/tools/regVariation/getIndels_2way.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 59 lines · 43 code · 16 blank · 0 comment · 0 complexity · ce380c755b2935b67cc3d852a3f501fe MD5 · raw file
- <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>