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annotate samtools_stats.xml @ 9:1cc79f49b8d5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
author iuc
date Sat, 27 Nov 2021 12:33:04 +0000
parents e28839a4b932
children 3a0efe14891f
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1 <tool id="samtools_stats" name="Samtools stats" version="2.0.3" profile="@PROFILE@">
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2 <description>generate statistics for BAM dataset</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @ADDTHREADS@
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11 @PREPARE_IDX@
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12 @PREPARE_FASTA_IDX@
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13 samtools stats
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14 #if $coverage_cond.coverage_select == 'yes':
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15 --coverage ${coverage_cond.coverage_min},${coverage_cond.coverage_max},${coverage_cond.coverage_step}
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16 #end if
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17 ${remove_dups}
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18 #if str( $filter_by_flags.filter_flags ) == "filter":
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19 #set $filter = $filter_by_flags.require_flags
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20 @FLAGS@
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21 --required-flag $flags
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22 #set $filter = $filter_by_flags.exclude_flags
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23 @FLAGS@
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24 --filtering-flag $flags
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25 #end if
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26 #if str($gc_depth):
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27 --GC-depth ${gc_depth}
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28 #end if
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29 #if str($insert_size):
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30 --insert-size ${insert_size}
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31 #end if
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32 ## #if $read_group
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33 ## -I '$read_group'
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34 ## #end if
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35 #if str($read_length):
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36 --read-length ${read_length}
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37 #end if
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38 #if str($most_inserts):
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39 --most-inserts ${most_inserts}
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40 #end if
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41 #if str($trim_quality):
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42 --trim-quality ${trim_quality}
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43 #end if
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44
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45 #if $use_ref:
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46 --ref-seq "\$reffa"
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47 #end if
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48 ## TODO currently not implemented in Galaxy
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49 ## generates STR_VALUE.bamstat where STR is given by -P and VALUE is a value of the TAG given by -S
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50 ## needs some discover data sets action...
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51 ## -P, --split-prefix STR
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52 ## -S, --split TAG
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53 $sparse
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54 @REGIONS_FILE@
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55 $remove_overlaps
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56 #if str($cov_threshold):
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57 -g $cov_threshold
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58 #end if
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59 -@ \$addthreads
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60 infile
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61 @REGIONS_MANUAL@
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62 > '$output'
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63
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64 #if $split_output_cond.split_output_selector == "yes":
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65 #set outputs_to_split = str($split_output_cond.generate_tables).split(',')
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66 && mkdir split
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67 #for s in str($split_output_cond.generate_tables).split(','):
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68 && name=`cat '$output' | grep '\^$s' | cut -d'.' -f 1 | sed 's/^# //'`
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69 && awk '/\^/{out=0} /\^$s/{out=1} {if(out==1){print $0}}' '$output' | sed 's/Use `grep .*` to extract this part.//' | sed 's/$s\t//' > "split/\$name.tab"
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70 #end for
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71 #end if
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72 ]]></command>
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73 <inputs>
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74 <param name="input" type="data" format="sam,bam,cram" label="BAM file" />
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75 <conditional name="coverage_cond">
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76 <param name="coverage_select" type="select" label="Set coverage distribution">
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77 <option value="no" selected="True">No</option>
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78 <option value="yes">Yes</option>
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79 </param>
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80 <when value="no"/>
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81 <when value="yes">
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82 <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="Minimum coverage" />
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83 <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="Maximum coverage" />
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84 <param name="coverage_step" type="integer" value="1" label="Coverage step" help="Step value for coverage" />
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85 </when>
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86 </conditional>
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87 <param name="remove_dups" argument="--remove-dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" />
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88 <conditional name="split_output_cond">
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89 <param name="split_output_selector" type="select" label="Output" help="Select between one single output or separate outputs for each statistics">
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90 <option value="no" selected="True">One single summary file</option>
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91 <option value="yes">Separate datasets for each statistic</option>
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92 </param>
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93 <when value="no" />
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94 <when value="yes">
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95 <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Desired output files">
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96 <option value="SN">Summary numbers</option>
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97 <option value="FFQ">First Fragment Qualities</option>
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98 <option value="LFQ">Last Fragment Qualities</option>
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99 <option value="MPC">Mismatches per cycle</option>
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100 <option value="GCF">GC Content of first fragments</option>
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101 <option value="GCL">GC Content of last fragments</option>
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102 <option value="GCC">ACGT content per cycle</option>
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103 <option value="FBC">ACGT content per cycle for first fragments</option>
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104 <option value="LBC">ACGT content per cycle for last fragments</option>
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105 <option value="IS">Insert sizes</option>
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106 <option value="RL">Read lengths</option>
