Mercurial > repos > ebi-gxa > fastq_quality_trimmer
annotate fastq_quality_trimmer.xml @ 0:27e997d5c273 draft default tip
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
author | ebi-gxa |
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date | Fri, 11 Mar 2022 03:56:00 +0000 |
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27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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1 <tool id="cshl_fastq_quality_trimmer" name="Trim By Quality" profile="18.01" version="0.0.14+galaxy0"> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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2 <description>Trims reads at the 3'-end based on quality, discarding reads with trimmed length less than threshold.</description> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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3 <requirements> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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4 <requirement type="package" version="0.0.14">fastx_toolkit</requirement> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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5 </requirements> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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6 <command><![CDATA[ |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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7 fastq_quality_trimmer |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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8 -i '$input' |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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9 -t '$cutoff' |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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10 -l '$minlen' |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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11 -Q '$phred' |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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12 -v |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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13 -o '$output' |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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14 ]]></command> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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15 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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16 <inputs> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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17 <param name="input" label="Library to clip" argument="-i" type="data" format="fastq,fastqsanger" optional="false" /> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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18 <param name="cutoff" size="4" type="integer" value="20"> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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19 <label>Minimum quality score</label> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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20 <help>Nucleotides below this quality will be trimmed</help> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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21 </param> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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22 <param name="minlen" size="4" type="integer" value="1"> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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23 <label>Minimum sequence length</label> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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24 <help>Sequences shorter than this length will be discard. Leave at zero to keep all sequences</help> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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25 </param> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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26 <param name="phred" label="PHRED Encoding" argument="-Q" type="select" help="PHRED encoding used in the input files"> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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27 <option value="33" selected="true">33</option> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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28 <option value="64">64</option> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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29 </param> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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30 </inputs> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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31 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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32 <outputs> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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33 <data label="${tool.name} on ${on_string}: Trimmed fastq" name="output" format_source="input" /> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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34 </outputs> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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35 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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36 <tests> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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37 <test> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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38 <param name="input" value="fastq_quality_trimmer.fastq" ftype="fastq" /> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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39 <param name="cutoff" value="30"/> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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40 <param name="minlen" value="16"/> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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41 <param name="phred" value="64"/> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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42 <output name="output" md5="5173e32392286a05e1317387cc0d567e" /> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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43 </test> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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44 </tests> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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45 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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46 <help> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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47 **What it does** |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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48 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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49 This tool scans the sequence from the end for the first nucleotide to possess the specified minimum quality score. It will then trim (remove nucleotides from) the sequence after this position. After trimming, sequences that are shorter than the minimum length are discarded. |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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50 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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51 -------- |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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52 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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53 **Example** |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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54 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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55 Input Fasta file (with 20 bases in each sequences):: |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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56 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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57 @1 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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58 TATGGTCAGAAACCATATGC |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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59 +1 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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60 40 40 40 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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61 @2 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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62 CAGCGAGGCTTTAATGCCAT |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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63 +2 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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64 40 40 40 40 40 40 40 40 30 20 19 20 19 19 19 19 19 19 19 19 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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65 @3 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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66 CAGCGAGGCTTTAATGCCAT |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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67 +3 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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68 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 19 19 19 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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69 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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70 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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71 Trimming with a cutoff of 20, we get the following FASTQ file:: |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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72 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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73 @1 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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74 TATGGTCAGAAA |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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75 +1 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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76 40 40 40 40 40 40 40 40 40 40 40 20 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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77 @2 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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78 CAGCGAGGCTTT |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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79 +2 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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80 40 40 40 40 40 40 40 40 30 20 19 20 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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81 @3 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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82 CAGCGAGGC |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
ebi-gxa
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83 +3 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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84 40 40 40 40 40 40 40 40 20 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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85 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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86 Trimming with a cutoff of 20 and a minimum length of 12, we get the following FASTQ file:: |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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87 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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88 @1 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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89 TATGGTCAGAAA |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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90 +1 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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91 40 40 40 40 40 40 40 40 40 40 40 20 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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92 @2 |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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93 CAGCGAGGCTTT |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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94 +2 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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95 40 40 40 40 40 40 40 40 30 20 19 20 |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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96 |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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97 ------ |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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98 |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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99 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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100 |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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101 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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102 |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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103 </help> |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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104 <citations> |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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105 <citation type="bibtex"><![CDATA[ |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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106 @ARTICLE{Gordon2009, |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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107 author = {Gordon, A.}, |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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108 title = {fastx_toolkit}, |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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109 year = {2009}, |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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110 publisher = {GitHub}, |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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111 journal = {GitHub repository}, |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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112 howpublished = {\url{https://github.com/agordon/fastx_toolkit}}, |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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113 commit = {ea0ca83ba24dce80c20ca589b838a281fe5deb0c} |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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114 }]]></citation> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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115 </citations> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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116 </tool> |
27e997d5c273
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer commit b8f23cd5bce0118cc9aab61253056b596e42a06f"
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117 <!-- FASTX-Quality-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |