Mercurial > repos > iuc > seqkit_split2

annotate seqkit_split2.xml @ 0:c19015f577a5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
author iuc
date Fri, 26 Sep 2025 16:48:57 +0000
parents
children 911de3a36b31
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0
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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1 <tool id="seqkit_split2" name="Seqkit Split2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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2 <description>Split sequences into files by part size, number of parts, or length</description>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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3 <macros>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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4 <import>macros.xml</import>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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5 </macros>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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6 <expand macro="bio_tools"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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7 <expand macro="requirements"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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8 <command detect_errors="exit_code"><![CDATA[
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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9 #import re
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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10 mkdir -p out &&
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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11
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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12 ## The preprocessing steps below are adapted from the cutadapt.xml tool wrapper.
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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13 ## Set things up for handling inputs and outputs in single- vs paired-end modes
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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14 #set input_type = str($input_file_type.type)
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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15 #if $input_type == 'single':
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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16 #set paired = False
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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17 #else:
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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18 #set paired = True
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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19 #end if
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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20
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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21 #if $input_type == 'paired_collection'
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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22 #set input_1 = $input_file_type.input_1.forward
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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23 #set input_2 = $input_file_type.input_1.reverse
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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24 #set read1 = re.sub('[^\w\-\s]', '_', str($input_file_type.input_1.name)) + "_1"
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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25 #set read2 = re.sub('[^\w\-\s]', '_', str($input_file_type.input_1.name)) + "_2"
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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26 #else
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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27 #set input_1 = $input_file_type.input_1
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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28 #set read1 = re.sub('[^\w\-\s]', '_', str($input_file_type.input_1.element_identifier))
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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29 #end if
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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30
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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31 #if $input_1.is_of_type("fastq", "fastq.gz"):
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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32 #set ext = ".fastqsanger"
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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33 #else
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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34 #set ext = ".fasta"
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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35 #end if
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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36 #if $input_1.ext.endswith(".gz"):
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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37 #set ext=ext+".gz"
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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38 #end if
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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39
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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40 #set read1 = $read1 + $ext
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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41
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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42 #if $paired:
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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43 #if $input_2.is_of_type("fastq", "fastq.gz"):
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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44 #set ext2 = ".fastqsanger"
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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45 #else
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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46 #set ext2 = ".fasta"
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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47 #end if
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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48 #if $input_2.ext.endswith(".gz"):
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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49 #set ext2=ext2+".gz"
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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50 #end if
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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51 #set read2 = $read2 + $ext2
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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52 #end if
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53
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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54 ## Link in the input files
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55 ln -fs '$input_1' '$read1' &&
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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56 #if $paired:
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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57 ln -fs '$input_2' '$read2' &&
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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58 #end if
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59
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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60 seqkit split2
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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61 #if $paired:
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62 -1 '$read1'
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63 -2 '$read2'
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64 #else:
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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65 '$read1'
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66 #end if
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67 #if str($split_type.split_selector) == 'by_part':
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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68 -p $split_type.by_part
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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69 #else if str($split_type.split_selector) == 'by_size':
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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70 -s $split_type.by_size
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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71 #else if str($split_type.split_selector) == 'by_length':
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72 -l $split_type.by_length
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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73 #end if
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74 -o seqkit_split2
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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75 -O out
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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76 -j "\${GALAXY_SLOTS:-4}"
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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77 ]]></command>
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78 <inputs>
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79 <conditional name="input_file_type">
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80 <param name="type" type="select" label="Single-end or Paired-end reads?">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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81 <option value="single">Single-end</option>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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82 <option value="paired_collection">Paired-end Collection</option>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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83 </param>
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84 <when value="single">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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85 <param name="input_1" type="data" format="@FASTQ_TYPES@" label="Input FASTQ/A file" help="Select a single FASTA or FASTQ file (gzipped or uncompressed)"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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86 </when>
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87 <when value="paired_collection">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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88 <param name="input_1" format="@FASTQ_TYPES@" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fasta&quot;" />
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
89 </when>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
90 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
91 <conditional name="split_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
92 <param name="split_selector" type="select" label="Split sequences by">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
93 <option value="by_part" selected="true">Number of parts</option>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
94 <option value="by_size">Number of sequences per part</option>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
95 <option value="by_length">Length of sequences</option>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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parents:
diff changeset
96 </param>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
97 <when value="by_part">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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parents:
diff changeset
98 <param name="by_part" type="integer" value="" min="1" label="Number of parts" help="Split sequences into N parts using round-robin distribution." />
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
99 </when>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
100 <when value="by_size">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
101 <param name="by_size" type="integer" value="" min="1" label="Number of sequences per part" help="Split sequences into parts with N sequences each." />
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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parents:
diff changeset
102 </when>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