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107 <option value="FRL">Read lengths for first fragments</option>
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108 <option value="LRL">Read lengths for last fragments</option>
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109 <option value="ID">Indel distribution</option>
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110 <option value="IC">Indels per cycle</option>
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111 <option value="COV">Coverage distribution</option>
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112 <option value="GCD">GC depth</option>
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113 </param>
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114 </when>
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115 </conditional>
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116 <conditional name="filter_by_flags">
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117 <param name="filter_flags" type="select" label="Filter by SAM flags" help="More info on the flags: https://samtools.github.io/hts-specs/SAMv1.pdf">
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118 <option value="nofilter" selected="True">Do not filter</option>
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119 <option value="filter">Filter by flags to exclude or require</option>
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120 </param>
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121 <when value="filter">
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122 <param name="require_flags" argument="-f" type="select" display="checkboxes" multiple="True" label="Require">
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123 <expand macro="flag_options" />
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124 </param>
2
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125 <param name="exclude_flags" argument="-F" type="select" display="checkboxes" multiple="True" label="Exclude">
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126 <expand macro="flag_options" />
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127 </param>
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128 </when>
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129 <when value="nofilter" />
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130
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131 </conditional>
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132 <!-- TODO I would like to set the default values of float and int parameters as on the samtools stats help page, but then the tests don't work. Hence I leave the optional and give the defaults in the help -->
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133 <param name="gc_depth" argument="--GC-depth" type="float" optional="True" label="Size of GC-depth bins" help="Decreasing bin size increases memory requirement. default=2e4" />
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134 <param name="insert_size" argument="--insert-size" type="integer" optional="True" label="Maximum insert size" help="default=8000" />
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135 <!-- TOOD https://github.com/samtools/samtools/issues/1489 -->
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136 <param name="read_group" argument="--id" type="select" optional="true" label="Limit to a specific read group name" >
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137 <options>
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138 <filter type="data_meta" ref="input" key="read_groups" />
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139 </options>
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140 </param>
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141 <param name="read_length" argument="--read-length" type="integer" optional="true" label="Minimum read length to generate statistics for" help="No cutoff if left empty" />
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142 <param name="most_inserts" argument="--most-inserts" type="float" optional="true" label="Report only the main part of inserts" help="default=0.99" />
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143 <param name="trim_quality" argument="--trim-quality" type="integer" optional="true" label="BWA trim parameter" help="default=0" />
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144
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145 <expand macro="optional_reference" argument="--ref-seq" help="Required for GC-depth and mismatches-per-cycle calculation"/>
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146 <!-- unfortunately -t takes tabular and not bed like view (otherwise a macro might have simplified this) -->
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147
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148 <expand macro="regions_macro"/>
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149
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150 <param name="sparse" argument="-x/--sparse" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Suppress absence of insertions" help="Suppress outputting IS rows where there are no insertions."/>
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151 <param name="remove_overlaps" argument="-p/--remove-overlaps" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Remove overlaps of paired-end reads from coverage and base count computations" />
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152 <param name="cov_threshold" argument="-g/--cov-threshold" optional="true" type="integer" label="Only bases with coverage above this value will be included in the target percentage computation" />
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153 </inputs>
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154
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155 <outputs>
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156 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
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157 <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="true" assign_primary_output="true"/>
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158 <filter>split_output_cond['split_output_selector'] == 'no'</filter>
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159 </data>
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160 <collection name="output_collection" type="list" label="${tool.name} on ${on_string}">
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161 <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="false"/>
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162 <filter>split_output_cond['split_output_selector'] == 'yes'</filter>
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163 </collection>
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164 </outputs>
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165 <tests>
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166 <!-- https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2402 -->
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167 <test>
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168 <param name="input" value="1_map_cigar.sam" ftype="sam" />
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169 <conditional name="addref_cond">
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170 <param name="addref_select" value="history" />
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171 <param name="ref" value="test.fa" ftype="fasta" />
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172 </conditional>
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173 <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="2" />
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174 </test>
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175 <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);-->
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176 <test>
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177 <param name="input" value="2_equal_cigar_full_seq.sam" ftype="sam" />
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178 <conditional name="addref_cond">
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179 <param name="addref_select" value="history" />
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180 <param name="ref" value="test.fa" ftype="fasta" />
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181 </conditional>
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182 <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="2" />
3
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183 </test>
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184 <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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185 <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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186 <!-- test_cmd($opts,out=>'stat/4.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/4_X_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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187 <!-- test_cmd($opts,out=>'stat/5.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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188 <test>
