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1 <tool id="samtools_slice_bam" name="Slice" version="2.0">
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2 <description>BAM by genomic regions</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 <!-- <code file="samtools_slice_options.py"/> -->
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7 <expand macro="requirements"></expand>
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8 <expand macro="stdio"></expand>
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9 <expand macro="version_command"></expand>
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10 <command>
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11 <![CDATA[
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12 ln -s "${input_bam}" temp_input.bam &&
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13 ln -s "${input_bam.metadata.bam_index}" temp_input.bam.bai &&
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14
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15 #if str($slice_method.slice_method_selector) == "bed":
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16
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17 samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam &&
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18
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19 #elif str($slice_method.slice_method_selector) == "chr":
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20
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21 samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
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22 ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } &&
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23
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24 #elif str($slice_method.slice_method_selector) == "man":
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25
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26 samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
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27
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28 #for $region in $slice_method.regions:
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29 "${region.chrom}:${region.start}-${region.end}"
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30 #end for
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31
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32 &&
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33
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34 #end if
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35
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36 samtools sort -O bam -T sorted -@ \${GALAXY_SLOTS:-1} -o "${output_bam}" unsorted_output.bam
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37 ]]>
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38 </command>
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39 <inputs>
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40 <param name="input_bam" format="bam" label="Select BAM dataset to slice" type="data" />
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41 <conditional name="slice_method">
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42 <param name="slice_method_selector" type="select" label="How do you want to slice your dataset?">
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43 <option value="bed">using a list of intervals from a BED dataset</option>
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44 <option value="chr">by chromosomes/contigs present in the BAM dataset</option>
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45 <option value="man">by chromosomes/contigs and coordinates</option>
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46 </param>
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47 <when value="bed">
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48 <param format="bed" label="BED file" name="input_interval" type="data" help="BED datasets can be obtained using "Get Data -> UCSC Main" datasource."/>
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49 </when>
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50 <when value="chr">
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51 <param name="refs" type="select" optional="False" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Click and type in the box above to see options. You can select multiple entries. If "No options available" is displayed, you need to re-detect metadata on the input dataset. See help section below.">
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52
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53 <!-- The options tagset below extracts reference names from bam file metadata -->
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54 <!-- This will not work with bed files with old style metadata. However this -->
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55 <!-- Can be easily fixed by re-deceting metadata on a bam dataset by clicking -->
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56 <!-- The pencil icon and settind datatype to "bam" -->
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57 <!-- This change has been commited in the following pull request: -->
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58 <!-- https://github.com/galaxyproject/galaxy/pull/107 -->
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59
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60 <options>
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61 <filter type="data_meta" ref="input_bam" key="reference_names" />
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62 </options>
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63 </param>
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64 </when>
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65 <when value="man">
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66 <repeat name="regions" title="Regions" min="1">
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67 <param name="chrom" type="select" optional="False" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Select chromosome/contig from the list. If "No options available" is displayed, you need to re-detect metadata on the input dataset. See help section below.">
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68
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69 <!-- See comments above -->
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70
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71 <options>
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72 <filter type="data_meta" ref="input_bam" key="reference_names" />
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73 </options>
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74 </param>
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75 <param name="start" type="integer" min="1" value="0" label="Enter START coordinate (1-based)"/>
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76 <param name="end" type="integer" min="1" value="100" label="Enter END coordinate"/>
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77 </repeat>
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78
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79
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80 </when>
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81 </conditional>
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82
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83 </inputs>
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84 <outputs>
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85 <data format="bam" name="output_bam" />
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86 </outputs>
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87 <tests>
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88 <test>
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89 <param ftype="bam" name="input_bam" value="bam-slice-input.bam" />
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90 <param name="slice_method_selector" value="bed"/>
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91 <param ftype="bed" name="input_interval" value="bam-slice.bed" />
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92 <output file="bam-slice-test1.bam" ftype="bam" name="output_bam" />
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93 </test>
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94 <test>
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95 <param ftype="bam" name="input_bam" value="bam-slice-input.bam" />
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96 <param name="slice_method_selector" value="chr"/>
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97 <param name="refs" value="chrM" />
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98 <output file="bam-slice-test2.bam" ftype="bam" name="output_bam" />
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99 </test>
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100 <test>
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101 <param ftype="bam" name="input_bam" value="bam-slice-input.bam" />
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102 <param name="slice_method_selector" value="man"/>
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103 <param name="chrom" value="chrM" />
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104 <param name="start" value="1" />
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105 <param name="end" value="1000" />
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106 <output file="bam-slice-test3.bam" ftype="bam" name="output_bam" />
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107 </test>
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108 </tests>
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109 <help>
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110 <![CDATA[
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111
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112 **What it does**
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113
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114 Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates. BED datasets can be obtained from **Get Data -> UCSC Main**.
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115
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116 This tool is based on ``samtools view`` command.
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117
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118 @no-chrom-options@
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119
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120 ]]>
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121 </help>
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122 <expand macro="citations"></expand>
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123 </tool>
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