Mercurial > repos > iuc > delly_rd

annotate rd.xml @ 0:8fff33666441 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
author iuc
date Thu, 29 Oct 2020 20:48:48 +0000
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0
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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1 <?xml version="1.0"?>
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2 <tool id="delly_rd" name="Delly read-depth (rd)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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3 <description>normalization on read-depth profiles</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ## run
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11 delly rd
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12 ## generic options
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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13 --genome '$generic.genome'
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14 --quality '$generic.quality'
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15 --mappability '$generic.mappability'
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16 --ploidy $generic.ploidy
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17 --fragment $generic.fragment
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18 #if 'stats' in $oo.out
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19 --statsfile 'stats.tsv.gz'
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20 #end if
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21 --outfile 'result.tsv.gz'
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22 $generic.adaptivewindowing
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23 ## window options
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24 --window-size $window.windowsize
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25 --window-offset $window.windowoffset
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26 #if $window.bedintervals
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27 --bed-intervals '$window.bedintervals'
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28 #end if
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29 --fraction-window $window.fractionwindow
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30 ## gc options
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31 --scan-window $gc.scanwindow
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32 --fraction-unique $gc.fractionunique
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33 #if $gc.scanregions
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34 --scan-regions '$gc.scanregions'
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35 #end if
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36 --mad-cutoff $gc.madcutoff
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37 --percentile $gc.percentile
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38 $gc.nowindowselection
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39 ## samples
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40 '$samples' ## input
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41
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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42 ## postprocessing
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43 @LOG@
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44 ]]></command>
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45 <inputs>
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46 <expand macro="samples" multiple="false" label="Select file"/>
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47 <section name="generic" title="Generic options" expanded="true">
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48 <expand macro="genome"/>
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49 <param argument="--quality" type="integer" value="10" label="Set minimum mapping quality"/>
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50 <param argument="--mappability" type="data" format="fasta" label="Select mappability map file"/>
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51 <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
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52 <param argument="--fragment" type="float" min="0.0" max="1.0" value="0.97" label="Set minimum fragment uniqueness"/>
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53 <param name="adaptivewindowing" type="boolean" truevalue="-a" falsevalue="" label="Use mappable bases for window size?" help="(--adaptive-windowing)"/>
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54 </section>
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55 <section name="window" title="Window options" expanded="true">
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56 <param name="windowsize" type="integer" value="10000" label="Set window size" help="(--window-size)"/>
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57 <param name="windowoffset" type="integer" value="10000" label="Set window offset" help="(--window-offset)"/>
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58 <param name="bedintervals" type="data" format="BED" optional="true" label="Select input BED file" help="(--bed-intervals)"/>
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59 <param name="fractionwindow" type="float" min="0.0" max="1.0" value="0.25" label="Set minimum callable window fraction" help="(--fraction-window)"/>
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60 </section>
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61 <section name="gc" title="GC options" expanded="true">
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62 <param name="scanwindow" type="integer" value="10000" label="Set scan window size" help="(--scan-window)"/>
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63 <param name="fractionunique" type="float" min="0.0" max="1.0" value="0.8" label="Set uniqueness filter for scanning windows" help="(--fraction-unique)"/>
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64 <param name="scanregions" type="data" format="BED" optional="true" label="Select file with scanning regions" help="(--scan-regions)"/>
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65 <param name="madcutoff" type="integer" value="3" label="Set count cutoff" help="(median + 3 * mad) (--mad-cutoff)"/>
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66 <param argument="--percentile" type="float" min="0.0" max="1.0" value="0.0005" label="Set threshold to exclude extreme GC fraction"/>
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67 <param name="nowindowselection" type="boolean" truevalue="-n" falsevalue="" label="Skip scan window selection?" help="(--no-window-selection)"/>
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68 </section>
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69 <section name="oo" title="Output options">
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70 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
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71 <option value="result" selected="true">Result</option>
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72 <option value="stats">Statistics (-s)</option>
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73 <option value="log">Log</option>
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74 </param>
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75 </section>
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76 </inputs>
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77 <outputs>
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78 <data name="out_result" format="tabular.gz" from_work_dir="result.tsv.gz" label="${tool.name} on ${on_string}: Result">
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79 <filter>'result' in oo['out']</filter>
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80 </data>
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81 <data name="out_stats" format="tabular.gz" from_work_dir="stats.tsv.gz" label="${tool.name} on ${on_string}: Statistics">
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82 <filter>'stats' in oo['out']</filter>
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83 </data>
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84 <expand macro="log"/>
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85 </outputs>
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86 <tests>
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87 <!-- no test implemented for parameter -b, -r -->
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88
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89 <!-- #1 default, test data not sufficient -->
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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90 <test expect_num_outputs="2">
