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