Mercurial > repos > nml > quasitools
annotate quality.xml @ 9:18aad692772a draft default tip
planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author | nml |
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date | Mon, 20 Jun 2022 20:06:36 +0000 |
parents | 9def47f3c1e4 |
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rev | line source |
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9
18aad692772a
planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
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1 <tool id="quality" name="Quality control" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
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b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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2 <description>Performs quality control on FASTQ reads.</description> |
9
18aad692772a
planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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3 <macros> |
18aad692772a
planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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4 <import>macros.xml</import> |
18aad692772a
planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
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5 </macros> |
18aad692772a
planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
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6 <expand macro="requirements"/> |
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b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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7 <command detect_errors="exit_code"><![CDATA[ |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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8 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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9 quasitools quality |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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10 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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11 ## Preparing file input. |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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12 #if $data_type.type == "paired": |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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13 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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14 '$data_type.fastq_input1' |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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15 '$data_type.fastq_input2' |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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16 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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17 #elif $data_type.type == "collection": |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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18 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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19 '$data_type.fastq_input1.forward' |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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20 '$data_type.fastq_input1.reverse' |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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21 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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22 #elif $data_type.type == "single": |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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23 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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24 '$data_type.fastq_input1' |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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25 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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26 #end if |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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27 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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28 #if $length_cutoff: |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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29 -lc '$length_cutoff' |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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30 #end if |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
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31 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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32 #if $score_cutoff: |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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33 -sc '$score_cutoff' |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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34 #end if |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
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35 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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36 #if $min_read_qual: |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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37 -rq '$min_read_qual' |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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38 #end if |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
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39 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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40 #if $low_quality.qual_selector == "filter_ns": |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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41 --ns |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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42 #elif $low_quality.qual_selector == "mask_reads": |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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43 --mask_reads |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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44 #end if |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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45 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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46 #if $score_type.score_selector == "median": |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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47 --median |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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48 #elif $score_type.score_selector == "mean": |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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49 --mean |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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50 #end if |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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51 |
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planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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52 $trim_reads |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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53 |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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54 -o output |
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planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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55 |
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planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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56 ]]></command> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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57 <inputs> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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58 <conditional name="data_type"> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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59 <param name="type" type="select" label="Specify the read type."> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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60 <option value="single">Single-end Data</option> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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61 <option value="paired">Paired-end Data</option> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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62 <option value="collection">Collection Paired-end Data</option> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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63 </param> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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64 <when value="single"> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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65 <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
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66 </when> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
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67 <when value="paired"> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
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68 <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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69 <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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70 </when> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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71 <when value="collection"> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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72 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" /> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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73 </when> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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parents:
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74 </conditional> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
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75 <param name="length_cutoff" type="integer" optional="true" min="1" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." /> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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76 <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose median or mean quality score (depending on the score type specified) is less than the specified score cutoff value will be filtered out. Defaults to 30." /> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
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77 <param name="min_read_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for a position in a read not to be masked, is masking is enabled. Defaults to 30." /> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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78 <param name="trim_reads" type="boolean" optional="true" checked="false" truevalue="-tr" falsevalue="" label="Trim reads" help="Iteratively trim reads based on filter values if enabled." /> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
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79 <conditional name="low_quality"> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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80 <param name="qual_selector" type="select" label="Filter out regions masked, or mask low coverage regions with n's." multiple="false" display="radio"> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
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81 <option value="filter_ns">Filter out regions with n's</option> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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82 <option value="mask_reads">Mask low coverage regions with n's</option> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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83 <option value="neither" selected="true">Do not filter or mask low coverage regions.</option> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
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84 </param> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
nml
parents:
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85 <when value="filter_ns"> |
b69e898b8109
planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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86 </when> |
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87 <when value="mask_reads"> |
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88 </when> |
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89 <when value="neither"> |
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90 </when> |
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91 </conditional> |
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92 <conditional name="score_type"> |
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93 <param name="score_selector" type="select" label="Use either median score (default) or mean score for the score cutoff value." multiple="false" display="radio"> |
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94 <option value="median" selected="true">Use median score</option> |
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95 <option value="mean">Use mean score</option> |
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96 </param> |
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97 <when value="median"> |
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98 </when> |
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99 <when value="mean"> |
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100 </when> |
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101 </conditional> |
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102 </inputs> |
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103 <outputs> |
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104 <data format="fastq" label="Quality control output" name="output_filtered" from_work_dir="output/filtered.fastq" /> |
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105 </outputs> |
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106 <tests> |
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107 <test> |
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108 <param name="type" value="single"/> |
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109 <param name="fastq_input1" value="forward.fastq" /> |
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110 <param name="score_selector" value="median" /> |
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111 <output name="output_filtered"> |
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112 <assert_contents> |
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113 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" /> |
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114 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" /> |
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115 </assert_contents> |
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116 </output> |
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117 </test> |
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118 <test> |
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119 <param name="type" value="single"/> |
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120 <param name="fastq_input1" value="forward.fastq" /> |
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121 <param name="score_selector" value="median" /> |
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122 <param name="qual_selector" value="filter_ns" /> |
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123 <output name="output_filtered"> |
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124 <assert_contents> |
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125 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" /> |
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126 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" /> |
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127 </assert_contents> |
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128 </output> |
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129 </test> |
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130 <test> |
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131 <param name="type" value="single"/> |
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132 <param name="fastq_input1" value="forward.fastq" /> |
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133 <param name="score_selector" value="median" /> |
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134 <param name="trim_reads" value="-tr" /> |
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135 <output name="output_filtered"> |
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136 <assert_contents> |
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137 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" /> |
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138 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" /> |
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139 </assert_contents> |
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140 </output> |
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141 </test> |
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142 <test> |
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143 <param name="type" value="single"/> |
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144 <param name="fastq_input1" value="forward.fastq" /> |
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145 <param name="score_selector" value="median" /> |
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146 <param name="qual_selector" value="mask_reads" /> |
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147 <output name="output_filtered"> |
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148 <assert_contents> |
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149 <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" /> |
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150 <has_text text="NNNNNNTACCACATCCCNCNNNNTTNNNNNNNNNNANNTCNNTNNCNNTNCTNNNTNTNNNTGNTGCNTNTTTTTCAGTTCCCTTNGNTGNNGNCTTCAGNNNNTATACTGCATTTACCNTNCNT" /> |
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151 </assert_contents> |
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152 </output> |
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153 </test> |
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154 <test> |
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155 <param name="type" value="single"/> |
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156 <param name="fastq_input1" value="forward.fastq" /> |
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157 <param name="score_selector" value="mean" /> |
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158 <output name="output_filtered"> |
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159 <assert_contents> |
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160 <has_text text="@M01647:10:000000000-ACPHB:1:1101:10485:1674 1:N:0:86" /> |
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161 <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" /> |
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162 </assert_contents> |
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163 </output> |
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164 </test> |
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165 </tests> |
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166 <help><![CDATA[ |
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167 Quality Control |
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168 =============== |
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169 |
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170 Perform quality control on FASTQ reads.]]></help> |
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171 <expand macro="citations" /> |
5
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planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1
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changeset
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172 </tool> |