Mercurial > repos > iuc > metabat2_jgi_summarize_bam_contig_depths

annotate jgi_summarize_bam_contig_depths.xml @ 3:ec045ca00b50 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 3a3dfd676076438bea1518eb731790edfb4da3c0
author iuc
date Thu, 09 Nov 2023 12:24:01 +0000
parents a4441f35f17b
children
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d27a4ed006ee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
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1 <tool id="metabat2_jgi_summarize_bam_contig_depths" name="Calculate contig depths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>for MetaBAT2</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="use_reference">
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6 <param name="use_reference" type="select" label="Select a reference genome?">
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7 <option value="no" selected="true">No</option>
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8 <option value="yes">Yes</option>
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9 </param>
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10 </xml>
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11 <xml name="reference_source">
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12 <param name="reference_source" type="select" label="Choose the source for the reference genome">
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13 <option value="cached" selected="true">locally cached</option>
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14 <option value="history">from history</option>
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15 </param>
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16 </xml>
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17 <xml name="referenceFasta">
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18 <param argument="--referenceFasta" type="data" format="fasta,fasta.gz" label="Using reference genome" help="Must be the reference used to map the input bam files"/>
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19 </xml>
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20 <xml name="gcWindow">
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21 <param argument="--gcWindow" type="integer" value ="100" label="Sliding window size for GC calculations"/>
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22 </xml>
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23 </macros>
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24 <expand macro="requirements"/>
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25 <command detect_errors="exit_code"><![CDATA[
1
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26 jgi_summarize_bam_contig_depths
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27 --outputDepth '$outputDepth'
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28 --percentIdentity $advanced.percentIdentity
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29 #if $advanced.output_paired_contigs
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30 --pairedContigs '$outputPairedContigs'
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31 #end if
1
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32 $advanced.noIntraDepthVariance
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33 $advanced.showDepth
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34 --minMapQual $advanced.minMapQual
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35 --weightMapQual $advanced.weightMapQual
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36 $advanced.includeEdgeBases
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37 --maxEdgeBases $advanced.maxEdgeBases
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38 #if str($mode.use_reference_cond.use_reference) == 'yes'
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39 #if str($mode.use_reference_cond.reference_cond.reference_source) == 'cached'
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40 --referenceFasta '$mode.use_reference_cond.reference_cond.referenceFasta.fields.path'
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41 #else
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42 --referenceFasta '$mode.use_reference_cond.reference_cond.referenceFasta'
0
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43 #end if
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44 --outputGC '$outputGC'
1
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45 --gcWindow $mode.use_reference_cond.gcWindow
0
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46 --outputReadStats '$outputReadStats'
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47 --outputKmers '$outputKmers'
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48 #end if
1
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49 --shredLength $shredding.shredLength
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50 --shredDepth $shredding.shredDepth
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51 --minContigLength $shredding.minContigLength
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52 --minContigDepth $shredding.minContigDepth
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53 #if $mode.type == 'individual'
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54 '$mode.bam_indiv_input'
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55 #else
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56 #for $bam_input in $mode.bam_co_inputs
0
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57 '$bam_input'
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58 #end for
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59 #end if
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60 ]]></command>
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61 <inputs>
1
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62 <conditional name="mode">
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63 <param name="type" type="select" label="Mode to process BAM files">
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64 <option value="individual">One by one</option>
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65 <option value="co">Together</option>
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66 </param>
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67 <when value="individual">
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68 <param name="bam_indiv_input" type="data" format="bam" label="Sorted bam files"/>
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69 <conditional name="use_reference_cond">
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70 <expand macro="use_reference"/>
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71 <when value="no"/>
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72 <when value="yes">
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73 <conditional name="reference_cond">
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74 <expand macro="reference_source"/>
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75 <when value="cached">
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76 <param argument="--referenceFasta" type="select" label="Using reference genome">
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77 <options from_data_table="fasta_indexes">
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78 <filter type="data_meta" column="1" key="dbkey" ref="bam_indiv_input"/>
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79 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected BAM file(s)"/>
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80 </options>
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81 </param>
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82 </when>
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83 <when value="history">
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84 <expand macro="referenceFasta"/>
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85 </when>
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86 </conditional>
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87 <expand macro="gcWindow"/>
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88 </when>
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89 </conditional>
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90 </when>
