Mercurial > repos > devteam > picard
annotate picard_ReorderSam.xml @ 3:bf1c3f9f8282
Fix for FastqToSam MAX_Q usage detection.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
|---|---|
| date | Fri, 03 May 2013 17:13:01 -0400 |
| parents | 9227b8c3093b |
| children | 3d4f1fa26f0e |
| rev | line source |
|---|---|
| 0 | 1 <tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0"> |
| 2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> | |
| 3 <command interpreter="python"> | |
| 4 picard_wrapper.py | |
|
2
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
5 --input="${inputFile}" |
| 0 | 6 #if $source.indexSource == "built-in" |
| 7 --ref="${source.ref.fields.path}" | |
| 8 #else | |
|
2
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
9 --ref-file="${refFile}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
10 --species-name="${source.speciesName}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
11 --build-name="${source.buildName}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
12 --trunc-names="${source.truncateSeqNames}" |
| 0 | 13 #end if |
|
2
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
14 --allow-inc-dict-concord="${allowIncDictConcord}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
15 --allow-contig-len-discord="${allowContigLenDiscord}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
16 --output-format="${outputFormat}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
17 --output="${outFile}" |
| 0 | 18 --tmpdir "${__new_file_path__}" |
| 19 -j "\$JAVA_JAR_PATH/ReorderSam.jar" | |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered" | |
| 23 help="If empty, upload or import a SAM/BAM dataset." /> | |
| 24 <conditional name="source"> | |
| 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."> | |
| 26 <option value="built-in">Locally cached</option> | |
| 27 <option value="history">History</option> | |
| 28 </param> | |
| 29 <when value="built-in"> | |
| 30 <param name="ref" type="select" label="Select a reference genome"> | |
| 31 <options from_data_table="picard_indexes" /> | |
| 32 </param> | |
| 33 </when> | |
| 34 <when value="history"> | |
| 35 <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" /> | |
| 36 <param name="speciesName" type="text" value="" label="Species name" /> | |
| 37 <param name="buildName" type="text" value="" label="Build name" /> | |
| 38 <param name="truncateSeqNames" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Truncate sequence names after first whitespace" /> | |
| 39 </when> | |
| 40 </conditional> | |
| 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." /> | |
| 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!" /> | |
| 43 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" /> | |
| 44 </inputs> | |
| 45 <outputs> | |
| 46 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: reordered ${outputFormat}"> | |
| 47 <change_format> | |
| 48 <when input="outputFormat" value="sam" format="sam" /> | |
| 49 </change_format> | |
| 50 </data> | |
| 51 </outputs> | |
| 52 <tests> | |
| 53 <test> | |
| 54 <!-- Commands: | |
| 55 cp test-data/phiX.fasta . | |
| 56 samtools faidx phiX.fasta | |
| 57 java -jar CreateSequenceDictionary.jar R=phiX.fasta O=phiX.dict URI=phiX.fasta TRUNCATE_NAMES_AT_WHITESPACE=false SPECIES=phiX174 | |
| 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 | |
| 59 --> | |
| 60 <param name="inputFile" value="picard_RS_input1.bam" /> | |
| 61 <param name="indexSource" value="history" /> | |
| 62 <param name="refFile" value="phiX.fasta" /> | |
| 63 <param name="speciesName" value="phiX174" /> | |
| 64 <param name="buildName" value="" /> | |
| 65 <param name="truncateSeqNames" value="false" /> | |
| 66 <param name="allowIncDictConcord" value="false" /> | |
| 67 <param name="allowContigLenDiscord" value="false" /> | |
| 68 <param name="outputFormat" value="True" /> | |
| 69 <output name="outFile" file="picard_RS_output1.bam" ftype="bam" lines_diff="4" compare="contains" /> | |
| 70 </test> | |
| 71 <test> | |
| 72 <!-- Command: | |
| 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 | |
| 74 /path/to/phiX/srma_index/phiX.fa is path to phiX.fa, phiX.fa.fai, and phiX.dict | |