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189 <param name="input" value="5_insert_cigar.sam" ftype="sam" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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190 <param name="insert_size" value="0" />
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191 <conditional name="addref_cond">
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192 <param name="addref_select" value="history" />
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193 <param name="ref" value="test.fa" ftype="fasta" />
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194 </conditional>
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195 <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="2" />
3
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196 </test>
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197 <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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198 <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); -->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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199 <!-- test_cmd($opts,out=>'stat/8.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/8_secondary.sam | tail -n+4", exp_fix=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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200 <!-- test_cmd($opts,out=>'stat/9.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/1_map_cigar.sam_s1_a_1.bamstat"=>"stat/1_map_cigar.sam_s1_a_1.expected.bamstat"},hskip=>3);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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201 <!-- test_cmd($opts,out=>'stat/10.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/10_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/10_map_cigar.sam_s1_a_1.bamstat"=>"stat/10_map_cigar.sam_s1_a_1.expected.bamstat", "stat/10_map_cigar.sam_s1_b_1.bamstat"=>"stat/10_map_cigar.sam_s1_b_1.expected.bamstat"},hskip=>3);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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202 <test>
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203 <param name="input" value="11_target.sam" ftype="sam" />
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204 <conditional name="addref_cond">
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205 <param name="addref_select" value="no" />
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206 </conditional>
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207 <conditional name="cond_region">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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208 <param name="select_region" value="tab"/>
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209 <param name="targetregions" value="11.stats.targets" ftype="tabular" />
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210 </conditional>
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211 <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="4" />
3
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212 </test>
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213 <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix); -->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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214
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215 <test>
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216 <param name="input" value="11_target.bam" ftype="bam" />
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217 <conditional name="addref_cond">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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218 <param name="addref_select" value="no" />
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219 </conditional>
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220 <conditional name="cond_region">
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221 <param name="select_region" value="text"/>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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222 <param name="regions_repeat_0|region" value="ref1:10-24"/>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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223 <param name="regions_repeat_1|region" value="ref1:30-46"/>
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224 <param name="regions_repeat_2|region" value="ref1:39-56"/>
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225 </conditional>
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226 <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="2" />
3
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227 </test>
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228 <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix);
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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229 -->
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230 <test>
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231 <param name="input" value="11_target.sam" ftype="sam" />
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232 <conditional name="addref_cond">
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233 <param name="addref_select" value="no" />
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234 </conditional>
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235 <conditional name="cond_region">
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236 <param name="select_region" value="tab"/>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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237 <param name="targetregions" value="11.stats.targets" ftype="tabular" />
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238 </conditional>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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239 <param name="cov_threshold" value="4" />
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240 <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="4" />
3
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241 </test>
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242 <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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243 <test>
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244 <param name="input" value="11_target.bam" ftype="bam" />
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245 <conditional name="addref_cond">
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246 <param name="addref_select" value="no" />
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247 </conditional>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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248 <conditional name="cond_region">
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249 <param name="select_region" value="text"/>
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250 <param name="regions_repeat_0|region" value="ref1:10-24"/>
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251 <param name="regions_repeat_1|region" value="ref1:30-46"/>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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252 <param name="regions_repeat_2|region" value="ref1:39-56"/>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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253 </conditional>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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254 <param name="cov_threshold" value="4" />
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255 <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="2" />
3
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256 </test>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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257 <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix); -->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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258 <test>
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259 <param name="input" value="12_overlaps.bam" ftype="bam" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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260 <conditional name="addref_cond">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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261 <param name="addref_select" value="no" />
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262 </conditional>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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263 <conditional name="cond_region">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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264 <param name="select_region" value="tab"/>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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265 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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266 </conditional>
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267 <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="4" />
3
