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annotate samtools_stats.xml @ 6:47035d167365 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 558d30ff047fe2f62658e8b57e27ebe8db77ede1"
author iuc
date Fri, 06 Sep 2019 11:23:05 -0400
parents 5a08c09b9311
children 145f6d74ff5e
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47035d167365 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 558d30ff047fe2f62658e8b57e27ebe8db77ede1"
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1 <tool id="samtools_stats" name="Samtools stats" version="2.0.2+galaxy2">
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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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47035d167365 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 558d30ff047fe2f62658e8b57e27ebe8db77ede1"
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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 #if $filter_by_flags.require_flags:
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20 #set $filter = $filter_by_flags.require_flags
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21 @FLAGS@
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22 --required-flag $flags
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23 #end if
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24 #if $filter_by_flags.exclude_flags:
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25 #set $filter = $filter_by_flags.exclude_flags
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26 @FLAGS@
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27 --filtering-flag $flags
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28 #end if
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29 #end if
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30 #if str($gc_depth):
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31 --GC-depth ${gc_depth}
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32 #end if
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33 #if str($insert_size):
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34 --insert-size ${insert_size}
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35 #end if
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36 ## The code below is commented out because using -I/--id options causes
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37 ## in samtools up to 1.9 the following exception
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38 ## Samtools-htslib: init_group_id() header parsing not yet implemented
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39 ##if str($read_group) != "":
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40 ## -I "${read_group}"
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41 ##end if
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42 #if str($read_length):
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43 --read-length ${read_length}
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44 #end if
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45 #if str($most_inserts):
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46 --most-inserts ${most_inserts}
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47 #end if
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48 #if str($trim_quality):
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49 --trim-quality ${trim_quality}
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50 #end if
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51
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52 #if $reffa != None:
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53 --ref-seq '$reffa'
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54 #end if
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55 ## TODO currently not implemented in Galaxy
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56 ## 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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57 ## needs some discover data sets action...
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58 ## -P, --split-prefix STR
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59 ## -S, --split TAG
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60 $sparse
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61 @REGIONS_FILE@
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62 $remove_overlaps
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63 #if str($cov_threshold):
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64 -g $cov_threshold
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65 #end if
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66 -@ \$addthreads
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67 infile
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68 @REGIONS_MANUAL@
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69 > '$output'
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70
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71 #if $split_output_cond.split_output_selector == "yes":
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72 #set outputs_to_split = str($split_output_cond.generate_tables).split(',')
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73 && mkdir split
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74 #for s in str($split_output_cond.generate_tables).split(','):
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75 && name=`cat '$output' | grep '\^$s' | cut -d'.' -f 1 | sed 's/^# //'`
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76 && awk '/\^/{out=0} /\^$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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77 #end for
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78 #end if
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79 ]]></command>
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80 <inputs>
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81 <param name="input" type="data" format="sam,bam,cram" label="BAM file" />
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82 <conditional name="coverage_cond">
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83 <param name="coverage_select" type="select" label="Set coverage distribution">
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84 <option value="no" selected="True">No</option>
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85 <option value="yes">Yes</option>
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86 </param>
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87 <when value="no"/>
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88 <when value="yes">
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89 <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="Minimum coverage" />
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90 <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="Maximum coverage" />
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91 <param name="coverage_step" type="integer" value="1" label="Coverage step" help="Step value for coverage" />
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92 </when>
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93 </conditional>
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94 <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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95 <conditional name="split_output_cond">
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96 <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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97 <option value="no" selected="True">One single summary file</option>
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98 <option value="yes">Separate datasets for each statistic</option>
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99 </param>
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100 <when value="no" />
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101 <when value="yes">
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102 <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Desired output files">
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103 <option value="SN">Summary numbers</option>
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104 <option value="FFQ">First Fragment Qualities</option>
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105 <option value="LFQ">Last Fragment Qualities</option>
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106 <option value="MPC">Mismatches per cycle</option>
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107 <option value="GCF">GC Content of first fragments</option>
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108 <option value="GCL">GC Content of last fragments</option>
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109 <option value="GCC">ACGT content per cycle</option>
