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1 <tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0">
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2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
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3 <command interpreter="python">
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4 picard_wrapper.py
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5 --input=$inputFile
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6 #if $source.indexSource == "built-in"
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7 --ref="${source.ref.fields.path}"
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8 #else
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9 --ref-file=$refFile
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10 --species-name=$source.speciesName
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11 --build-name=$source.buildName
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12 --trunc-names=$source.truncateSeqNames
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13 #end if
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14 --allow-inc-dict-concord=$allowIncDictConcord
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15 --allow-contig-len-discord=$allowContigLenDiscord
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16 --output-format=$outputFormat
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17 --output=$outFile
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18 --tmpdir "${__new_file_path__}"
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19 -j "\$JAVA_JAR_PATH/ReorderSam.jar"
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20 </command>
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21 <inputs>
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22 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"
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23 help="If empty, upload or import a SAM/BAM dataset." />
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24 <conditional name="source">
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25 <param name="indexSource" type="select" label="Select Reference Genome" help="This tool will re-order SAM/BAM in the same order as reference selected below.">
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26 <option value="built-in">Locally cached</option>
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27 <option value="history">History</option>
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28 </param>
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29 <when value="built-in">
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30 <param name="ref" type="select" label="Select a reference genome">
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31 <options from_data_table="picard_indexes" />
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32 </param>
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33 </when>
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34 <when value="history">
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35 <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
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36 <param name="speciesName" type="text" value="" label="Species name" />
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37 <param name="buildName" type="text" value="" label="Build name" />
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38 <param name="truncateSeqNames" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Truncate sequence names after first whitespace" />
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39 </when>
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40 </conditional>
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41 <param name="allowIncDictConcord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow incomplete dict concordance?" help="Allows a partial overlap of the BAM contigs with the new reference sequence contigs." />
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42 <param name="allowContigLenDiscord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow contig length discordance?" help="This is dangerous--don't check it unless you know exactly what you're doing!" />
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43 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
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44 </inputs>
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45 <outputs>
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46 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: reordered ${outputFormat}">
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47 <change_format>
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48 <when input="outputFormat" value="sam" format="sam" />
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49 </change_format>
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50 </data>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <!-- Commands:
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55 cp test-data/phiX.fasta .
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56 samtools faidx phiX.fasta
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57 java -jar CreateSequenceDictionary.jar R=phiX.fasta O=phiX.dict URI=phiX.fasta TRUNCATE_NAMES_AT_WHITESPACE=false SPECIES=phiX174
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58 java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input1.bam O=picard_RS_output1.bam REFERENCE=phiX.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
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59 -->
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60 <param name="inputFile" value="picard_RS_input1.bam" />
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61 <param name="indexSource" value="history" />
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62 <param name="refFile" value="phiX.fasta" />
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63 <param name="speciesName" value="phiX174" />
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64 <param name="buildName" value="" />
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65 <param name="truncateSeqNames" value="false" />
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66 <param name="allowIncDictConcord" value="false" />
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67 <param name="allowContigLenDiscord" value="false" />
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68 <param name="outputFormat" value="True" />
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69 <output name="outFile" file="picard_RS_output1.bam" ftype="bam" lines_diff="4" compare="contains" />
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70 </test>
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71 <test>
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72 <!-- Command:
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73 java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input2.sam O=picard_RS_output2.sam REFERENCE=/path/to/phiX/picard_index/phiX.fa ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false
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74 /path/to/phiX/srma_index/phiX.fa is path to phiX.fa, phiX.fa.fai, and phiX.dict
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75 -->
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76 <param name="inputFile" value="picard_RS_input2.sam" />
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77 <param name="indexSource" value="built-in" />
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78 <param name="ref" value="phiX" />
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79 <param name="allowIncDictConcord" value="false" />
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80 <param name="allowContigLenDiscord" value="false" />
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81 <param name="outputFormat" value="False" />
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82 <output name="outFile" file="picard_RS_output2.sam" ftype="sam" lines_diff="4" sort="True" />
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83 </test>
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84 <test>
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85 <!-- Commands:
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86 cp test-data/picard_RS_input4.fasta .
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87 samtools faidx picard_RS_input4.fasta
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88 java -jar CreateSequenceDictionary.jar R=picard_RS_input4.fasta O=picard_RS_input4.dict URI=picard_RS_input4.fasta TRUNCATE_NAMES_AT_WHITESPACE=true SPECIES=phiX174 GENOME_ASSEMBLY=phiX_buildBlah1.1
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89 java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input3.bam O=picard_RS_output3.sam REFERENCE=picard_RS_input4.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false
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90 picard_RS_input3.bam can be made from picard_RS_input3.sam
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91 -->
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92 <param name="inputFile" value="picard_RS_input3.bam" />
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93 <param name="indexSource" value="history" />
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94 <param name="refFile" value="picard_RS_input4.fasta" />
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95 <param name="speciesName" value="phiX174" />
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96 <param name="buildName" value="phiX_buildBlah1.1" />
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97 <param name="truncateSeqNames" value="true" />
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98 <param name="allowIncDictConcord" value="true" />
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99 <param name="allowContigLenDiscord" value="false" />
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100 <param name="outputFormat" value="False" />
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101 <output name="outFile" file="picard_RS_output3.sam" ftype="sam" lines_diff="12" sort="True" />
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102 </test>
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103 </tests>
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104 <help>
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105
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106 .. class:: infomark
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107
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108 **Purpose**
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109
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110 Reorder SAM/BAM to match contig ordering in a particular reference file. Note that this is
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111 not the same as sorting as done by the SortSam tool, which sorts by either coordinate
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112 values or query name. The ordering in ReorderSam is based on exact name matching of
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113 contigs/chromosomes. Reads that are mapped to a contig that is not in the new reference file are
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114 not included in the output.
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115
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116 **Picard documentation**
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117
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118 This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_.
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119
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120 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
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121
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122 ------
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123
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124 .. class:: infomark
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125
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126 **Inputs, outputs, and parameters**
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127
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128 For the file that needs to be reordered, either a sam file or a bam file must be supplied.
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129 If a bam file is used, it must be coordinate-sorted. A reference file is also required,
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130 so either a fasta file should be supplied or a built-in reference can be selected.
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131
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132 The output contains the same reads as the input file but the reads have been rearranged so
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133 they appear in the same order as the provided reference file. The tool will output either
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134 bam (the default) or sam, according to user selection. Bam is recommended since it is smaller.
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135
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136 The only extra parameters that can be set are flags for allowing incomplete dict concordance
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137 and allowing contig length discordance. If incomplete dict concordance is allowed, only a
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138 partial overlap of the bam contigs with the new reference sequence contigs is required. By
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139 default it is off, requiring a corresponding contig in the new reference for each read contig.
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140 If contig length discordance is allowed, contig names that are the same between a read and the
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141 new reference contig are allowed even if they have different lengths. This is usually not a
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142 good idea, unless you know exactly what you're doing. It's off by default.
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143
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144 .. class:: warningmark
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145
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146 **Warning on SAM/BAM quality**
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147
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148 Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
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149 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
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150 to be the only way to deal with SAM/BAM that cannot be parsed.
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151
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152
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153 </help>
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154 </tool>
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