41
+ − 1 <tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.106.0">
+ − 2 <!-- taken from Inserthttps://github.com/najoshi/ucd-biocore-galaxy/tree/master/tools/picard -->
43
+ − 3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
41
+ − 4 <command interpreter="python">
+ − 5 picard_wrapper.py
+ − 6 --input=$inputFile
+ − 7 #if $source.indexSource == "built-in"
+ − 8 --ref="${source.ref.fields.path}"
+ − 9 #else
+ − 10 --ref-file=$refFile
+ − 11 --species-name=$source.speciesName
+ − 12 --build-name=$source.buildName
+ − 13 --trunc-names=$source.truncateSeqNames
+ − 14 #end if
+ − 15 --allow-inc-dict-concord=$allowIncDictConcord
+ − 16 --allow-contig-len-discord=$allowContigLenDiscord
+ − 17 --output-format=$outputFormat
+ − 18 --output=$outFile
+ − 19 --tmpdir "${__new_file_path__}"
+ − 20 -j "\$JAVA_JAR_PATH/ReorderSam.jar"
+ − 21 </command>
+ − 22 <inputs>
+ − 23 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"
+ − 24 help="If empty, upload or import a SAM/BAM dataset." />
+ − 25 <conditional name="source">
+ − 26 <param name="indexSource" type="select" label="Select Reference Genome" help="This tool will re-order SAM/BAM in the same order as reference selected below.">
+ − 27 <option value="built-in">Locally cached</option>
+ − 28 <option value="history">History</option>
+ − 29 </param>
+ − 30 <when value="built-in">
+ − 31 <param name="ref" type="select" label="Select a reference genome">
+ − 32 <options from_data_table="picard_indexes" />
+ − 33 </param>
+ − 34 </when>
+ − 35 <when value="history">
+ − 36 <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />
+ − 37 <param name="speciesName" type="text" value="" label="Species name" />
+ − 38 <param name="buildName" type="text" value="" label="Build name" />
+ − 39 <param name="truncateSeqNames" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Truncate sequence names after first whitespace" />
+ − 40 </when>
+ − 41 </conditional>
+ − 42 <param name="allowIncDictConcord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow incomplete dict concordance?" help="Allows a partial overlap of the BAM contigs with the new reference sequence contigs." />
+ − 43 <param name="allowContigLenDiscord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow contig length discordance?" help="This is dangerous--don't check it unless you know exactly what you're doing!" />
+ − 44 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
+ − 45 </inputs>
+ − 46 <outputs>
+ − 47 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: reordered ${outputFormat}">
+ − 48 <change_format>
+ − 49 <when input="outputFormat" value="sam" format="sam" />
+ − 50 </change_format>
+ − 51 </data>
+ − 52 </outputs>
+ − 53 <tests>
+ − 54 <test>
+ − 55 <!-- Commands:
+ − 56 cp test-data/phiX.fasta .
+ − 57 samtools faidx phiX.fasta
+ − 58 java -jar CreateSequenceDictionary.jar R=phiX.fasta O=phiX.dict URI=phiX.fasta TRUNCATE_NAMES_AT_WHITESPACE=false SPECIES=phiX174
+ − 59 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
+ − 60 -->
+ − 61 <param name="inputFile" value="picard_RS_input1.bam" />
+ − 62 <param name="indexSource" value="history" />
+ − 63 <param name="refFile" value="phiX.fasta" />
+ − 64 <param name="speciesName" value="phiX174" />
+ − 65 <param name="buildName" value="" />
+ − 66 <param name="truncateSeqNames" value="false" />
+ − 67 <param name="allowIncDictConcord" value="false" />
+ − 68 <param name="allowContigLenDiscord" value="false" />
+ − 69 <param name="outputFormat" value="True" />
+ − 70 <output name="outFile" file="picard_RS_output1.bam" ftype="bam" lines_diff="4" compare="contains" />
+ − 71 </test>
+ − 72 <test>
+ − 73 <!-- Command:
+ − 74 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
+ − 75 /path/to/phiX/srma_index/phiX.fa is path to phiX.fa, phiX.fa.fai, and phiX.dict
+ − 76 -->
+ − 77 <param name="inputFile" value="picard_RS_input2.sam" />
+ − 78 <param name="indexSource" value="built-in" />
+ − 79 <param name="ref" value="phiX" />
+ − 80 <param name="allowIncDictConcord" value="false" />
+ − 81 <param name="allowContigLenDiscord" value="false" />
+ − 82 <param name="outputFormat" value="False" />
+ − 83 <output name="outFile" file="picard_RS_output2.sam" ftype="sam" lines_diff="4" sort="True" />
+ − 84 </test>
+ − 85 <test>
+ − 86 <!-- Commands:
+ − 87 cp test-data/picard_RS_input4.fasta .