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91 <when value="co">
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92 <param name="bam_co_inputs" type="data" format="bam" multiple="true" label="Sorted bam files"/>
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93 <conditional name="use_reference_cond">
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94 <expand macro="use_reference"/>
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95 <when value="no"/>
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96 <when value="yes">
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97 <conditional name="reference_cond">
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98 <expand macro="reference_source"/>
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99 <when value="cached">
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100 <param argument="--referenceFasta" type="select" label="Using reference genome">
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101 <options from_data_table="fasta_indexes">
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102 <filter type="data_meta" column="1" key="dbkey" ref="bam_co_inputs"/>
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103 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected BAM file(s)"/>
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104 </options>
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105 </param>
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106 </when>
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107 <when value="history">
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108 <expand macro="referenceFasta"/>
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109 </when>
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110 </conditional>
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111 <expand macro="gcWindow"/>
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112 </when>
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113 </conditional>
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114 </when>
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115 </conditional>
0
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116 <section name="advanced" title="Advanced options">
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117 <param argument="--percentIdentity" type="integer" value="97" label="Minimum end-to-end percent identity of qualifying reads"/>
1
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118 <param name="output_paired_contigs" type="boolean" checked="false" label="Output the sparse matrix of contigs which paired reads span?"/>
0
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119 <param argument="--noIntraDepthVariance" type="boolean" truevalue="--noIntraDepthVariance" falsevalue="" checked="false" label="Remove variance from mean depth along the contig?"/>
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120 <param argument="--showDepth" type="boolean" truevalue="--showDepth" falsevalue="" checked="false" label="Output a depth file per bam for each contig base?"/>
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121 <param argument="--minMapQual" type="integer" value="0" label="Minimum mapping quality necessary to count a read as mapped"/>
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122 <param argument="--weightMapQual" type="float" value="0.0" label="Weight per-base depth based on the MQ of the read" help="Zero value disables"/>
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123 <param argument="--includeEdgeBases" type="boolean" truevalue="--includeEdgeBases" falsevalue="" checked="false" label="Include 1-readlength edges when calculating depth and variance?"/>
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124 <param argument="--maxEdgeBases" type="integer" value="75" label="Maximum length when calculating depth and variance" help="Ignored when including 1-readlength edges when calculating depth and variance"/>
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125 </section>
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126 <section name="shredding" title="Options to control shredding contigs that are under-represented by the reads">
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127 <param argument="--shredLength" type="integer" value="16000" label="Maximum length of the shreds"/>
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128 <param argument="--shredDepth" type="integer" value="5" label="Depth to generate overlapping shreds"/>
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129 <param argument="--minContigLength" type="integer" value="1" label="Mimimum length of contig to include for mapping and shredding"/>
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130 <param argument="--minContigDepth" type="float" value="0.0" label="Minimum depth along the contig at which to break the contig"/>
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131 </section>
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132 </inputs>
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133 <outputs>
1
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134 <data name="outputDepth" format="tabular" label="${tool.name} on ${on_string}: Depth matrix"/>
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135 <data name="outputPairedContigs" format="fasta" label="${tool.name} on ${on_string}: Paired contigs">
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136 <filter>advanced["output_paired_contigs"]</filter>
0
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137 </data>
1
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138 <data name="outputGC" format="tabular" label="${tool.name} on ${on_string}: GC coverage histogram">
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139 <filter>mode["use_reference_cond"]["use_reference"] == 'yes'</filter>
0
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140 </data>
1
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141 <data name="outputReadStats" format="tabular" label="${tool.name} on ${on_string}: Read statistics">
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142 <filter>mode["use_reference_cond"]["use_reference"] == 'yes'</filter>
0
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143 </data>
1
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144 <data name="outputKmers" format="tabular" label="${tool.name} on ${on_string}: Perfect kmer counts">
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145 <filter>mode["use_reference_cond"]["use_reference"] == 'yes'</filter>
0
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146 </data>
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147 </outputs>
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148 <tests>
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149 <!-- Single input, default settings -->
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150 <test expect_num_outputs="1">
1
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151 <conditional name="mode">
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152 <param name="type" value="individual"/>
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153 <param name="bam_indiv_input" value="input1.bam" ftype="bam"/>
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154 </conditional>
0
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155 <output name="outputDepth" file="jgi_output1.tabular" ftype="tabular" compare="contains"/>
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156 </test>
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157 <!-- Multiple inputs, default settings -->
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158 <test expect_num_outputs="1">
1
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159 <conditional name="mode">
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160 <param name="type" value="co"/>
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161 <param name="bam_co_inputs" value="input1.bam,input1.bam" ftype="bam"/>
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162 </conditional>
0
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163 <output name="outputDepth" file="jgi_output2.tabular" ftype="tabular" compare="contains"/>
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164 </test>
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165 <!-- Single input, output paired contigs, reference from history -->
