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annotate picard_FilterSamReads.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
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1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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2 <description>include or exclude aligned and unaligned reads and read lists</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 <token name="@WRAPPER_VERSION@">0</token>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 @java_options@
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10 @symlink_element_identifier@
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11 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
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12
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13 picard SortSam
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14 --INPUT '$escaped_element_identifier'
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15 --OUTPUT query_sorted_bam.bam
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16 --SORT_ORDER queryname
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17 --VALIDATION_STRINGENCY LENIENT
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18 --QUIET true
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19 --VERBOSITY ERROR
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20
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21 &&
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22
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23 picard FilterSamReads
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24 --INPUT query_sorted_bam.bam
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25 --FILTER '${filter_type.filter}'
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26
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27 #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):
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28 --READ_LIST_FILE '${filter_type.read_list_file}'
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29 #end if
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30
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31 --OUTPUT '${outFile}'
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32 --SORT_ORDER coordinate
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33 --VALIDATION_STRINGENCY '${validation_stringency}'
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34 --QUIET true
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35 --VERBOSITY ERROR
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36
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37 ]]></command>
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38 <inputs>
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39 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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40 <conditional name="filter_type">
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41 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
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42 <option value="includeAligned">Include aligned</option>
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43 <option value="excludeAligned">Exclude aligned</option>
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44 <option value="includeReadList">Include read list</option>
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45 <option value="excludeReadList">Exclude read list</option>
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46 </param>
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47 <when value="includeAligned"/>
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48 <!-- do nothing -->
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49 <when value="excludeAligned"/>
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50 <!-- do nothing -->
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51 <when value="includeReadList">
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52 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be INCLUDED in the output" help="READ_LIST_FILE"/>
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53 </when>
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54 <when value="excludeReadList">
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55 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/>
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56 </when>
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57 </conditional>
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58 <expand macro="VS"/>
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59 </inputs>
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60 <outputs>
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61 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
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66 <param name="filter" value="includeReadList"/>
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67 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
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68 <param name="validation_stringency" value="LENIENT"/>
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69 <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="4"/>
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70 </test>
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71 <test>
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72 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
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73 <param name="filter" value="excludeReadList"/>
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74 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
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75 <param name="validation_stringency" value="LENIENT"/>
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76 <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/>
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77 </test>
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78 </tests>
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79 <help>
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80
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81 **Purpose**
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82
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83 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
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84
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85 ------
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86
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87 .. class:: warningmark
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88
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89 **Warning on using this tool on BWA-MEM output**
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90
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91 This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts.
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92
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93 @dataset_collections@
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94
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95 @description@
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96
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97 FILTER=Filter Filter. Required. Possible values:
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98 includeAligned [OUTPUT SAM/BAM will contain aligned
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99 reads only. (Note that *both* first and
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100 second of paired reads must be aligned to be included
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101 in the OUTPUT SAM or BAM)],
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102
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103 excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only.
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104 (Note that *both* first and second of pair must be aligned to be
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105 excluded from the OUTPUT SAM or BAM)]
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106
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107 includeReadList [OUTPUT SAM/BAM will contain reads
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108 that are supplied in the READ_LIST_FILE file]
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109
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110 excludeReadList [OUTPUT bam will contain
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111 reads that are *not* supplied in the READ_LIST_FILE file]}
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112
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113 READ_LIST_FILE=File
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114 RLF=File Read List File containing reads that will be included or excluded from the OUTPUT SAM or
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115 BAM file. Default value: null.
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116
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117 @more_info@
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118
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119 </help>
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120 <expand macro="citations"/>
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121 </tool>