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comparison tools/maf/interval_maf_to_merged_fasta.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks" version="1.0.1">
2 <description>given a set of genomic intervals</description>
3 <command interpreter="python">
4 #if $maf_source_type.maf_source == "user" #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
5 #else #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
6 #end if# --overwrite_with_gaps=$overwrite_with_gaps
7 </command>
8 <inputs>
9 <page>
10 <param format="interval" name="input1" type="data" label="Choose intervals">
11 <validator type="unspecified_build" />
12 </param>
13 <conditional name="maf_source_type">
14 <param name="maf_source" type="select" label="MAF Source">
15 <option value="cached" selected="true">Locally Cached Alignments</option>
16 <option value="user">Alignments in Your History</option>
17 </param>
18 <when value="user">
19 <param name="maf_file" type="data" format="maf" label="MAF File">
20 <options>
21 <filter type="data_meta" ref="input1" key="dbkey" />
22 </options>
23 <validator type="dataset_ok_validator" />
24 </param>
25 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
26 <options>
27 <filter type="data_meta" ref="maf_file" key="species" />
28 </options>
29 </param>
30 </when>
31 <when value="cached">
32 <param name="maf_identifier" type="select" label="MAF Type" >
33 <options from_file="maf_index.loc">
34 <column name="name" index="0"/>
35 <column name="value" index="1"/>
36 <column name="dbkey" index="2"/>
37 <column name="species" index="3"/>
38 <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/>
39 <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
40 </options>
41 </param>
42 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
43 <options from_file="maf_index.loc">
44 <column name="uid" index="1"/>
45 <column name="value" index="3"/>
46 <column name="name" index="3"/>
47 <filter type="param_value" ref="maf_identifier" name="uid" column="1"/>
48 <filter type="multiple_splitter" column="3" separator=","/>
49 </options>
50 </param>
51 </when>
52 </conditional>
53 <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occurring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block.">
54 <option value="True" selected="true">No</option>
55 <option value="False">Yes</option>
56 </param>
57 </page>
58 </inputs>
59 <outputs>
60 <data format="fasta" name="out_file1" />
61 </outputs>
62 <tests>
63 <test>
64 <param name="input1" value="13.bed" dbkey="hg18" ftype="bed"/>
65 <param name="maf_source" value="cached"/>
66 <param name="maf_identifier" value="17_WAY_MULTIZ_hg18"/>
67 <param name="species" value="hg18,mm8"/>
68 <param name="overwrite_with_gaps" value="True"/>
69 <output name="out_file1" file="interval_maf_to_merged_fasta_out3.fasta" />
70 </test>
71 <test>
72 <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/>
73 <param name="maf_source" value="cached"/>
74 <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/>
75 <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>
76 <param name="overwrite_with_gaps" value="True"/>
77 <output name="out_file1" file="interval_maf_to_merged_fasta_out.dat" />
78 </test>
79 <test>
80 <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/>
81 <param name="maf_source" value="user"/>
82 <param name="maf_file" value="5.maf"/>
83 <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>
84 <param name="overwrite_with_gaps" value="True"/>
85 <output name="out_file1" file="interval_maf_to_merged_fasta_user_out.dat" />
86 </test>
87 </tests>
88 <help>
89 **What it does**
90
91 A single genomic region can be covered by multiple alignment blocks. In many cases it is desirable to stitch these alignment blocks together. This tool accepts a list of genomic intervals. For every interval it performs the following:
92
93 * finds all MAF blocks that overlap the interval;
94 * sorts MAF blocks by alignment score;
95 * stitches blocks together and resolves overlaps based on alignment score;
96 * outputs alignments in FASTA format.
97
98 ------
99
100 **Example**
101
102 Here three MAF blocks overlapping a single interval are stitched together. Space between blocks 2 and 3 is filled with gaps:
103
104 .. image:: ./static/images/maf_icons/stitchMaf.png
105
106 ------
107
108 **Citation**
109
110 If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21775304&gt;`_
111
112
113 </help>
114 </tool>