Mercurial > repos > xuebing > sharplabtool
comparison tools/sr_mapping/mosaik.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <?xml version="1.0"?> | |
2 <tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1"> | |
3 <description/> | |
4 <requirements><requirement type="package">mosaik</requirement></requirements> | |
5 <command> | |
6 #set $processors = '-p 4' | |
7 #set $lm = '' | |
8 #if $paired.kind == 'single': | |
9 #set $mfl = '' | |
10 #set $ls = '' | |
11 #else: | |
12 #set $ls = '-ls $mfl' | |
13 #end if | |
14 MosaikBuild -fr | |
15 #if $genomeSource.refGenomeSource == 'indexed': | |
16 ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } | |
17 #else: | |
18 $genomeSource.historyReference | |
19 #end if | |
20 -oa mosaik_ref_file; | |
21 MosaikBuild -q $reads $mfl -st $st -out mosaik_reads_file; | |
22 MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls -mm $mm -mhp $mhp -act $act -bw $bw $processors $lm -hs 15; | |
23 MosaikText -in mosaik_aligned_file -$outFormat sam_bam_file; | |
24 #if str($outFormat) == 'bam': | |
25 samtools sort sam_bam_file sorted_bam; | |
26 mv sorted_bam.bam $output | |
27 #else: | |
28 gunzip sam_bam_file.gz; | |
29 mv sam_bam_file $output | |
30 #end if | |
31 </command> | |
32 <inputs> | |
33 <conditional name="genomeSource"> | |
34 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> | |
35 <option value="indexed">Use a built-in index</option> | |
36 <option value="history">Use one from the history</option> | |
37 </param> | |
38 <when value="indexed"> | |
39 <param name="indexReference" type="select" label="Select a reference genome"> | |
40 <options from_data_table="mosaik_indexes"> | |
41 <filter type="sort_by" column="2"/> | |
42 <validator type="no_options" message="No indexes are available" /> | |
43 </options> | |
44 </param> | |
45 </when> | |
46 <when value="history"> | |
47 <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history"/> | |
48 </when> | |
49 </conditional> | |
50 <param format="fastq" name="reads" type="data" label="Fastq Reads File"/> | |
51 <param name="outFormat" type="select" label="Output Format"> | |
52 <option value="sam">Sam</option> | |
53 <option value="bam">Bam</option> | |
54 </param> | |
55 <param name="st" type="select" label="Sequencing Technology Used"> | |
56 <option value="454">454</option> | |
57 <option value="illumina">Illumina</option> | |
58 <option value="solid">Solid</option> | |
59 <option value="sanger">Sanger</option> | |
60 <option value="helicos">Helicos</option> | |
61 </param> | |
62 <conditional name="paired"> | |
63 <param name="kind" type="select" label="Is this library mate-paired?"> | |
64 <option value="single">Single-end</option> | |
65 <option value="paired">Paired-end</option> | |
66 </param> | |
67 <when value="single"/> | |
68 <when value="paired"> | |
69 <param name="mfl" type="integer" value="200" label="Insert Size" help="the length between the paired reads"/> | |
70 <param name="ls" type="integer" value="50" label="Realignment Window" help="Window size to realign mate pairs that are out of position. Large values slow down performance"/> | |
71 </when> | |
72 </conditional> | |
73 <param name="mm" size="5" type="integer" value="6" label="Mismatches allowed" help="mismatches allowed per sequence"/> | |
74 <param name="act" size="5" type="integer" value="35" label="Alignment Candidate Threshold" help="determines which hash regions will be aligned with Smith Waterman"/> | |
75 <param name="bw" size="5" type="integer" value="19" label="Smith-Waterman band width"/> | |
76 <param name="mhp" size="5" type="integer" value="100" label="Maximum # Of Positions Stored Per Seed" help="number of places in the reference the aligner will try to place a particular hash"/> | |
77 </inputs> | |
78 <outputs> | |
79 <data format="sam" name="output"> | |
80 <change_format> | |
81 <when input="outFormat" value="bam" format="bam" /> | |
82 </change_format> | |
83 <actions> | |
84 <conditional name="genomeSource.refGenomeSource"> | |
85 <when value="indexed"> | |
86 <action type="metadata" name="dbkey"> | |
87 <option type="from_data_table" name="mosaik_indexes" column="1"> | |
88 <filter type="param_value" column="0" value="#" compare="startswith" keep="False" /> | |
89 <filter type="param_value" ref="genomeSource.indexReference" column="0" /> | |
90 </option> | |
91 </action> | |
92 </when> | |
93 <when value="history"> | |
94 <action type="metadata" name="dbkey"> | |
95 <option type="from_param" name="genomeSource.historyReference" param_attribute="dbkey" /> | |
96 </action> | |
97 </when> | |
98 </conditional> | |
99 </actions> | |
100 </data> | |
101 </outputs> | |
102 <tests> | |
103 <test> | |
104 <param name="refGenomeSource" value="history"/> | |
105 <param name="historyReference" ftype="fasta" value="mosaik_test_ref.fasta"/> | |
106 <param name="reads" ftype="fastq" value="mosaik_test_input.fastq"/> | |
107 <param name="outFormat" value="sam"/> | |
108 <param name="st" value="454"/> | |
109 <param name="kind" value="single"/> | |
110 <param name="mm" value="6"/> | |
111 <param name="act" value="35"/> | |
112 <param name="bw" value="19"/> | |
113 <param name="mhp" value="100"/> | |
114 <output name="output" file="mosaik_test_out.sam" compare="sim_size" delta="0"/> | |
115 </test> | |
116 </tests> | |
117 <help> | |
118 This tool uses Mosaik to align reads to a reference sequence. | |
119 </help> | |
120 </tool> |