+ − 88 samtools faidx picard_RS_input4.fasta
+ − 89 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
+ − 90 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
+ − 91 picard_RS_input3.bam can be made from picard_RS_input3.sam
+ − 92 -->
+ − 93 <param name="inputFile" value="picard_RS_input3.bam" />
+ − 94 <param name="indexSource" value="history" />
+ − 95 <param name="refFile" value="picard_RS_input4.fasta" />
+ − 96 <param name="speciesName" value="phiX174" />
+ − 97 <param name="buildName" value="phiX_buildBlah1.1" />
+ − 98 <param name="truncateSeqNames" value="true" />
+ − 99 <param name="allowIncDictConcord" value="true" />
+ − 100 <param name="allowContigLenDiscord" value="false" />
+ − 101 <param name="outputFormat" value="False" />
+ − 102 <output name="outFile" file="picard_RS_output3.sam" ftype="sam" lines_diff="12" sort="True" />
+ − 103 </test>
+ − 104 </tests>
+ − 105 <help>
+ − 106
+ − 107 .. class:: infomark
+ − 108
+ − 109 **Purpose**
+ − 110
+ − 111 Reorder SAM/BAM to match contig ordering in a particular reference file. Note that this is
+ − 112 not the same as sorting as done by the SortSam tool, which sorts by either coordinate
+ − 113 values or query name. The ordering in ReorderSam is based on exact name matching of
+ − 114 contigs/chromosomes. Reads that are mapped to a contig that is not in the new reference file are
+ − 115 not included in the output.
+ − 116
+ − 117 **Picard documentation**
+ − 118
+ − 119 This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_.
+ − 120
+ − 121 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
+ − 122
+ − 123 ------
+ − 124
+ − 125 .. class:: infomark
+ − 126
+ − 127 **Inputs, outputs, and parameters**
+ − 128
+ − 129 For the file that needs to be reordered, either a sam file or a bam file must be supplied.
+ − 130 If a bam file is used, it must be coordinate-sorted. A reference file is also required,
+ − 131 so either a fasta file should be supplied or a built-in reference can be selected.
+ − 132
+ − 133 The output contains the same reads as the input file but the reads have been rearranged so
+ − 134 they appear in the same order as the provided reference file. The tool will output either
+ − 135 bam (the default) or sam, according to user selection. Bam is recommended since it is smaller.
+ − 136
+ − 137 The only extra parameters that can be set are flags for allowing incomplete dict concordance
+ − 138 and allowing contig length discordance. If incomplete dict concordance is allowed, only a
+ − 139 partial overlap of the bam contigs with the new reference sequence contigs is required. By
+ − 140 default it is off, requiring a corresponding contig in the new reference for each read contig.
+ − 141 If contig length discordance is allowed, contig names that are the same between a read and the
+ − 142 new reference contig are allowed even if they have different lengths. This is usually not a
+ − 143 good idea, unless you know exactly what you're doing. It's off by default.
+ − 144
+ − 145 .. class:: warningmark
+ − 146
+ − 147 **Warning on SAM/BAM quality**
+ − 148
+ − 149 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**
+ − 150 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
+ − 151 to be the only way to deal with SAM/BAM that cannot be parsed.
+ − 152
+ − 153
+ − 154 </help>
+ − 155 </tool>
+ − 156
+ − 157
+ − 158