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

リビジョン 2, 6.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
91A 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
102Here 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  </help>
107</tool>
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