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annotate samtools_depth.xml @ 2:6bb273ed8785 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 15:59:58 +0000
parents b0cebea6e9df
children ad06afad0c44
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6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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1 <tool id="samtools_depth" name="Samtools depth" version="@TOOL_VERSION@" profile="@PROFILE@">
0
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2 <description>compute the depth at each position or region</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 ## create symlinks to bams and index files (0,..., n-1 + 0.[bai|crai],...,n-1.[bai|crai] )
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11 @PREPARE_IDX_MULTIPLE@
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12
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13 samtools depth
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14 $all
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15 #if $cond_region.select_region == 'bed':
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16 -b '$cond_region.input_bed'
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17 #else if $cond_region.select_region == 'text':
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18 -r $cond_region.region
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19 #end if
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20 #if str($minlength) != '':
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21 -l $minlength
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22 #end if
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23 #if str($maxdepth) != '':
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24 -m $maxdepth
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25 #end if
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26 #if str($basequality) != '':
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27 -q $basequality
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28 #end if
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29 #if str($mapquality) != '':
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30 -Q $mapquality
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31 #end if
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32 #for $i in range(len( $input_bams )):
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33 ${i}
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34 #end for
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35 #set $filter = $additional_options.required_flags
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36 @FLAGS@
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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37 -g $flags
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38 #set $filter = $additional_options.skipped_flags
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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39 @FLAGS@
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40 -G $flags
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41 $additional_options.deletions
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42 $additional_options.single_read
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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43 $output_options.header
0
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44 > '${output}'
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45 ]]></command>
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46 <inputs>
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47 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
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48 <conditional name="cond_region">
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49 <param name="select_region" type="select" label="Filter by regions">
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50 <option value="no" selected="True">No</option>
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51 <option value="text">Manualy specify a region</option>
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52 <option value="bed">Regions from BED file</option>
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53 </param>
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54 <when value="no"/>
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55 <when value="text">
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56 <param name="region" type="text" optional="false" argument="-r" label="Only report depth in a specified region" help="Format is CHROMOSOME:FROM-TO"/>
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57 </when>
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58 <when value="bed">
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59 <param name="input_bed" type="data" format="bed" argument="-b" label="Genomic intervals (in BED format)" help="Compute depth at list of positions or regions in specified BED FILE." />
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60 </when>
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61 </conditional>
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62
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63 <param name="all" type="select" argument="-a/-aa" label="Output all positions" help="Note that if the all option (-a) is used in conjunction with a BED file it may sometimes operate as if -aa was specified if the reference sequence has coverage outside of the region specified in the BED file.">
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64 <option value="" selected="True">Default</option>
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65 <option value="-a">Output all positions (including those with zero depth) (-a)</option>
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66 <option value="-aa">Output absolutely all positions, including unused reference sequences. (-aa)</option>
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67 </param>
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68 <param name="minlength" type="integer" argument="-l" min="0" optional="true" label="Ignore reads shorter than" />
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69 <param name="maxdepth" type="integer" argument="-m" min="0" optional="true" label="Limits the maximum number of considered alignments starting at any sequence position to INT. Note that, the reported depths values might be larger than INT. If 0, depth is set to the maximum integer value, effectively removing any depth limit. (default = 8000)" />
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70
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71 <param name="basequality" type="integer" argument="-q" min="0" optional="true" label="Only count reads with base quality greater than" />
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72 <param name="mapquality" type="integer" argument="-Q" min="0" optional="true" label="Only count reads with mapping quality greater than" />
2
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6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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74 <section name="additional_options" title="Additional Filter Options">
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75 <param name="required_flags" argument="-g" type="select" multiple="True" label="Require that these flags are set.">
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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76 <expand macro="flag_options" />
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77 </param>
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78
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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79 <param name="skipped_flags" argument="-G" type="select" multiple="True" label="Exclude reads with any of the following flags set (the default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704).">
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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80 <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
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81 </param>
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82
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83 <param name="deletions" type="boolean" argument="-J" truevalue="-J" falsevalue="" checked="false" label="Include reads with deletions in depth computation." />
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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84 <param name="single_read" type="boolean" argument="-s" truevalue="-s" falsevalue="" checked="false" label="For the overlapping section of a read pair, count only the bases of a single read." />
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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85 </section>
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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86
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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87 <section name="output_options" title="Output Options" expanded="true">
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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88 <param name="header" type="boolean" argument="-H" truevalue="-H" falsevalue="" checked="false" label="Print a file header to file." />
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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89 </section>
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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90
0
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91 </inputs>
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92 <outputs>
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93 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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94 </outputs>
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95 <tests>
2
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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96 <!-- 1) -->
0
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97 <test>
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98 <conditional name="cond_region">
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99 <param name="select_region" value="bed"/>
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100 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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101 </conditional>
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102 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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103 <output name="output" file="samtools_depth_out1.tab" />
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104 </test>
2
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105 <!-- 2) -->
0
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106 <test>
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107 <conditional name="cond_region">
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108 <param name="select_region" value="text"/>
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109 <param name="region" value="eboVir3:500-1500" />
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110 </conditional>
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111 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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112 <output name="output" file="samtools_depth_out2.tab" />
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113 </test>
2
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114 <!-- 3) -->
0
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115 <test>
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116 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
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117 <param name="all" value="-a"/>
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118 <output name="output" file="samtools_depth_out3.tab" />
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119 </test>
2
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120 <!-- 4) -->
0
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121 <test>
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122 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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123 <param name="minlength" value="10" />
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124 <!-- Odd thing: I did not expect values > 4 in the output, but there are ... ?
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125 see https://github.com/samtools/samtools/issues/889 -->
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126 <param name="maxdepth" value="4" />
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127 <param name="basequality" value="11" />
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128 <param name="mapquality" value="12" />
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129 <output name="output" file="samtools_depth_out4.tab" />
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130 </test>
2
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131 <!-- 5) Testing argument -H -->
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132 <test>
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133 <conditional name="cond_region">
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134 <param name="select_region" value="bed"/>
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135 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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136 </conditional>
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137 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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138 <param name="header" value="true" />
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139 <output name="output" file="samtools_depth_out5.tab" />
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140 </test>
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141 <!-- 6) Tetsing argument -g -->
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142 <test>
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143 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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144 <param name="required_flags" value="2,16,64" />
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145 <output name="output" file="samtools_depth_out6.tab" />
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146 </test>
6bb273ed8785 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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147 <!-- 7) Tetsing argument -G -->
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148 <test>
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149 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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150 <param name="skipped_flags" value="2,16,64" />
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151 <output name="output" file="samtools_depth_out7.tab" />
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152 </test>
0
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153 </tests>
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154 <help>
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155 **What it does**
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156
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157 Computes the depth at each position or region using the ``samtools depth`` command.
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158
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159 The output is a tabular file, with one line for each base of each reference
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160 with any coverage (bases with no coverage may not appear).
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161
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162 The first column is the reference name, the second column is the reference
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163 position, and then there is one column for each SAM/BAM file giving the
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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164 coverage depth at that position.
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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165 </help>
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166 <expand macro="citations"/>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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167 </tool>