Mercurial > repos > iuc > sickle

annotate sickle.xml @ 5:3905ccd5c631 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
author iuc
date Thu, 13 Apr 2017 16:06:10 -0400
parents edaa8572219d
children 6756c87dc2d4
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5
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
diff changeset
1 <tool id="sickle" name="Sickle" version="1.33.1" profile="17.01">
0
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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2 <description>windowed adaptive trimming of FASTQ data</description>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
iuc
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3 <requirements>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
iuc
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4 <requirement type="package" version="1.33">sickle</requirement>
2
013275060443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 9cf2e1454bf23a11ca0e7eeb26b4eaa446832bf8-dirty
iuc
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5 <!-- conda dependency -->
013275060443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 9cf2e1454bf23a11ca0e7eeb26b4eaa446832bf8-dirty
iuc
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6 <requirement type="package" version="1.33">sickle-trim</requirement>
0
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
iuc
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7 </requirements>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
iuc
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8 <version_command>sickle --version | head -n 1</version_command>
5
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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9 <command><![CDATA[
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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10 ## Link in the input files, which also determines the type of the output
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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11 #set compressed = ""
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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12 #if str($readtype.single_or_paired) == "se":
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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13 #if $readtype.input_single.is_of_type('fastq.gz'):
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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14 #set read1 = "input_1.fastq.gz"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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15 #set compressed = "-g"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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16 #else
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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17 #set read1 = "input_1.fastq"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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18 #end if
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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19 ln -f -s '${readtype.input_single}' ${read1} &&
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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20 #else if str($readtype.single_or_paired) == "pe_combo":
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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21 #if $readtype.input_combo.is_of_type('fastq.gz'):
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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22 #set read1 = "input_1.fastq.gz"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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23 #set compressed = "-g"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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24 #else
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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25 #set read1 = "input_1.fastq"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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26 #end if
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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27 ln -f -s '${readtype.input_combo}' ${read1} &&
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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28 #else if str($readtype.single_or_paired) == "pe_sep":
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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29 #if $readtype.input_paired1.is_of_type('fastq.gz'):
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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30 #set read1 = "input_1.fastq.gz"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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31 #set compressed = "-g"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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32 #else
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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33 #set read1 = "input_1.fastq"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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34 #end if
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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35 ln -f -s '${readtype.input_paired1}' ${read1} &&
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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36
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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37 #if $readtype.input_paired2.is_of_type('fastq.gz'):
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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diff changeset
38 #set read2 = "input_2.fastq.gz"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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39 #else
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
parents: 4
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40 #set read2 = "input_2.fastq"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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41 #end if
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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42 ln -f -s '${readtype.input_paired2}' ${read2} &&
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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43 #else
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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44 #if $readtype.input_paired.forward.is_of_type('fastq.gz'):
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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45 #set read1 = "input_1.fastq.gz"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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46 #set compressed = "-g"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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47 #else
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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48 #set read1 = "input_1.fastq"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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49 #end if
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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50 ln -f -s '${readtype.input_paired.forward}' ${read1} &&
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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51
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52 #if $readtype.input_paired.reverse.is_of_type('fastq.gz'):
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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53 #set read2 = "input_2.fastq.gz"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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54 #else
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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55 #set read2 = "input_2.fastq"
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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56 #end if
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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57 ln -f -s '${readtype.input_paired.reverse}' ${read2} &&
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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58 #end if
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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59
0
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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60 sickle
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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61
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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62 #if str($readtype.single_or_paired) == "se":
5
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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63 se -f ${read1} -o '${output_single}'
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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64
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65 #if $readtype.input_single.is_of_type('fastqillumina', 'fastqillumina.gz'):
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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66 -t illumina
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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67 #else if $readtype.input_single.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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68 -t solexa
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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69 #else:
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70 -t sanger
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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71 #end if
