mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
60 lines
1.4 KiB
XML
60 lines
1.4 KiB
XML
<tool id="getIndels_2way" name="Fetch Indels">
|
|
<description> from pairwise alignments</description>
|
|
<command interpreter="python">
|
|
getIndels.py $input1 $out_file1
|
|
</command>
|
|
<inputs>
|
|
<page>
|
|
<param format="maf" name="input1" type="data" label="Select data"/>
|
|
</page>
|
|
</inputs>
|
|
<outputs>
|
|
<data format="tabular" name="out_file1" metadata_source="input1"/>
|
|
</outputs>
|
|
<requirements>
|
|
<requirement type="python-module">numpy</requirement>
|
|
</requirements>
|
|
<tests>
|
|
<test>
|
|
<param name="input1" value="6.maf"/>
|
|
<output name="out_file1" file="6_indels.tabular"/>
|
|
</test>
|
|
</tests>
|
|
<help>
|
|
|
|
.. class:: infomark
|
|
|
|
**What it does**
|
|
|
|
This tool estimates the number of indels for every alignment block of the MAF file.
|
|
|
|
-----
|
|
|
|
.. class:: warningmark
|
|
|
|
**Note**
|
|
|
|
Any block/s not containing exactly 2 species will be omitted.
|
|
|
|
-----
|
|
|
|
**Example**
|
|
|
|
- For the following alignment block::
|
|
|
|
a score=7233.0
|
|
s hg18.chr1 100 35 + 247249719 AT--GACTGAGGACTTAGTTTAAGATGTTCCTACT
|
|
s rheMac2.chr11 200 31 + 134511895 ATAAG-CGGACGACTTAGTTTAAGATGTTCC----
|
|
|
|
- running this tool will return::
|
|
|
|
#Block Source Seq1_Start Seq1_End Seq2_Start Seq2_End Indel_length
|
|
1 hg18.chr1 101 102 202 204 2
|
|
1 rheMac2.chr11 103 104 204 205 1
|
|
1 rheMac2.chr11 129 133 229 230 4
|
|
|
|
</help>
|
|
|
|
|
|
</tool>
|