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annotate overlapping_reads.xml @ 2:320e06bf99b9 draft

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author artbio
date Wed, 30 Aug 2017 05:40:18 -0400
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320e06bf99b9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 5cf421cdafd250995172684a9db0ac8acbb350b5
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1 <tool id="overlapping_reads" name="Get overlapping reads" version="0.9.1">
1
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2 <description />
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3 <requirements>
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4 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Tool exception" />
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8 </stdio>
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9 <command detect_errors="exit_code"><![CDATA[
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10 samtools index '$input' &&
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11 python '$__tool_directory__'/overlapping_reads.py
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12 --input '$input'
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13 --minquery '$minquery'
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14 --maxquery '$maxquery'
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15 --mintarget '$mintarget'
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16 --maxtarget '$maxtarget'
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17 --overlap '$overlap'
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18 --output '$output'
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19 ]]></command>
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20 <inputs>
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21 <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
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22 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
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23 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
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24 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
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25 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
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26 <param help="'10' = 10 nucleotides overlap" label="Overlap (in nt)" name="overlap" size="3" type="integer" value="10" />
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27 </inputs>
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28 <outputs>
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29 <data format="fasta" label="pairable reads" name="output" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param ftype="bam" name="input" value="sr_bowtie.bam" />
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34 <param name="minquery" value="23" />
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35 <param name="maxquery" value="29" />
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36 <param name="mintarget" value="23" />
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37 <param name="maxtarget" value="29" />
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38 <param name="overlap" value="10" />
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39 <output file="paired.fa" ftype="fasta" name="output" />
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40 </test>
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41 </tests>
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42 <help>
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43
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44 **What it does**
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45
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46 Extract reads with overlap signatures of the specified overlap (in nt) and
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47 return a fasta file of these "pairable" reads.
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48
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49 See `Antoniewski (2014)`_ for background and details
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51 .. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12
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53 **Input**
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54
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55 A **sorted** BAM alignment file.
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56
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57 **Outputs**
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58
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59 a fasta file of pairable reads such as :
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61 >FBgn0000004_17.6|5839|R|26
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63 TTTTCGTCAATTGTGCCAAATAGGTA
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64
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65 >FBgn0000004_17.6|5855|F|23
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66
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67 TTGACGAAAATGATCGAGTGGAT
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68
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69 where FBgn0000004_17.6 stands for the chromosome, 5839 stands for the 1-based read position,
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70 R stand for reverse strand (F forward strand) and 26 stands for the size of the read.
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71
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72 the second sequence in this example is a read that overlap by 10 nt with the first read.
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73
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74 </help>
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75 <citations>
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76 <citation type="doi">10.1007/978-1-4939-0931-5_12</citation>
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77 </citations>
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78 </tool>