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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72 #else if str($readtype.single_or_paired) == "pe_combo":
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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73 #if $readtype.output_n:
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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74 pe -c ${read1} -M '${output_combo}'
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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75 #else
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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76 pe -c ${read1} -m '${output_combo}' -s '${output_combo_single}'
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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77 #end if
0
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1
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78
5
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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79 #if $readtype.input_combo.is_of_type('fastqillumina', 'fastqillumina.gz'):
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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80 -t illumina
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
iuc
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81 #else if $readtype.input_combo.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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82 -t solexa
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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83 #else:
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84 -t sanger
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85 #end if
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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86 #else if str($readtype.single_or_paired) == "pe_sep":
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87 pe -f ${read1} -r ${read2} -o '${output_paired1}' -p '${output_paired2}' -s '${output_paired_single}'
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88
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89 #if $readtype.input_paired1.is_of_type('fastqillumina', 'fastqillumina.gz'):
0
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90 -t illumina
5
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91 #else if $readtype.input_paired1.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
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92 -t solexa
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93 #else:
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94 -t sanger
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95 #end if
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96 #else if str($readtype.single_or_paired) == "pe_collection":
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97 pe -f ${read1} -r ${read2} -o '${output_paired_coll.forward}' -p '${output_paired_coll.reverse}' -s '${output_paired_coll_single}'
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98
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99 #if $readtype.input_paired.forward.is_of_type('fastqillumina', 'fastqillumina.gz'):
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100 -t illumina
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101 #else if $readtype.input_paired.forward.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
0
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102 -t solexa
4
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103 #else:
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104 -t sanger
0
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105 #end if
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106 #end if
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107
5
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108 $compressed
1
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109
0
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110 #if str($qual_threshold) != "":
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111 -q $qual_threshold
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112 #end if
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113
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114 #if str($length_threshold) != "":
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115 -l $length_threshold
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116 #end if
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117
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118 #if $no_five_prime:
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119 -x
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120 #end if
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121
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122 #if $trunc_n:
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123 -n
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124 #end if
5
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125 ]]>
0
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126 </command>
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127
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128 <inputs>
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129 <conditional name="readtype">
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130 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger.">
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131 <option value="se" selected="true">Single-end</option>
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132 <option value="pe_combo">Paired-end (one interleaved input file)</option>
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133 <option value="pe_sep">Paired-end (two separate input files)</option>
1
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134 <option value="pe_collection">Paired-end (as collection)</option>
0
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135 </param>
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136
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137 <when value="se">
5
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138 <param format="fastq,fastq.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" />
0
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139 </when>
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140
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141 <when value="pe_combo">
5
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142 <param format="fastq,fastq.gz" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)" />
0
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143 <param name="output_n" type="boolean" label="Output only one file with all reads" help="This will output only one file with all the reads, where the reads that did not pass filter will be replaced with a single 'N', rather than discarded."/>
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144 </when>
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145
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146 <when value="pe_sep">
5
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147 <param format="fastq,fastq.gz" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" />
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148 <param format="fastq,fastq.gz" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" />
0
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149 </when>
1
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150
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151 <when value="pe_collection">
5
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152 <param format="fastq,fastq.gz" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" />
1
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153 </when>
0
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154 </conditional>
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155
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156 <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)" />
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157
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158 <param name="length_threshold" value="20" min="0" type="integer" optional="true" label="Length threshold" help="Threshold to keep a read based on length after trimming (-l)" />
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159
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160 <param name="no_five_prime" type="boolean" label="Don't do 5' trimming" help="(-x)" />
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161 <param name="trunc_n" type="boolean" label="Truncate sequences with Ns at first N position" help="(-n)" />
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162 </inputs>
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163
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164 <outputs>
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165 <data name="output_single" format_source="input_single" label="Single-end output of ${tool.name} on ${on_string}">
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166 <filter>readtype['single_or_paired'] == 'se'</filter>
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167 </data>
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168
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169 <data name="output_combo" format_source="input_combo" label="Paired-end interleaved output of ${tool.name} on ${on_string}">
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170 <filter>readtype['single_or_paired'] == 'pe_combo'</filter>
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171 </data>
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172
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173 <data name="output_combo_single" format_source="input_combo" label="Singletons from paired-end interleaved output of ${tool.name} on ${on_string}">
