Mercurial > repos > xuebing > sharplabtool
comparison tools/maf/maf_stats.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 <tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1"> | |
2 <description>Alignment coverage information</description> | |
3 <command interpreter="python"> | |
4 maf_stats.py | |
5 #if $maf_source_type.maf_source == "user": | |
6 $maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary | |
7 #else: | |
8 $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary | |
9 #end if | |
10 ${GALAXY_DATA_INDEX_DIR} | |
11 #if $maf_source_type.maf_source == "user": | |
12 $input2.metadata.maf_index | |
13 #end if | |
14 </command> | |
15 <inputs> | |
16 <param format="interval" name="input1" label="Interval File" type="data"> | |
17 <validator type="unspecified_build" /> | |
18 </param> | |
19 <conditional name="maf_source_type"> | |
20 <param name="maf_source" type="select" label="MAF Source"> | |
21 <option value="cached" selected="true">Locally Cached Alignments</option> | |
22 <option value="user">Alignments in Your History</option> | |
23 </param> | |
24 <when value="user"> | |
25 <param format="maf" name="input2" label="MAF File" type="data"> | |
26 <options> | |
27 <filter type="data_meta" ref="input1" key="dbkey" /> | |
28 </options> | |
29 <validator type="dataset_ok_validator" /> | |
30 </param> | |
31 </when> | |
32 <when value="cached"> | |
33 <param name="mafType" type="select" label="MAF Type"> | |
34 <options from_file="maf_index.loc"> | |
35 <column name="name" index="0"/> | |
36 <column name="value" index="1"/> | |
37 <column name="dbkey" index="2"/> | |
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 </when> | |
43 </conditional> | |
44 <param name="summary" type="select" label="Type of Output"> | |
45 <option value="false" selected="true">Coverage by Region</option> | |
46 <option value="true">Summarize Coverage</option> | |
47 </param> | |
48 </inputs> | |
49 <outputs> | |
50 <data format="interval" name="out_file1" metadata_source="input1"> | |
51 <change_format> | |
52 <when input="summary" value="true" format="tabular" /> | |
53 </change_format> | |
54 </data> | |
55 </outputs> | |
56 <requirements> | |
57 <requirement type="python-module">numpy</requirement> | |
58 </requirements> | |
59 <tests> | |
60 <test> | |
61 <param name="input1" value="1.bed" dbkey="hg17" format="bed"/> | |
62 <param name="maf_source" value="cached"/> | |
63 <param name="mafType" value="8_WAY_MULTIZ_hg17"/> | |
64 <output name="out_file1" file="maf_stats_interval_out.dat"/> | |
65 <param name="summary" value="false"/> | |
66 </test> | |
67 <test> | |
68 <param name="input1" value="1.bed" dbkey="hg17" format="bed"/> | |
69 <param name="maf_source" value="cached"/> | |
70 <param name="mafType" value="8_WAY_MULTIZ_hg17"/> | |
71 <output name="out_file1" file="maf_stats_summary_out.dat"/> | |
72 <param name="summary" value="true"/> | |
73 </test> | |
74 </tests> | |
75 <help> | |
76 | |
77 **What it does** | |
78 | |
79 This tool takes a MAF file and an interval file and relates coverage information by interval for each species. | |
80 If a column does not exist in the reference genome, it is not included in the output. | |
81 | |
82 Consider the interval: "chrX 1000 1100 myInterval" | |
83 Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this: | |
84 | |
85 chrX 1000 1100 myInterval H XXX YYY | |
86 | |
87 chrX 1000 1100 myInterval M XXX YYY | |
88 | |
89 chrX 1000 1100 myInterval R XXX YYY | |
90 | |
91 | |
92 where XXX and YYY are: | |
93 | |
94 XXX = number of nucleotides | |
95 | |
96 YYY = number of gaps | |
97 | |
98 ---- | |
99 | |
100 Alternatively, you can request only summary information for a set of intervals: | |
101 | |
102 ======== =========== ======== | |
103 #species nucleotides coverage | |
104 ======== =========== ======== | |
105 hg18 30639 0.2372 | |
106 rheMac2 7524 0.0582 | |
107 panTro2 30390 0.2353 | |
108 ======== =========== ======== | |
109 | |
110 where **coverage** is the number of nucleotides divided by the total length of the provided intervals. | |
111 | |
112 ------ | |
113 | |
114 **Citation** | |
115 | |
116 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. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ | |
117 | |
118 | |
119 </help> | |
120 </tool> |