Mercurial > repos > devteam > getindels_2way
annotate getIndels_2way.xml @ 1:51ee76168a2d default tip
Corrected version string.
| author | devteam <devteam@galaxyproject.org> |
|---|---|
| date | Thu, 10 Apr 2014 13:47:13 -0400 |
| parents | d6d2391a1cbb |
| children |
| rev | line source |
|---|---|
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51ee76168a2d
Corrected version string.
devteam <devteam@galaxyproject.org>
parents:
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1 <tool id="getIndels_2way" name="Fetch Indels" version="1.0.0"> |
| 0 | 2 <description> from pairwise alignments</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.7.1">numpy</requirement> | |
| 5 <requirement type="package" version="0.7.1">bx-python</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="python"> | |
| 8 getIndels.py $input1 $out_file1 | |
| 9 </command> | |
| 10 <inputs> | |
| 11 <page> | |
| 12 <param format="maf" name="input1" type="data" label="Select data"/> | |
| 13 </page> | |
| 14 </inputs> | |
| 15 <outputs> | |
| 16 <data format="tabular" name="out_file1" metadata_source="input1"/> | |
| 17 </outputs> | |
| 18 <requirements> | |
| 19 <requirement type="python-module">numpy</requirement> | |
| 20 </requirements> | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="input1" value="6.maf"/> | |
| 24 <output name="out_file1" file="6_indels.tabular"/> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help> | |
| 28 | |
| 29 .. class:: infomark | |
| 30 | |
| 31 **What it does** | |
| 32 | |
| 33 This tool estimates the number of indels for every alignment block of the MAF file. | |
| 34 | |
| 35 ----- | |
| 36 | |
| 37 .. class:: warningmark | |
| 38 | |
| 39 **Note** | |
| 40 | |
| 41 Any block/s not containing exactly 2 species will be omitted. | |
| 42 | |
| 43 ----- | |
| 44 | |
| 45 **Example** | |
| 46 | |
| 47 - For the following alignment block:: | |
| 48 | |
| 49 a score=7233.0 | |
| 50 s hg18.chr1 100 35 + 247249719 AT--GACTGAGGACTTAGTTTAAGATGTTCCTACT | |
| 51 s rheMac2.chr11 200 31 + 134511895 ATAAG-CGGACGACTTAGTTTAAGATGTTCC---- | |
| 52 | |
| 53 - running this tool will return:: | |
| 54 | |
| 55 #Block Source Seq1_Start Seq1_End Seq2_Start Seq2_End Indel_length | |
| 56 1 hg18.chr1 101 102 202 204 2 | |
| 57 1 rheMac2.chr11 103 104 204 205 1 | |
| 58 1 rheMac2.chr11 129 133 229 230 4 | |
| 59 | |
| 60 </help> | |
| 61 | |
| 62 | |
| 63 </tool> |