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174 <filter>readtype['single_or_paired'] == 'pe_combo' and not readtype['output_n']</filter>
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175 </data>
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176
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177 <data name="output_paired1" format_source="input_paired1" label="Paired-end forward strand output of ${tool.name} on ${on_string}">
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178 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
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179 </data>
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180
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181 <data name="output_paired2" format_source="input_paired2" label="Paired-end reverse strand output of ${tool.name} on ${on_string}">
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182 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
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183 </data>
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184
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185 <data name="output_paired_single" format_source="input_paired1" label="Singletons from paired-end output of ${tool.name} on ${on_string}">
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186 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
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187 </data>
1
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188
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189 <collection name="output_paired_coll" type="paired" structured_like="input_paired" inherit_format="true" label="Paired-end output of ${tool.name} on ${on_string}">
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190 <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
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191 </collection>
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192
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193 <data name="output_paired_coll_single" format_source="input_paired['forward']" label="Singletons from paired-end output of ${tool.name} on ${on_string}">
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194 <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
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195 </data>
0
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196 </outputs>
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197 <tests>
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198 <test>
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199 <param name="single_or_paired" value="pe_combo" />
5
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200 <param name="input_combo" ftype="fastqillumina" value="test.fastq" />
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201 <param name="qual_threshold" value="3" />
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202 <output name="output_combo" ftype="fastqillumina" file="output.c1.fastq" />
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203 <output name="output_combo_single" ftype="fastqillumina" file="output.s.fastq" />
0
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204 </test>
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205 <test>
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206 <param name="single_or_paired" value="pe_combo" />
5
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207 <param name="input_combo" ftype="fastqillumina" value="test.fastq" />
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208 <param name="qual_threshold" value="3" />
0
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209 <param name="output_n" value="true" />
5
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210 <output name="output_combo" ftype="fastqillumina" file="output.c2.fastq" />
0
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211 </test>
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212 <test>
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213 <param name="single_or_paired" value="pe_sep" />
5
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214 <param name="input_paired1" ftype="fastqillumina" value="test.f.fastq" />
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215 <param name="input_paired2" ftype="fastqillumina" value="test.r.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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216 <param name="qual_threshold" value="3" />
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217 <output name="output_paired1" ftype="fastqillumina" file="output.f.fastq" />
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218 <output name="output_paired2" ftype="fastqillumina" file="output.r.fastq" />
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219 <output name="output_paired_single" ftype="fastqillumina" file="output.s.fastq" />
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220 </test>
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221 <test> <!-- as above, but gzipped -->
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222 <param name="single_or_paired" value="pe_sep" />
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223 <param name="input_paired1" ftype="fastqillumina.gz" value="test.f.fastq.gz" />
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224 <param name="input_paired2" ftype="fastqillumina.gz" value="test.r.fastq.gz" />
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225 <param name="qual_threshold" value="3" />
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226 <output name="output_paired1" ftype="fastqillumina.gz" file="output.f.fastq.gz" />
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227 <output name="output_paired2" ftype="fastqillumina.gz" file="output.r.fastq.gz" />
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228 <output name="output_paired_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" />
1
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229 </test>
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230 <test>
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231 <param name="single_or_paired" value="pe_collection" />
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232 <param name="input_paired">
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233 <collection type="paired">
5
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234 <element name="forward" ftype="fastqillumina" value="test.f.fastq" />
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235 <element name="reverse" ftype="fastqillumina" value="test.r.fastq" />
1
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236 </collection>
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237 </param>
5
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238 <param name="qual_threshold" value="3" />
1
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239 <output_collection name="output_paired_coll" type="paired">
5
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240 <element name="forward" ftype="fastqillumina" file="output.f.fastq" />
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241 <element name="reverse" ftype="fastqillumina" file="output.r.fastq" />
1
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242 </output_collection>
5
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243 <output name="output_paired_coll_single" ftype="fastqillumina" file="output.s.fastq" />
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244 </test>
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245
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246 <test> <!-- as above, but gzipped -->
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247 <param name="single_or_paired" value="pe_collection" />
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248 <param name="input_paired">
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249 <collection type="paired">
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250 <element name="forward" ftype="fastqillumina.gz" value="test.f.fastq.gz" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35
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251 <element name="reverse" ftype="fastqillumina.gz" value="test.r.fastq.gz" />
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252 </collection>
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253 </param>
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254 <param name="qual_threshold" value="3" />
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255 <output_collection name="output_paired_coll" type="paired">
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256 <element name="forward" ftype="fastqillumina.gz" file="output.f.fastq.gz" />
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257 <element name="reverse" ftype="fastqillumina.gz" file="output.r.fastq.gz" />
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258 </output_collection>
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259 <output name="output_paired_coll_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" />
0
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260 </test>
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261 </tests>
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262 <help>
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263 **What it does**
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264
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265 Most modern sequencing technologies produce reads that have
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266 deteriorating quality towards the 3'-end and some towards the 5'-end
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267 as well. Incorrectly called bases in both regions negatively impact
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268 assembles, mapping, and downstream bioinformatics analyses.