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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91 <param name="samples" value="normal.bam"/>
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92 <section name="generic">
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93 <param name="genome" value="genome.fasta"/>
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94 <param name="mappability" value="map.fasta"/>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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95 </section>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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96 <section name="oo">
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97 <param name="out" value="result,log"/>
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98 </section>
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99 <output name="out_result">
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iuc
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100 <assert_contents>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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101 <has_n_lines n="0"/>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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102 </assert_contents>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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103 </output>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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104 <output name="out_log">
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iuc
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105 <assert_contents>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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106 <has_text_matching expression=".+Scanning Windows"/>
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107 </assert_contents>
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108 </output>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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109 </test>
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110 <!-- #2 default, test data not sufficient -->
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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111 <test expect_num_outputs="3">
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112 <param name="samples" value="normal.bam"/>
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113 <section name="generic">
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114 <param name="genome" value="genome.fasta"/>
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115 <param name="quality" value="11"/>
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iuc
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116 <param name="mappability" value="map.fasta"/>
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117 <param name="ploidy" value="3"/>
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iuc
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118 <param name="fragment" value="0.96"/>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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119 <param name="adaptivewindowing" value="true"/>
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120 </section>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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121 <section name="window">
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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122 <param name="windowsize" value="10001"/>
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123 <param name="windowoffset" value="9999"/>
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124 <param name="fractionwindow" value="0.24"/>
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125 </section>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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126 <section name="gc">
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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127 <param name="scanwindow" value="10001"/>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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128 <param name="fractionunique" value="0.79"/>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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129 <param name="madcutoff" value="2"/>
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130 <param name="percentile" value="0.0006"/>
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131 <param name="nowindowselection" value="true"/>
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132 </section>
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133 <section name="oo">
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134 <param name="out" value="result,stats,log"/>
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135 </section>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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136 <output name="out_result">
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137 <assert_contents>
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138 <has_n_lines n="1"/>
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139 </assert_contents>
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140 </output>
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141 <output name="out_stats">
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142 <assert_contents>
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143 <has_n_lines n="12"/>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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144 </assert_contents>
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145 </output>
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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146 <output name="out_log">
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147 <assert_contents>
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148 <has_text_matching expression=".+Scanning Windows"/>
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149 </assert_contents>
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150 </output>
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151 </test>
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152 </tests>
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153 <help><![CDATA[
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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154 .. class:: infomark
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155
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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156 **What it does**
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157
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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158 @WID@
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159
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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160 Delly *read-depth normalization (rd)* generates read-depth profiles.
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161
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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162 **Input**
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163
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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164 Required inputs are a sample (BAM), a genome (FASTA) and a mappability map (FASTA), which can be downloaded `here <https://gear.embl.de/data/delly/>`_. Optionally intervals (BED) and scanning regions (BED) ca be provided.
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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165
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166 **Output**
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167
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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168 Read-depth profiles (tabular) and optionally statistics (tabular) are created.
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169
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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170 .. class:: infomark
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171
8fff33666441 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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172 **References**
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173
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174 @REFERENCES@
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175 ]]></help>
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176 <expand macro="citations"/>
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177 </tool>