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110 <option value="FBC">ACGT content per cycle for first fragments</option>
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111 <option value="LBC">ACGT content per cycle for last fragments</option>
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112 <option value="IS">Insert sizes</option>
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113 <option value="RL">Read lengths</option>
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114 <option value="FRL">Read lengths for first fragments</option>
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115 <option value="LRL">Read lengths for last fragments</option>
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116 <option value="ID">Indel distribution</option>
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117 <option value="IC">Indels per cycle</option>
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118 <option value="COV">Coverage distribution</option>
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119 <option value="GCD">GC depth</option>
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120 </param>
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121 </when>
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122 </conditional>
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123 <conditional name="filter_by_flags">
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124 <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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125 <option value="nofilter" selected="True">Do not filter</option>
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126 <option value="filter">Filter by flags to exclude or require</option>
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127 </param>
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128 <when value="filter">
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129 <param name="require_flags" argument="-f" type="select" display="checkboxes" multiple="True" label="Require">
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130 <expand macro="flag_options" />
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131 </param>
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132 <param name="exclude_flags" argument="-F" type="select" display="checkboxes" multiple="True" label="Exclude">
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133 <expand macro="flag_options" />
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134 </param>
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135 </when>
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136 <when value="nofilter" />
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137
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138 </conditional>
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139 <!-- 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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140 <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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141 <param name="insert_size" argument="--insert-size" type="integer" optional="True" label="Maximum insert size" help="default=8000" />
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142 <!--
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143 The -I option of samtools stats returns the following message up to version 1.9:
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144 Samtools-htslib: init_group_id() header parsing not yet implemented
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145 Because of this the section below is commented out until this stats bug is fixed
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146 <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" >
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147 <options>
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148 <filter type="data_meta" ref="input" key="read_groups" />
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149 </options>
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150 </param>
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151 -->
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152 <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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153 <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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154 <param name="trim_quality" argument="--trim-quality" type="integer" optional="true" label="BWA trim parameter" help="default=0" />
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155
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156 <conditional name="addref_cond">
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157 <param name="addref_select" type="select" label="Use a reference sequence" help="Required for GC-depth and mismatches-per-cycle calculation">
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158 <option value="no">No</option>
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159 <option value="cached">Locally cached</option>
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160 <option value="history">History</option>
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161 </param>
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162 <when value="no"/>
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163 <when value="cached">
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164 <param name="ref" type="select" label="Using genome">
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165 <options from_data_table="fasta_indexes">
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166 <filter type="data_meta" ref="input" key="dbkey" column="1" />
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167 </options>
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168 </param>
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169 </when>
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170 <when value="history">
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171 <param name="ref" type="data" format="fasta" label="Using file" />
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172 </when>
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173 </conditional>
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174 <!-- unfortunately -t takes tabular and not bed like view (otherwise a macro might have simplified this) -->
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175
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176 <expand macro="regions_macro"/>
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177
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178 <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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179 <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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180 <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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181 </inputs>
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182
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183 <outputs>
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184 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
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185 <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="true" assign_primary_output="true"/>
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186 <filter>split_output_cond['split_output_selector'] == 'no'</filter>
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187 </data>
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188 <collection name="output_collection" type="list" label="${tool.name} on ${on_string}">
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189 <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="false"/>
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190 <filter>split_output_cond['split_output_selector'] == 'yes'</filter>
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191 </collection>
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192 </outputs>
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193 <tests>
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194 <!-- https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2402 -->
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195 <test>
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196 <param name="input" value="1_map_cigar.sam" ftype="sam" />
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197 <conditional name="addref_cond">
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198 <param name="addref_select" value="history" />
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199 <param name="ref" value="test.fa" ftype="fasta" />
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200 </conditional>