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268 </test>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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269 <!-- test_cmd($opts,out=>'stat/12.3reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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270 <test>
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271 <param name="input" value="12_overlaps.bam" ftype="bam" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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272 <conditional name="addref_cond">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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273 <param name="addref_select" value="no" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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274 </conditional>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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275 <conditional name="cond_region">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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276 <param name="select_region" value="tab"/>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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277 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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278 </conditional>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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279 <param name="remove_overlaps" value="-p"/>
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280 <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
3
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281 </test>
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282 <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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283 <test>
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284 <param name="input" value="12_overlaps.bam" ftype="bam" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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285 <conditional name="addref_cond">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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286 <param name="addref_select" value="no" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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287 </conditional>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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diff changeset
288 <conditional name="cond_region">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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289 <param name="select_region" value="tab"/>
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290 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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291 </conditional>
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292 <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="4" />
3
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293 </test>
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294 <!-- test_cmd($opts,out=>'stat/12.2reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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295 <test>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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296 <param name="input" value="12_overlaps.bam" ftype="bam" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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297 <conditional name="addref_cond">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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298 <param name="addref_select" value="no" />
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299 </conditional>
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300 <conditional name="cond_region">
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301 <param name="select_region" value="tab"/>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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302 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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303 </conditional>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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304 <param name="remove_overlaps" value="-p"/>
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305 <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
3
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306 </test>
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307 <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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308 <test>
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309 <param name="input" value="samtools_stats_input.bam" ftype="bam" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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310 <conditional name="addref_cond">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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311 <param name="addref_select" value="history" />
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312 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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313 </conditional>
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314 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="2" />
0
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315 </test>
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316 <test>
3
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317 <param name="input" value="samtools_stats_input.bam" ftype="bam" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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318 <conditional name="addref_cond">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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319 <param name="addref_select" value="history" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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320 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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321 </conditional>
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322 <conditional name="split_output_cond">
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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323 <param name="split_output_selector" value="yes" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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324 <param name="generate_tables" value="SN,MPC,GCC" />
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325 </conditional>
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326 <output_collection name="output_collection" type="list">
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327 <element name="ACGT content per cycle" ftype="tabular" file="samtools_stats_out1__gcc.tab"/>
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328 <element name="Mismatches per cycle and quality" ftype="tabular" file="samtools_stats_out1__mpc.tab" />
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329 <element name="Summary Numbers" ftype="tabular" file="samtools_stats_out1__sn.tab" />
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330 </output_collection>
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331 </test>
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332 <!-- test filtering by read group -->
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333 <!-- <test>
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334 <param name="input" value="11_target.sam" ftype="sam" />
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335 <conditional name="addref_cond">
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336 <param name="addref_select" value="no" />
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337 </conditional>
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338 <param name="read_group" value="grp1" />
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339 <output name="output" file="11.stats.read_groups.expected" ftype="tabular" lines_diff="2" />
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340 <assert_command>
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341 <has_text text="-I 'grp1'"/>
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342 </assert_command>
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343 </test> -->
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344 </tests>
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345 <help><![CDATA[
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346 **What it does**
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347
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348 This tool runs the ``samtools stats`` command.
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349
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350 The results of samtools stats can be visualized with MultiQC (for this the default of a single output file needs to be selected).
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351 ]]></help>
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352 <expand macro="citations"/>
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353 </tool>