmapped_Sample3_total.fasta" ftype="fasta"/>
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131 </conditional>
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132 <conditional name="adv_cond">
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133 <param name="adv_select" value="no"/>
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134 </conditional>
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135 <output_collection name="bins" type="list" count="2">
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136 <element name="001" file="1/out.001.fasta" ftype="fasta"/>
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137 <element name="002" file="1/out.002.fasta" ftype="fasta"/>
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138 </output_collection>
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139 <output name="summary" file="1/out.summary" ftype="tabular" />
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140 <output name="log" file="1/out.log" ftype="txt" compare="diff" lines_diff="17" />
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141 <output name="abundout" file="1/out.abund1" ftype="tabular" />
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142 <output name="marker" file="1/out.marker" ftype="tabular" />
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143 <output name="noclass" file="1/out.noclass" ftype="fasta" />
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144 <output name="toshort" file="1/out.tooshort" ftype="fasta" />
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145 <output_collection name="markers" type="list" count="1">
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146 <element name="001" file="1/out.001.marker.fasta" ftype="fasta"/>
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147 </output_collection>
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148 </test>
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149 <test><!--test w contigs and abundances as input + advanced options -->
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150 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
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151 <conditional name="intype_cond">
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152 <param name="intype_select" value="abdc"/>
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153 <param name="abund" value="abundances.tsv" ftype="tabular"/>
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154 </conditional>
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155 <conditional name="adv_cond">
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156 <param name="adv_select" value="yes"/>
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157 <param name="min_contig_length" value="500"/>
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158 <param name="max_iteration" value="10"/>
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159 <param name="prob_threshold" value="0.95"/>
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160 <param name="plotmarker" value="-plotmarker"/>
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161 <param name="markerset" value="107"/>
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162 </conditional>
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163 <output_collection name="bins" type="list" count="2">
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164 <element name="001" file="2/out.001.fasta" ftype="fasta"/>
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165 <element name="002" file="2/out.002.fasta" ftype="fasta"/>
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166 </output_collection>
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167 <output name="summary" file="2/out.summary" ftype="tabular" />
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168 <output name="log" file="2/out.log" ftype="txt" compare="diff" lines_diff="17" />
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169 <output name="marker" file="2/out.marker" ftype="tabular" />
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170 <output name="plot" file="2/out.marker.pdf" ftype="pdf" compare="sim_size" />
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171 <output name="noclass" file="2/out.noclass" ftype="fasta" />
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172 <output name="toshort" file="2/out.tooshort" ftype="fasta" />
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173 <output_collection name="markers" type="list" count="1">
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174 <element name="001" file="2/out.001.marker.fasta" ftype="fasta"/>
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175 </output_collection>
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176 </test>
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177 <test><!-- test w contigs and reads as input + reassembly-->
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178 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
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179 <conditional name="intype_cond">
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180 <param name="intype_select" value="rds"/>
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181 <param name="reads" value="interleavedPE_unmapped_Sample3_total.fasta" ftype="fasta"/>
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182 <param name="reassembly" value="-reassembly"/>
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183 </conditional>
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184 <conditional name="adv_cond">
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185 <param name="adv_select" value="no"/>
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186 </conditional>
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187 <output_collection name="bins" type="list" count="2">
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188 <element name="001" file="3/out.001.fasta" ftype="fasta"/>
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189 <element name="002" file="3/out.002.fasta" ftype="fasta"/>
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190 </output_collection>
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191 <output name="summary" file="3/out.summary" ftype="tabular" />
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192 <output name="log" file="3/out.log" ftype="txt" compare="diff" lines_diff="17" />
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193 <output name="abundout" file="3/out.abund1" ftype="tabular" />
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194 <output name="marker" file="3/out.marker" ftype="tabular" />
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195 <output name="noclass" file="3/out.noclass" ftype="fasta" />
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196 <output name="toshort" file="3/out.tooshort" ftype="fasta" />
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197 <output_collection name="markers" type="list" count="1">
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198 <element name="001" file="3/out.001.marker.fasta" ftype="fasta"/>
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199 </output_collection>
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200 <output_collection name="reassembly_bins" type="list" count="2">
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201 <element name="001" file="3/out.reassem/out.001.fasta" ftype="fasta"/>
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202 <element name="002" file="3/out.reassem/out.002.fasta" ftype="fasta"/>
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203 </output_collection>
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204 <output_collection name="reassembly_reads" type="list" count="2">
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205 <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/>
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206 <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/>
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207 </output_collection>
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208 <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />
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209 <output name="reassembly_n50" file="3/out.reassem/N50.txt" ftype="text" />
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210 </test>
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211 </tests>
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212 <help><![CDATA[
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213 MaxBin is a software that clusters metagenomic contigs into different bins,
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214 each consists (hopefully) of contigs from one species. MaxBin uses the
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215 nucleotide composition information and contig abundance information to do
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216 achieve binning through an Expectation-Maximization algorithm.
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217
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218
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219 **Input**:
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220
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221 MaxBin need the contigs and contig abundance information. The contig abundance
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222 information can be provided in two ways: the user can choose to provide
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223
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224 - the abundance file or
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225 - the sequencing reads in fasta format (and MaxBin will use Bowtie2 to map the
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226 sequencing reads against the contigs and generate the abundance information)
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227
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228 The abundance information can be provided as tabular file:
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229
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230 For example, assume I have three contigs named A0001, A0002, and A0003, then my abundance file will look like
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231
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232 A0001 30.89
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233 A0002 20.02
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234 A0003 78.93
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235
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236 Reads/Abundundance files can be given in multiple files.
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237
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238 By default MaxBin will look for 107 marker genes present in >95% of bacteria.
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239 Alternatively you can also choose 40 marker gene sets that are universal among
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240 bacteria and archaea (Wu et al., PLoS ONE 2013). This option may be better
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241 suited for environment dominated by archaea; however it tend to split genomes
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242 into more bins. You can choose between different marker gene sets and see which
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243 one works better.
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244
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245 **Outputs**
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246
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247 - bins: binned sequences
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248 - summary: a summary file describing which contigs are being classified into which bin.
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249 - log: a log file recording the core steps of MaxBin algorithm
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250 - abundances (only if reads are used as input): a summary file describing which contigs are being classified into which bin
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251 - 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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252 - 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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253 - unclassified sequences: this file stores all sequences that pass the minimum length threshold but are not classified successfully.
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254 - to short sequences: this file stores all sequences that do not meet the minimum length threshold.
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255 - markers prediced for bins: these data sets store all markers predicted from the individual bins.
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256
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257 **Reassembly**
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258
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259 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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260
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261 ]]></help>
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262 <citations>
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263 <citation type="doi">10.1093/bioinformatics/btv638</citation>
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264 <citation type="bibtex">
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265 @misc{renameTODO,
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266 author = {LastTODO, FirstTODO},
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267 year = {TODO},
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268 title = {TODO},
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269 url = {https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html},
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270 }</citation>
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271 </citations>
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272 </tool>