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1 <tool name="ReorderSam" id="picard_ReorderSam" version="1.135">
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2 <description>reorder reads to match ordering in reference sequences</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command>
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8 @java_options@
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9 #set $picard_dict = "localref.dict"
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10 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
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11
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12 ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
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13
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14 #if str( $reference_source.reference_source_selector ) == "history":
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15
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16 java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
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17 QUIET=true
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18 VERBOSITY=ERROR
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19
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20 &&
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21
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22 #else:
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23
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24 #set $ref_fasta = str( $reference_source.ref_file.fields.path )
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25
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26 #end if
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27
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28 java -jar \$JAVA_JAR_PATH/picard.jar
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29 ReorderSam
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30 INPUT="${inputFile}"
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31 OUTPUT="${outFile}"
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32 REFERENCE="${ref_fasta}"
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33 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
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34 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"
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35
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36 VALIDATION_STRINGENCY="${validation_stringency}"
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37 QUIET=true
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38 VERBOSITY=ERROR
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39
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40 </command>
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41
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42 <inputs>
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43
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44 <conditional name="reference_source">
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45 <param name="reference_source_selector" type="select" label="Load reference genome from">
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46 <option value="cached">Local cache</option>
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47 <option value="history">History</option>
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48 </param>
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49 <when value="cached">
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50 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
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51 <options from_data_table="picard_indexes">
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52 <filter type="sort_by" column="2" />
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53 <validator type="no_options" message="No indexes are available" />
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54 </options>
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55 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
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56 </param>
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57 </when>
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58 <when value="history">
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59 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
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60 </when>
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61 </conditional>
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62
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63 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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64 <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/>
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65 <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/>
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66 <expand macro="VS" />
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67
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68 </inputs>
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69 <outputs>
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70 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
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71 </outputs>
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72 <tests>
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73 <test>
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74 <param name="reference_source_selector" value="history" />
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75 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" />
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76 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
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77 <param name="allow_incomplete_dict_concordance" value="false"/>
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78 <param name="allow_contig_length_discordance" value="false"/>
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79 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="2"/>
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80 </test>
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81 </tests>
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82
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83 <stdio>
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84 <exit_code range="1:" level="fatal"/>
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85 </stdio>
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86
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87 <help>
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88
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89 .. class:: infomark
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90
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91 **Purpose**
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92
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93 ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped.
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94
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95 @dataset_collections@
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96
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97 ----
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98
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99 .. class:: warningmark
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100
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101 Not to be confused with **SortSam**.
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102
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103 @description@
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104
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105 ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean
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106 S=Boolean If true, then allows only a partial overlap of the BAM contigs with the new reference
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107 sequence contigs. By default, this tool requires a corresponding contig in the new
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108 reference for each read contig Default value: false. Possible values: {true, false}
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109
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110 ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean
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111 U=Boolean If true, then permits mapping from a read contig to a new reference contig with the same
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112 name but a different length. Highly dangerous, only use if you know what you are doing.
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113 Default value: false. Possible values: {true, false}
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114
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115 @more_info@
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116 </help>
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117 </tool>
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118
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119
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120
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121
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125
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126
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