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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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