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201 <output name="output" file="1.stats.expected" ftype="tabular" lines_diff="3" />
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202 </test>
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203 <!-- test_cmd($opts,out=>'stat/1.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix);-->
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204 <test>
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205 <param name="input" value="2_equal_cigar_full_seq.sam" ftype="sam" />
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206 <conditional name="addref_cond">
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207 <param name="addref_select" value="history" />
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208 <param name="ref" value="test.fa" ftype="fasta" />
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209 </conditional>
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210 <output name="output" file="2.stats.expected" ftype="tabular" lines_diff="3" />
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211 </test>
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212 <!-- test_cmd($opts,out=>'stat/2.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/2_equal_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
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213 <!-- test_cmd($opts,out=>'stat/3.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/3_map_cigar_equal_seq.sam | tail -n+4", exp_fix=>$efix);-->
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214 <!-- test_cmd($opts,out=>'stat/4.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/4_X_cigar_full_seq.sam | tail -n+4", exp_fix=>$efix);-->
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215 <!-- test_cmd($opts,out=>'stat/5.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
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216 <test>
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217 <param name="input" value="5_insert_cigar.sam" ftype="sam" />
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218 <param name="insert_size" value="0" />
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219 <conditional name="addref_cond">
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220 <param name="addref_select" value="history" />
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221 <param name="ref" value="test.fa" ftype="fasta" />
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222 </conditional>
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223 <output name="output" file="6.stats.expected" ftype="tabular" lines_diff="3" />
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224 </test>
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225 <!-- test_cmd($opts,out=>'stat/6.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa -i 0 $$opts{path}/stat/5_insert_cigar.sam | tail -n+4", exp_fix=>$efix); -->
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226 <!-- test_cmd($opts,out=>'stat/7.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/7_supp.sam | tail -n+4", exp_fix=>$efix); -->
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227 <!-- test_cmd($opts,out=>'stat/8.stats.expected',cmd=>"$$opts{bin}/samtools stats -r $$opts{path}/stat/test.fa $$opts{path}/stat/8_secondary.sam | tail -n+4", exp_fix=>$efix);-->
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228 <!-- test_cmd($opts,out=>'stat/9.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/1_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/1_map_cigar.sam_s1_a_1.bamstat"=>"stat/1_map_cigar.sam_s1_a_1.expected.bamstat"},hskip=>3);-->
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229 <!-- test_cmd($opts,out=>'stat/10.stats.expected',cmd=>"$$opts{bin}/samtools stats -S RG -r $$opts{path}/stat/test.fa $$opts{path}/stat/10_map_cigar.sam | tail -n+4", exp_fix=>$efix,out_map=>{"stat/10_map_cigar.sam_s1_a_1.bamstat"=>"stat/10_map_cigar.sam_s1_a_1.expected.bamstat", "stat/10_map_cigar.sam_s1_b_1.bamstat"=>"stat/10_map_cigar.sam_s1_b_1.expected.bamstat"},hskip=>3);-->
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230 <test>
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231 <param name="input" value="11_target.sam" ftype="sam" />
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232 <conditional name="addref_cond">
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233 <param name="addref_select" value="no" />
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234 </conditional>
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235 <conditional name="cond_region">
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236 <param name="select_region" value="tab"/>
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237 <param name="targetregions" value="11.stats.targets" ftype="tabular" />
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238 </conditional>
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239 <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="3" />
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240 </test>
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241 <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix); -->
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242
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243 <test>
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244 <param name="input" value="11_target.bam" ftype="bam" />
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245 <conditional name="addref_cond">
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246 <param name="addref_select" value="no" />
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247 </conditional>
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248 <conditional name="cond_region">
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249 <param name="select_region" value="text"/>
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250 <param name="regions_repeat_0|region" value="ref1:10-24"/>
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251 <param name="regions_repeat_1|region" value="ref1:30-46"/>
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252 <param name="regions_repeat_2|region" value="ref1:39-56"/>
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253 </conditional>
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254 <output name="output" file="11.stats.expected" ftype="tabular" lines_diff="3" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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255 </test>
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256 <!-- test_cmd($opts,out=>'stat/11.stats.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4", exp_fix=>$efix);
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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257 -->
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258 <test>
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259 <param name="input" value="11_target.sam" ftype="sam" />
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260 <conditional name="addref_cond">
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261 <param name="addref_select" value="no" />
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262 </conditional>
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263 <conditional name="cond_region">
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264 <param name="select_region" value="tab"/>
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265 <param name="targetregions" value="11.stats.targets" ftype="tabular" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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266 </conditional>
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267 <param name="cov_threshold" value="4" />
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268 <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="3" />
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269 </test>
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270 <!-- test_cmd($opts,out=>'stat/11.stats.g4.expected',cmd=>"$$opts{bin}/samtools stats -g 4 -t $$opts{path}/stat/11.stats.targets $$opts{path}/stat/11_target.sam | tail -n+4", exp_fix=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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271 <test>
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272 <param name="input" value="11_target.bam" ftype="bam" />
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273 <conditional name="addref_cond">
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274 <param name="addref_select" value="no" />
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275 </conditional>
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276 <conditional name="cond_region">
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277 <param name="select_region" value="text"/>
