root/galaxy-central/tools/extract/extract_genomic_dna.xml

リビジョン 2, 5.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.1">
2  <description>using coordinates from assembled/unassembled genomes</description>
3  <command interpreter="python">
4      extract_genomic_dna.py $input $out_file1 -d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR}
5      #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
6        -1 1,4,5,7 --gff
7      #else:
8        -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
9      #end if
10  </command>
11  <inputs>
12    <param format="interval,gff" name="input" type="data" label="Fetch sequences corresponding to Query">
13        <validator type="unspecified_build" />
14        <validator type="dataset_metadata_in_file" filename="alignseq.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="seq" />
15    </param>
16        <param name="out_format" type="select" label="Output data type">
17        <option value="fasta">FASTA</option>
18        <option value="interval">Interval</option>
19        </param>
20  </inputs>
21  <outputs>
22    <data format="input" name="out_file1" metadata_source="input">
23      <change_format>
24        <when input="out_format" value="fasta" format="fasta" />
25      </change_format>
26    </data>
27  </outputs>
28  <tests>
29    <test>
30      <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
31      <param name="out_format" value="fasta"/>   
32      <output name="out_file1" file="extract_genomic_dna_out1.fasta" />
33    </test>
34    <test>
35      <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
36      <param name="out_format" value="fasta"/>
37      <output name="out_file1" file="extract_genomic_dna_out2.fasta" />
38    </test>
39    <test>
40      <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
41      <param name="out_format" value="interval"/>
42      <output name="out_file1" file="extract_genomic_dna_out3.interval" />
43    </test>
44    <!-- Test GFF file support. -->
45    <test>
46      <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
47      <param name="out_format" value="interval"/>
48      <output name="out_file1" file="extract_genomic_dna_out4.gff" />
49    </test>
50    <test>
51      <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
52      <param name="out_format" value="fasta"/>
53      <output name="out_file1" file="extract_genomic_dna_out5.fasta" />
54    </test>
55  </tests>
56  <help>
57
58.. class:: warningmark
59
60This tool requires tabular formatted data.  If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*.
61
62.. class:: warningmark
63
64Make sure that the genome build is specified for the dataset from which you are extracting sequences (click the pencil icon in the history item if it is not specified).
65
66.. class:: warningmark
67
68All of the following will cause a line from the input dataset to be skipped and a warning generated.  The number of warnings and skipped lines is documented in the resulting history item.
69 - Any lines that do not contain at least 3 columns, a chromosome and numerical start and end coordinates.
70 - Sequences that fall outside of the range of a line's start and end coordinates.
71 - Chromosome, start or end coordinates that are invalid for the specified build.
72 - Any lines whose data columns are not separated by a **TAB** character ( other white-space characters are invalid ).
73
74.. class:: infomark
75
76 **Extract genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes** previously were achieved by two separate tools.
77
78-----
79
80**What it does**
81
82This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format.
83
84If strand is not defined, the default value is "+".
85
86-----
87
88**Example**
89
90If the input dataset is::
91
92    chr7  127475281  127475310  NM_000230  0  +
93    chr7  127485994  127486166  NM_000230  0  +
94    chr7  127486011  127486166  D49487     0  +
95
96Extracting sequences with **FASTA** output data type returns::
97
98    &gt;hg17_chr7_127475281_127475310_+
99    GTAGGAATCGCAGCGCCAGCGGTTGCAAG
100    &gt;hg17_chr7_127485994_127486166_+
101    GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
102    GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
103    CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
104    GATCAATGACATTTCACACACG
105    &gt;hg17_chr7_127486011_127486166_+
106    TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
107    CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
108    CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC
109    ACACG
110
111Extracting sequences with **Interval** output data type returns::
112
113    chr7    127475281       127475310       NM_000230       0       +       GTAGGAATCGCAGCGCCAGCGGTTGCAAG
114    chr7    127485994       127486166       NM_000230       0       +       GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
115    chr7    127486011       127486166       D49487  0       +       TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
116
117</help>
118</tool>
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