Mercurial > repos > devteam > samtools_bedcov

annotate samtools_bedcov.xml @ 4:46c6639921f1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:11:43 +0000
parents 9149ad20699a
children 6856f8a01905
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46c6639921f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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1 <tool id="samtools_bedcov" name="Samtools bedcov" version="2.0.3" profile="@PROFILE@">
2
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2 <description>calculate read depth for a set of genomic intervals</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 @PREPARE_IDX_MULTIPLE@
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11
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12 samtools bedcov
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13 #if $mapq:
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14 -Q $mapq
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15 #end if
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16 $countdel
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17 #set $filter = $additional_options.required_flags
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18 @FLAGS@
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19 -g $flags
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20 #set $filter = $additional_options.skipped_flags
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21 @FLAGS@
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22 -G $flags
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23 #if $depth_thresh:
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24 -d $depth_thresh
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25 #end if
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26 '${input_bed}'
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27 #for $i in range(len($input_bams)):
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28 '${i}'
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29 #end for
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30 > '${output}'
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31 ]]></command>
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32 <inputs>
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33 <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
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34 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
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35 <param name="mapq" argument="-Q" type="integer" value="" optional="true" label="Minimum MAPQ" help="Only count reads with mapping quality greater than this value" />
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36 <param name="countdel" argument="-j" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Exclude deletions and ref skips" help=" Do not include deletions (D) and ref skips (N) in bedcov computation" />
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37 <param name="depth_thresh" argument="-d" type="integer" value="" min="0" optional="true" label="Depth threshold" help="Number of reference bases with coverage above and including this value will be displayed in a separate column." />
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38
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39 <section name="additional_options" title="Additional Filter Options">
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40 <param name="required_flags" argument="-g" type="select" multiple="True" label="Require that these flags are set.">
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41 <expand macro="flag_options" />
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42 </param>
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43
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44 <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).">
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45 <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
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46 </param>
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47 </section>
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48 </inputs>
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49 <outputs>
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50 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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51 </outputs>
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52 <tests>
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53 <!-- 1) -->
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54 <test>
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55 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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56 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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57 <output name="output" file="samtools_bedcov_out1.tab" />
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58 </test>
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59 <!-- 2) -->
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60 <test>
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61 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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62 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
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63 <output name="output" file="samtools_bedcov_out2.tab" />
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64 </test>
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65 <!-- 3) -->
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66 <test>
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67 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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68 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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69 <param name="mapq" value="40"/>
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70 <output name="output" file="samtools_bedcov_out1.tab" />
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71 </test>
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72 <!-- 4) -->
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73 <test>
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74 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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75 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
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76 <param name="countdel" value="-j" />
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77 <output name="output" file="samtools_bedcov_out2.tab" />
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78 </test>
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79 <!-- 5) Testing argument -g -->
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80 <test>
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81 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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82 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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83 <param name="required_flags" value="2,16,64" />
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84 <output name="output" file="samtools_depth_out5.tab" />
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85 </test>
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86 <!-- 6) Testing argument -G -->
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87 <test>
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88 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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89 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
46c6639921f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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90 <param name="skipped_flags" value="2,16,64" />
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91 <output name="output" file="samtools_depth_out6.tab" />
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92 </test>
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93 <!-- 7) Testing depth threshold -d -->
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94 <test>
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95 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
46c6639921f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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96 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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97 <param name="depth_thresh" value="10" />
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98 <output name="output" file="samtools_bedcov_out7.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 Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::
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105
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106 samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
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107 </help>
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108 <expand macro="citations"/>
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109 </tool>