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comparison picard_ReorderSam.xml @ 41:468673afa348 draft

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date Thu, 13 Feb 2014 21:39:50 -0500
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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 -->
3 <requirements><requirement type="package">picard</requirement></requirements>
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
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158