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annotate samtools_depth.xml @ 0:11649ca077f8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
author iuc
date Sun, 14 Oct 2018 19:14:37 -0400
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children b0cebea6e9df
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0
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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1 <tool id="samtools_depth" name="Samtools depth" version="1.8">
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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2 <description>compute the depth at each position or region</description>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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3 <macros>
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4 <import>macros.xml</import>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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5 </macros>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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6 <expand macro="requirements"/>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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7 <expand macro="stdio"/>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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8 <expand macro="version_command"/>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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9 <command><![CDATA[
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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10 ## create symlinks to bams and index files (0,..., n-1 + 0.[bai|crai],...,n-1.[bai|crai] )
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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11 @PREPARE_IDX_MULTIPLE@
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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12
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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13 samtools depth
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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14 $all
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15 #if $cond_region.select_region == 'bed':
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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16 -b '$cond_region.input_bed'
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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17 #else if $cond_region.select_region == 'text':
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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18 -r $cond_region.region
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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19 #end if
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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20 #if str($minlength) != '':
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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21 -l $minlength
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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22 #end if
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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23 #if str($maxdepth) != '':
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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24 -m $maxdepth
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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25 #end if
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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26 #if str($basequality) != '':
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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27 -q $basequality
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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28 #end if
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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29 #if str($mapquality) != '':
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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30 -Q $mapquality
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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31 #end if
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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32 #for $i in range(len( $input_bams )):
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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33 ${i}
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34 #end for
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35 > '${output}'
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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36 ]]></command>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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37 <inputs>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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38 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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39 <conditional name="cond_region">
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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40 <param name="select_region" type="select" label="Filter by regions">
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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41 <option value="no" selected="True">No</option>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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42 <option value="text">Manualy specify a region</option>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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43 <option value="bed">Regions from BED file</option>
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44 </param>
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45 <when value="no"/>
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46 <when value="text">
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47 <param name="region" type="text" optional="false" argument="-r" label="Only report depth in a specified region" help="Format is CHROMOSOME:FROM-TO"/>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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48 </when>
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49 <when value="bed">
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50 <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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51 </when>
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52 </conditional>
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53
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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54 <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.">
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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55 <option value="" selected="True">Default</option>
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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56 <option value="-a">Output all positions (including those with zero depth) (-a)</option>
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57 <option value="-aa">Output absolutely all positions, including unused reference sequences. (-aa)</option>
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58 </param>
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59 <param name="minlength" type="integer" argument="-l" min="0" optional="true" label="Ignore reads shorter than" />
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60 <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)" />
11649ca077f8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit b75040a9832972a60a964bc5a35da029d2bcf86c
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61
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62 <param name="basequality" type="integer" argument="-q" min="0" optional="true" label="Only count reads with base quality greater than" />
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63 <param name="mapquality" type="integer" argument="-Q" min="0" optional="true" label="Only count reads with mapping quality greater than" />
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64 </inputs>
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65 <outputs>
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66 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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67 </outputs>
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68 <tests>
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69 <test>
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70 <conditional name="cond_region">
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71 <param name="select_region" value="bed"/>
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72 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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73 </conditional>
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74 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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75 <output name="output" file="samtools_depth_out1.tab" />
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76 </test>
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77 <test>
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78 <conditional name="cond_region">
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79 <param name="select_region" value="text"/>
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80 <param name="region" value="eboVir3:500-1500" />
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81 </conditional>
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82 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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83 <output name="output" file="samtools_depth_out2.tab" />
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84 </test>
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85 <test>
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86 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
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87 <param name="all" value="-a"/>
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88 <output name="output" file="samtools_depth_out3.tab" />
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89 </test>
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90 <test>
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91 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
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92 <param name="minlength" value="10" />
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93 <!-- Odd thing: I did not expect values > 4 in the output, but there are ... ?
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94 see https://github.com/samtools/samtools/issues/889 -->
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95 <param name="maxdepth" value="4" />
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96 <param name="basequality" value="11" />
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97 <param name="mapquality" value="12" />
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98 <output name="output" file="samtools_depth_out4.tab" />
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99 </test>
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100 </tests>
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101 <help>
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102 **What it does**
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103
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104 Computes the depth at each position or region using the ``samtools depth`` command.
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105
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106 The output is a tabular file, with one line for each base of each reference
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107 with any coverage (bases with no coverage may not appear).
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108
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109 The first column is the reference name, the second column is the reference
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110 position, and then there is one column for each SAM/BAM file giving the
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111 coverage depth at that position.
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112 </help>
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113 <expand macro="citations"/>
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114 </tool>