root/galaxy-central/tools/maf/maf_stats.xml

リビジョン 2, 4.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
79This tool takes a MAF file and an interval file and relates coverage information by interval for each species.
80If a column does not exist in the reference genome, it is not included in the output.
81
82Consider 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
100Alternatively, 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  </help>
112</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。