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comparison mosaik2.xml @ 0:6adb6e16b00f draft

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author crs4
date Wed, 02 Apr 2014 12:32:52 -0400
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1 <?xml version="1.0"?>
2 <tool id="mosaik2" name="Map with MOSAIK v. 2" version="2.0.0">
3 <description/>
4 <requirements>
5 <requirement type="package" version="2.2.26">mosaik</requirement>
6 <requirement type="package" version="0.1.19">samtools</requirement>
7 </requirements>
8 <version_command>MosaikJump | sed -e 's/\x1b\[[[:digit:]]\{1,2\}\(;[[:digit:]]\{1,2\}\)\{0,1\}m//g' | sed -n 's/MosaikJump \([[:digit:].]\{1,\}\).*/\1/p'</version_command>
9 <command>
10 MosaikBuild -fr
11 #if $genomeSource.refGenomeSource == 'indexed'
12 ${genomeSource.indexReference.fields.path}
13 #else
14 ${genomeSource.historyReference}
15 #end if
16 -oa mosaik_ref_file;
17 MosaikBuild -q $reads
18 #if $paired.kind == 'single'
19 #set $ls_string = ''
20 #else
21 -q2 ${paired.reads2}
22 -mfl ${paired.mfl}
23 #set $ls_string = '-ls %s' % $paired.ls
24 #end if
25 -st $st -out mosaik_reads_file;
26 MosaikAligner -p \${GALAXY_SLOTS:-4} -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file -annpe \$MOSAIK_NETWORK_DIR/2.1.26.pe.100.0065.ann -annse \$MOSAIK_NETWORK_DIR/2.1.26.se.100.005.ann $ls_string
27 #if str($mm)
28 -mm $mm
29 #end if
30 #if str($act)
31 -act $act
32 #end if
33 #if str($bw)
34 -bw $bw
35 #end if
36 #if str($mhp)
37 -mhp $mhp
38 #end if
39 -hs 15;
40 #if str($outFormat) == 'bam'
41 samtools sort -o mosaik_aligned_file.bam out_prefix &gt; $output
42 #else
43 samtools view mosaik_aligned_file.bam -o $output
44 #end if
45 </command>
46 <inputs>
47 <conditional name="genomeSource">
48 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
49 <option value="indexed">Use a built-in index</option>
50 <option value="history">Use one from the history</option>
51 </param>
52 <when value="indexed">
53 <param name="indexReference" type="select" label="Select a reference genome">
54 <options from_data_table="mosaik_indexes">
55 <filter type="sort_by" column="2" />
56 <validator type="no_options" message="No indexes are available" />
57 </options>
58 </param>
59 </when>
60 <when value="history">
61 <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history" />
62 </when>
63 </conditional>
64 <param name="st" type="select" label="Sequencing technology used">
65 <option value="454">454</option>
66 <option value="illumina">Illumina</option>
67 <option value="solid">Solid</option>
68 <option value="sanger">Sanger</option>
69 <option value="helicos">Helicos</option>
70 </param>
71 <param format="fastq" name="reads" type="data" label="FASTQ reads file" />
72 <conditional name="paired">
73 <param name="kind" type="select" label="Is this library mate-paired?">
74 <option value="single">Single-end</option>
75 <option value="paired">Paired-end</option>
76 </param>
77 <when value="single" />
78 <when value="paired">
79 <param format="fastq" name="reads2" type="data" label="FASTQ 2nd mate" />
80 <param name="mfl" type="integer" value="200" label="Median fragment length" />
81 <param name="ls" type="integer" min="0" value="50" label="Local alignment search radius to rescue mates" help="A large value slows down performances" />
82 </when>
83 </conditional>
84 <param name="mm" type="integer" value="6" optional="true" label="Number of mismatches allowed per sequence" />
85 <param name="act" type="integer" value="35" optional="true" label="Alignment candidate threshold" help="Determines which hash regions will be aligned with Smith-Waterman" />
86 <param name="bw" type="integer" value="9" optional="true" label="Smith-Waterman band width" />
87 <param name="mhp" type="integer" value="100" optional="true" label="Maximum number of positions stored per seed" help="Number of places in the reference the aligner will try to place a particular hash" />
88 <param name="outFormat" type="select" label="Output format">
89 <option value="sam">SAM</option>
90 <option value="bam">BAM</option>
91 </param>
92 </inputs>
93 <outputs>
94 <data format="sam" name="output">
95 <change_format>
96 <when input="outFormat" value="bam" format="bam" />
97 </change_format>
98 <actions>
99 <conditional name="genomeSource.refGenomeSource">
100 <when value="indexed">
101 <action type="metadata" name="dbkey">
102 <option type="from_data_table" name="mosaik_indexes" column="1">
103 <filter type="param_value" column="0" value="#" compare="startswith" keep="False" />
104 <filter type="param_value" ref="genomeSource.indexReference" column="0" />
105 </option>
106 </action>
107 </when>
108 <when value="history">
109 <action type="metadata" name="dbkey">
110 <option type="from_param" name="genomeSource.historyReference" param_attribute="dbkey" />
111 </action>
112 </when>
113 </conditional>
114 </actions>
115 </data>
116 </outputs>
117 <tests>
118 <test>
119 <param name="refGenomeSource" value="history" />
120 <param name="historyReference" ftype="fasta" value="mosaik_test_ref.fasta" />
121 <param name="st" value="454" />
122 <param name="reads" ftype="fastq" value="mosaik_test_input.fastq" />
123 <param name="kind" value="single" />
124 <param name="mm" value="6" />
125 <param name="act" value="35" />
126 <param name="bw" value="9" />
127 <param name="mhp" value="100" />
128 <param name="outFormat" value="sam" />
129 <output name="output" file="mosaik_test_out.sam" compare="sim_size" delta="0" />
130 </test>
131 </tests>
132 <help>
133 **What it does**
134
135 This tool uses `MOSAIK`_ v. 2 to align reads to a reference sequence.
136
137 **License and citation**
138
139 This Galaxy tool is Copyright © 2005-2013 Pennsylvania State University, © 2013-2014 `CRS4 Srl.`_ and is released under the `Academic Free License v. 3.0`_.
140
141 .. _CRS4 Srl.: http://www.crs4.it/
142 .. _Academic Free License v. 3.0: http://opensource.org/licenses/AFL-3.0
143
144 If you use this tool in Galaxy, please cite |Cuccuru2014|_.
145
146 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
147 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/03/10/bioinformatics.btu135
148
149 This tool uses `MOSAIK`_, which is licensed separately. Please cite |Lee2014|_.
150
151 .. _MOSAIK: https://code.google.com/p/mosaik-aligner/
152 .. |Lee2014| replace:: Lee, W.-P., *et al.* (2014) MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping. *PLoS ONE* 9(3), e90581
153 .. _Lee2014: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090581
154 </help>
155 </tool>