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166 <test expect_num_outputs="5">
1
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167 <conditional name="mode">
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168 <param name="type" value="individual"/>
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169 <param name="bam_indiv_input" value="input2.bam" ftype="bam" dbkey="89"/>
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170 <conditional name="use_reference_cond">
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171 <param name="use_reference" value="yes"/>
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172 <conditional name="reference_cond">
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173 <param name="reference_source" value="history"/>
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174 <param name="referenceFasta" value="NC_002945v4.fasta" ftype="fasta"/>
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175 </conditional>
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176 </conditional>
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177 </conditional>
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178 <section name="advanced">
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179 <param name="output_paired_contigs" value="true"/>
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180 </section>
0
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181 <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/>
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182 <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/>
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183 <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/>
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184 <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/>
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185 <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/>
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186 </test>
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187 <!-- Single input, output paired contigs, cached reference -->
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188 <test expect_num_outputs="5">
1
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189 <conditional name="mode">
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190 <param name="type" value="individual"/>
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191 <param name="bam_indiv_input" value="input2.bam" ftype="bam" dbkey="89"/>
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192 <conditional name="use_reference_cond">
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193 <param name="use_reference" value="yes"/>
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194 <conditional name="reference_cond">
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195 <param name="reference_source" value="cached"/>
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196 </conditional>
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197 </conditional>
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198 </conditional>
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199 <section name="advanced">
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200 <param name="output_paired_contigs" value="true"/>
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201 </section>
0
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202 <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/>
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203 <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/>
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204 <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/>
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205 <output name="outputReadStats" file="jgi_output_read_stats1.tabular" ftype="tabular"/>
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206 <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/>
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207 </test>
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208 </tests>
1
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209 <help><![CDATA[
0
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210 **What it does**
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211
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212 Calculates coverage depth for each sequence in one or more selected BAM files, producing a tabular file (for each input)
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213 having mean and variance of base coverage depth that can be used as one of the inputs for the MetaBAT2 metagenome binning
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214 tool.
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215
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216 The algorithm used for calculating the coverage depth is adjusted by a few factors to improve the fidelity of the metrics
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217 when correlating abundance coverage in the binning stage. By default the following adjustments are applied.
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218
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219 **Edge bases are ignored**
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220
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221 Edge bases are not counted as coverage, by the lesser of 1 AverageReadLength or (--maxEdgeBases=75). This is because most
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222 mappers can not reliably place a read that would extend off the edge of a sequence, and coverage depth tends to drop towards
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223 0 at the edge of a contig or scaffold. Use --includeEdgeBases to include the coverage in this region.
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224
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225 **Reads with high mapping errors are skipped**
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226
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227 Reads that map imperfectly are excluded when the %ID of the mapping drops below a threshold (--percentIdentity=97).
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228 MetaBAT2 is designed to resolve strain variation and mapping reads with low %ID indicate that the read actually came from
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229 a different strain/species.
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230
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231 %ID is calculated from the CIGAR string and/or NM/MD fields and == 100 * MatchedBases / (MatchedBases + Substituions +
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232 Insertions + Deletions). This ensures that clips, insertions, deletions and mismatches are excluded from the coverage count.
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233 Only the read bases that exactly match the reference are counted as coverage. This generally has a small effect, except in
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234 the case of long reads from PacBio and Nanopore.
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235
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236 **More information**
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237
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238 https://bitbucket.org/berkeleylab/metabat/src/master/
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239
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240 **Options**
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241
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242 * **Select a reference genome** - optionally select the reference genome that was used to map the input bam file(s) and 3 additional outputs will be produced; gc coverage histogram, read statistics and perfect kmer counts.
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243
1
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244 ]]></help>
0
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245 <expand macro="citations"/>
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246 </tool>
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247