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269
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270 Sickle is a tool that uses sliding windows along with quality and
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271 length thresholds to determine when quality is sufficiently low to
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272 trim the 3'-end of reads and also determines when the quality is
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273 sufficiently high enough to trim the 5'-end of reads. It will also
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274 discard reads based upon the length threshold. It takes the quality
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275 values and slides a window across them whose length is 0.1 times the
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276 length of the read. If this length is less than 1, then the window is
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277 set to be equal to the length of the read. Otherwise, the window
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278 slides along the quality values until the average quality in the
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279 window rises above the threshold, at which point the algorithm
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280 determines where within the window the rise occurs and cuts the read
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281 and quality there for the 5'-end cut. Then when the average quality
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282 in the window drops below the threshold, the algorithm determines
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283 where in the window the drop occurs and cuts both the read and quality
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284 strings there for the 3'-end cut. However, if the length of the
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285 remaining sequence is less than the minimum length threshold, then the
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286 read is discarded entirely (or replaced with an "N" record). 5'-end
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287 trimming can be disabled. Sickle also has an option to truncate reads
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288 with Ns at the first N position.
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289
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290 Sickle supports three types of quality values: Illumina, Solexa, and
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291 Sanger. Note that the Solexa quality setting is an approximation (the
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292 actual conversion is a non-linear transformation). The end
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293 approximation is close. Illumina quality refers to qualities encoded
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294 with the CASAVA pipeline between versions 1.3 and 1.7. Illumina
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295 quality using CASAVA >= 1.8 is Sanger encoded. The quality value will
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296 be determined from the datatype of the data, i.e. a fastqsanger datatype
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297 is assumed to be Sanger encoded.
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298
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299 Note that Sickle will remove the 2nd FASTQ record header (on the "+"
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300 line) and replace it with simply a "+". This is the default format for
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301 CASAVA >= 1.8.
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302
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303 -----
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304
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305 **Options**
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306
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307 **Single-end**
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308
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309 This option takes one single-end input file and outputs one single-end
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310 output file of reads that passed the filters.
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311
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312 **Paired-End (one interleaved input file)**
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313
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314 This option takes as input one interleaved paired-end file. If you then
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315 check the "Output only one file with all reads" checkbox, it will output
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316 one interleaved file where any read that did not pass filter will be replaced
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317 with a FASTQ record where the sequence is a single "N" and the quality is the
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318 lowest quality possible for that quality type. This will preserve the paired
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319 nature of the data. If you leave the checkbox unchecked, it will output two files,
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320 one interleaved file with all the passed pairs and one singletons file where only
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321 one of the pair passed filter.
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322
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323 **Paired-End (two separate input files)**
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324
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325 This option takes two separate (forward and reverse) paired-end files as input.
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326 The output is three files: Two paired-end files with pairs that passed filter and
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327 a singletons file where only one of the pair passed filter.
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328
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329 **Quality threshold**
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330
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331 Input your desired quality threshold. This threshold is phred-scaled, which is typically
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332 values between 0-41 for FASTQ data.
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333
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334 **Length threshold**
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335
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336 Input your desired length threshold. This is the threshold to determine if a read is kept
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337 after all the trimming steps are done.
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338
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339 **Disable 5-prime trimming**
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340
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341 An option to disable trimming the read on the 5-prime end. This trimming trims the read
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342 if the average quality values dip below the quality threshold at the 5-prime end.
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343
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344 **Truncate sequences with Ns**
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345
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346 This option will trim a read at the first "N" base in the read after doing quality trimming.
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347 It is then still subject to the length threshold.
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348
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349 -----
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350
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351 Copyright: Nikhil Joshi
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352
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353 http://bioinformatics.ucdavis.edu
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354
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355 http://github.com/najoshi/sickle
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356 </help>
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357 <citations>
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358 <citation type="bibtex">
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359 @unpublished{sickle_link,
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360 author = {Joshi, Nikhil A. and Fass, Joseph N.},
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361 title = {Sickle: A windowed adaptive trimming tool for FASTQ files using quality},
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362 year = 2011,
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363 url = { https://github.com/najoshi/sickle }
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364 }
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365 </citation>
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366 </citations>
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367 </tool>