| 75 --> | |
| 76 <param name="inputFile" value="picard_RS_input2.sam" /> | |
| 77 <param name="indexSource" value="built-in" /> | |
| 78 <param name="ref" value="phiX" /> | |
| 79 <param name="allowIncDictConcord" value="false" /> | |
| 80 <param name="allowContigLenDiscord" value="false" /> | |
| 81 <param name="outputFormat" value="False" /> | |
| 82 <output name="outFile" file="picard_RS_output2.sam" ftype="sam" lines_diff="4" sort="True" /> | |
| 83 </test> | |
| 84 <test> | |
| 85 <!-- Commands: | |
| 86 cp test-data/picard_RS_input4.fasta . | |
| 87 samtools faidx picard_RS_input4.fasta | |
| 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 | |
| 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 | |
| 90 picard_RS_input3.bam can be made from picard_RS_input3.sam | |
| 91 --> | |
| 92 <param name="inputFile" value="picard_RS_input3.bam" /> | |
| 93 <param name="indexSource" value="history" /> | |
| 94 <param name="refFile" value="picard_RS_input4.fasta" /> | |
| 95 <param name="speciesName" value="phiX174" /> | |
| 96 <param name="buildName" value="phiX_buildBlah1.1" /> | |
| 97 <param name="truncateSeqNames" value="true" /> | |
| 98 <param name="allowIncDictConcord" value="true" /> | |
| 99 <param name="allowContigLenDiscord" value="false" /> | |
| 100 <param name="outputFormat" value="False" /> | |
| 101 <output name="outFile" file="picard_RS_output3.sam" ftype="sam" lines_diff="12" sort="True" /> | |
| 102 </test> | |
| 103 </tests> | |
| 104 <help> | |
| 105 | |
| 106 .. class:: infomark | |
| 107 | |
| 108 **Purpose** | |
| 109 | |
| 110 Reorder SAM/BAM to match contig ordering in a particular reference file. Note that this is | |
| 111 not the same as sorting as done by the SortSam tool, which sorts by either coordinate | |
| 112 values or query name. The ordering in ReorderSam is based on exact name matching of | |
| 113 contigs/chromosomes. Reads that are mapped to a contig that is not in the new reference file are | |
| 114 not included in the output. | |
| 115 | |
| 116 **Picard documentation** | |
| 117 | |
| 118 This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_. | |
| 119 | |
| 120 .. _Picard-tools: http://www.google.com/search?q=picard+samtools | |
| 121 | |
| 122 ------ | |
| 123 | |
| 124 .. class:: infomark | |
| 125 | |
| 126 **Inputs, outputs, and parameters** | |
| 127 | |
| 128 For the file that needs to be reordered, either a sam file or a bam file must be supplied. | |
| 129 If a bam file is used, it must be coordinate-sorted. A reference file is also required, | |
| 130 so either a fasta file should be supplied or a built-in reference can be selected. | |
| 131 | |
| 132 The output contains the same reads as the input file but the reads have been rearranged so | |
| 133 they appear in the same order as the provided reference file. The tool will output either | |
| 134 bam (the default) or sam, according to user selection. Bam is recommended since it is smaller. | |
| 135 | |
| 136 The only extra parameters that can be set are flags for allowing incomplete dict concordance | |
| 137 and allowing contig length discordance. If incomplete dict concordance is allowed, only a | |
| 138 partial overlap of the bam contigs with the new reference sequence contigs is required. By | |
| 139 default it is off, requiring a corresponding contig in the new reference for each read contig. | |
| 140 If contig length discordance is allowed, contig names that are the same between a read and the | |
| 141 new reference contig are allowed even if they have different lengths. This is usually not a | |
| 142 good idea, unless you know exactly what you're doing. It's off by default. | |
| 143 | |
| 144 .. class:: warningmark | |
| 145 | |
| 146 **Warning on SAM/BAM quality** | |
| 147 | |
| 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** | |
| 149 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears | |
| 150 to be the only way to deal with SAM/BAM that cannot be parsed. | |
| 151 | |
| 152 | |
| 153 </help> | |
| 154 </tool> | |
| 155 | |
| 156 | |
| 157 | |
| 158 | |
| 159 | |
| 160 | |
| 161 | |
| 162 | |
| 163 | |
| 164 | |
| 165 | |
| 166 |