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1 <tool id="yac" name="Clip adapter" version="1.0.0">
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2 <description></description>
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3 <command interpreter="python">yac.py $input $output $clip_source.clip_sequence $min $max $Nmode</command>
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4 <inputs>
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5 <param format="fastq" name="input" type="data" label="Source file"/>
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6 <param name="min" type="integer" size="4" value="15" label="min size"/>
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7 <param name="max" type="integer" size="4" value="36" label="max size"/>
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8 <param name="Nmode" type="select" label="Reads containing Nst">
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9 <option value="accept" selected="True">accept</option>
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10 <option value="reject">reject</option>
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11 </param>
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12 <conditional name="clip_source">
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13 <param name="clip_source_list" type="select" label="Source" help="Built-in adapters or User-provided">
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14 <option value="prebuilt" selected="True">Use a built-in adapter (select from the list below)</option>
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15 <option value="user">Use custom sequence</option>
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16 </param>
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17 <when value="prebuilt">
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18 <param name="clip_sequence" type="select" label="Select Adapter to clip" help="if your adapter is not listed, input your own sequence">
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19 <option value="TCGTATGCCGTCTTCTGCTTG">Solexa TCGTATGCCGTCTTCTGCTTG</option>
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20 <option value="ATCTCGTATGCCGTCTTCTGCTT">Illumina ATCTCGTATGCCGTCTTCTGCTT</option>
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21 <option value="TGGAATTCTCGGGTGCCAAG" selected="True">Illumina TruSeq TGGAATTCTCGGGTGCCAAG</option>
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22 <option value="CTGTAGGCACCATCAATCGT">IdT CTGTAGGCACCATCAATCGT</option>
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23 </param>
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24 </when>
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25 <when value="user">
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26 <param name="clip_sequence" type="text" size="35" label="Enter your Sequence" value="GAATCC"/>
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27 </when>
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28 </conditional>
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29 </inputs>
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30 <outputs>
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31 <data format="fasta" name="output" metadata="input" />
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32 </outputs>
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33
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34 <help>
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35 <!-- write a decent doc ! -->
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36 This tool clips adapter sequences from a fastq file and fasta file of clipped reads with renumbered fasta headers.
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37
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38 Clipped sequences with Ns can be discarded.
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39
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40 Min size and max size filter clipped reads on their size.
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41
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42 Note that unclipped reads that satisfy the min and max size conditions are kept.
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43 </help>
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44
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45 <!-- write a <test> section -->
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46 <tests>
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47 <test>
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48 <param name="input" value="yac.fastq" ftype="fastqsanger"/>
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49 <param name="min" value="18" />
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50 <param name="max" value="29" />
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51 <param name="clip_source_list" value="prebuilt" />
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52 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
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53 <param name="Nmode" value="accept" />
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54 <output name="output" file="yac.out" />
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55 </test>
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56 </tests>
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57
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58 </tool>
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