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278 <param name="regions_repeat_0|region" value="ref1:10-24"/>
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279 <param name="regions_repeat_1|region" value="ref1:30-46"/>
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280 <param name="regions_repeat_2|region" value="ref1:39-56"/>
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281 </conditional>
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282 <param name="cov_threshold" value="4" />
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283 <output name="output" file="11.stats.g4.expected" ftype="tabular" lines_diff="3" />
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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284 </test>
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285 <!-- test_cmd($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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286 <test>
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287 <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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288 <conditional name="addref_cond">
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289 <param name="addref_select" value="no" />
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290 </conditional>
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291 <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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292 <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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293 <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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294 </conditional>
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295 <output name="output" file="12.3reads.overlap.expected" ftype="tabular" lines_diff="3" />
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296 </test>
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297 <!-- 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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298 <test>
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299 <param name="input" value="12_overlaps.bam" ftype="bam" />
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300 <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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301 <param name="addref_select" value="no" />
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302 </conditional>
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303 <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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304 <param name="select_region" value="tab"/>
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305 <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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306 </conditional>
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307 <param name="remove_overlaps" value="-p"/>
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308 <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="3" />
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309 </test>
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310 <!-- 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=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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311 <test>
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312 <param name="input" value="12_overlaps.bam" ftype="bam" />
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313 <conditional name="addref_cond">
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314 <param name="addref_select" value="no" />
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315 </conditional>
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316 <conditional name="cond_region">
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317 <param name="select_region" value="tab"/>
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318 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
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319 </conditional>
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320 <output name="output" file="12.2reads.overlap.expected" ftype="tabular" lines_diff="3" />
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321 </test>
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322 <!-- test_cmd($opts,out=>'stat/12.2reads.overlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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323 <test>
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324 <param name="input" value="12_overlaps.bam" ftype="bam" />
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325 <conditional name="addref_cond">
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326 <param name="addref_select" value="no" />
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327 </conditional>
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328 <conditional name="cond_region">
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329 <param name="select_region" value="tab"/>
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330 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
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331 </conditional>
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332 <param name="remove_overlaps" value="-p"/>
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333 <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="3" />
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334 </test>
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335 <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->
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336 <test>
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337 <param name="input" value="samtools_stats_input.bam" ftype="bam" />
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338 <conditional name="addref_cond">
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339 <param name="addref_select" value="history" />
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340 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
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341 </conditional>
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342 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="2" />
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343 </test>
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344 <test>
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345 <param name="input" value="samtools_stats_input.bam" ftype="bam" />
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346 <conditional name="addref_cond">
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347 <param name="addref_select" value="history" />
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348 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
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349 </conditional>
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350 <conditional name="split_output_cond">
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351 <param name="split_output_selector" value="yes" />
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352 <param name="generate_tables" value="SN,MPC,GCC" />
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353 </conditional>
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354 <output_collection name="output_collection" type="list">
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355 <element name="ACGT content per cycle" ftype="tabular" file="samtools_stats_out1__gcc.tab"/>
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356 <element name="Mismatches per cycle and quality" ftype="tabular" file="samtools_stats_out1__mpc.tab" />
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357 <element name="Summary Numbers" ftype="tabular" file="samtools_stats_out1__sn.tab" />
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358 </output_collection>
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359 </test>
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360 </tests>
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361 <help><![CDATA[
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362 **What it does**
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363
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364 This tool runs the ``samtools stats`` command.
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365
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366 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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367 ]]></help>
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368 <expand macro="citations"/>
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369 </tool>
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370