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author | yqiancolumbia |
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date | Mon, 30 Apr 2018 05:25:11 -0400 |
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1 <tool id="trimming3" name="Trim 3' adapter"> |
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2 <description></description> |
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3 |
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4 <command> |
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5 fastx_clipper -a $Adapter -l $DiscardShort $DiscardNonclipped $DiscardClipped $AdapterOnly $KeepUnknown |
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6 #if $minAdapterAlignment.Mrequired =="yes": |
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7 -M $minAdapterAlignment.Min |
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8 #end if |
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9 -v -i $input 2>/dev/null | fastq_quality_trimmer -v -l $DiscardShort $CompressOutput -t $Qualitythreshold -o $output |
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10 </command> |
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11 |
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12 <inputs> |
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13 <param name="input" type="data" format="fastq" label="Input FASTQ file"/> |
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14 |
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15 <param name="Adapter" type="text" value="" label="Adapter sequence (the 3' adapter will vary for different CLIP protocol variations)"/> |
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16 <param name="DiscardShort" type="integer" value="" label="Discard sequences shorter than N nucleotides (see help below for parameter suggestion)"/> |
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17 <param name="DiscardNonclipped" type="boolean" truevalue="-c" falsevalue="" checked="no" label="Discard non-trimmed sequences (i.e. - keep only sequences which contained the adapter)" /> |
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18 <param name="DiscardClipped" type="boolean" truevalue="-C" falsevalue="" checked="no" label="Discard trimmed sequences (i.e. - keep only sequences which did not contained the adapter)" /> |
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19 <param name="AdapterOnly" type="boolean" truevalue="-k" falsevalue="" checked="no" label="Report Adapter-Only sequences"/> |
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20 <param name="KeepUnknown" type="boolean" truevalue="-n" falsevalue="" checked="yes" label="Keep sequences with unknown nucleotides"/> |
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21 <conditional name="minAdapterAlignment"> |
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22 <param name="Mrequired" type="select" label="Require minimum adapter alignment length of N. If less than N nucleotides aligned with the adapter - don't trim it."> |
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23 <option value="yes">Yes</option> |
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24 <option value="no" selected="True">No</option> |
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25 </param> |
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26 <when value="yes"> |
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27 <param name="Min" type="integer" value="" label="Input the length"/> |
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28 </when> |
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29 <when value="no"> |
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30 </when> |
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31 </conditional> |
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32 <param name="Qualitythreshold" type="integer" value="5" label="Quality threshold - nucleotides with lower quality will be trimmed (from the end of the sequence)"/> |
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33 <param name="CompressOutput" type="boolean" truevalue="-z" falsevalue="" checked="no" label="Compress output with GZIP"/> |
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34 |
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35 </inputs> |
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36 |
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37 <outputs> |
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38 <data name="output" format="fastq" label="Trim 3' adapter on ${on_string} "/> |
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39 </outputs> |
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40 <help> |
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41 |
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42 .. class:: infomark |
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43 |
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44 **What this tool does** |
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45 |
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46 For long reads that are common now, collapsing before trimming is not very helpful. Therefore, trim the 3' adapter first. |
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47 |
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48 This tool (fastx_clipper and fastq_quality_trimmer) will take as input FASTQ files and output FASTQ files with 3' adapters and extremely low quality bases (e.g. score less than 5) removed. |
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49 |
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50 It is a part of FASTX Toolkit. |
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51 |
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52 ----- |
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53 |
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54 **Parameter suggestion for discarding sequences** |
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55 |
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56 * For standard CLIP: discard sequences shorter than 20 nucleotides. |
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57 * For BrdU CLIP: discard sequences shorter than 29 nucleotides. |
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58 |
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59 </help> |
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60 |
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61 </tool> |