103 <when value="by_length">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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104 <param name="by_length" type="text" value="" label="Chunk size" help="Split sequences into chunks of >=N bases. Supports K/M/G suffix (e.g., 10K, 1M)">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
105 <validator type="regex" message="Invalid characters in field">^[0-9KMG]+$</validator>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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diff changeset
106 </param>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
107 </when>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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108 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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diff changeset
109 </inputs>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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110 <outputs>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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111 <collection name="outputs_files" type="list" label="${tool.name} on ${on_string}: Splitted files">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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112 <discover_datasets pattern="(?P&lt;designation&gt;seqkit_split2\.part_\d+)\.(?P&lt;ext&gt;.+)" directory="out"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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113 </collection>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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114 </outputs>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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115 <tests>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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116 <!-- Test 01: for Seqkit Split with Single End FASTQ file; splitting by parts -->
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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117 <test expect_num_outputs="1">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
118 <conditional name="input_file_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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119 <param name="type" value="single"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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120 <param name="input_1" value="reads_1.fq.gz"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
121 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
122 <conditional name="split_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
123 <param name="split_selector" value="by_part"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
124 <param name="by_part" value="2"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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diff changeset
125 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
126 <output_collection name="outputs_files" type="list" count="2">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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127 <element name="seqkit_split2.part_001" ftype="fastqsanger.gz">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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128 <assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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129 <has_n_lines n="4958"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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130 </assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
131 </element>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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132 <element name="seqkit_split2.part_002" ftype="fastqsanger.gz">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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133 <assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
134 <has_n_lines n="4949"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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135 </assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
136 </element>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
137 </output_collection>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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138 </test>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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139
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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140 <!-- Test 02: for Seqkit Split with Paired FASTQ Collection; splitting by parts -->
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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141 <test expect_num_outputs="1">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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142 <conditional name="input_file_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
143 <param name="type" value="paired_collection"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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144 <param name="input_1">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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145 <collection type="paired">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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146 <element name="forward" ftype="fastq.gz" value="reads_1.fq.gz"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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147 <element name="reverse" ftype="fastq.gz" value="reads_2.fq.gz"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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148 </collection>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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149 </param>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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150 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
151 <conditional name="split_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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152 <param name="split_selector" value="by_part"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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153 <param name="by_part" value="2"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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154 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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155 <output_collection name="outputs_files" type="list" count="2">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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156 <element name="seqkit_split2.part_001" ftype="fastqsanger.gz">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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157 <assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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158 <has_n_lines n="4958"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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159 </assert_contents>
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iuc
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160 </element>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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161 <element name="seqkit_split2.part_002" ftype="fastqsanger.gz">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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162 <assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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163 <has_n_lines n="4949"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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164 </assert_contents>
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165 </element>
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166 </output_collection>
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167 </test>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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168
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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169 <!-- Test 03: for Seqkit Split with Single End FASTA file; splitting by parts -->
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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170 <test expect_num_outputs="1">
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iuc
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171 <conditional name="input_file_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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172 <param name="type" value="single"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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173 <param name="input_1" value="hairpin.fa.gz"/>
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174 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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diff changeset
175 <conditional name="split_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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176 <param name="split_selector" value="by_part"/>
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177 <param name="by_part" value="2"/>
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178 </conditional>
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179 <output_collection name="outputs_files" type="list" count="2">
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180 <element name="seqkit_split2.part_001" ftype="fasta.gz">
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181 <assert_contents>
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182 <has_n_lines n="2988"/>
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183 </assert_contents>
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184 </element>
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185 <element name="seqkit_split2.part_002" ftype="fasta.gz">
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186 <assert_contents>
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187 <has_n_lines n="2987"/>
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188 </assert_contents>
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189 </element>
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190 </output_collection>
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191 </test>
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192
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193 <!-- Test 04: for Seqkit Split with Single End FASTA file; splitting by size -->
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194 <test expect_num_outputs="1">
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195 <conditional name="input_file_type">
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196 <param name="type" value="single"/>
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197 <param name="input_1" value="hairpin.fa.gz"/>
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198 </conditional>
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199 <conditional name="split_type">
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200 <param name="split_selector" value="by_size"/>
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201 <param name="by_size" value="200"/>
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202 </conditional>
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203 <output_collection name="outputs_files" type="list" count="25">
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204 <element name="seqkit_split2.part_001" ftype="fasta.gz">
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205 <assert_contents>
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206 <has_n_lines n="224"/>
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207 </assert_contents>
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208 </element>
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209 <element name="seqkit_split2.part_002" ftype="fasta.gz">
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210 <assert_contents>
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211 <has_n_lines n="281"/>
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212 </assert_contents>
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213 </element>
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214 </output_collection>
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215 </test>
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216
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217 <!-- Test 05: for Seqkit Split with Single End FASTA file; splitting by length -->
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218 <test expect_num_outputs="1">
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219 <conditional name="input_file_type">
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220 <param name="type" value="single"/>
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221 <param name="input_1" value="hairpin.fa.gz"/>
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222 </conditional>
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223 <conditional name="split_type">
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224 <param name="split_selector" value="by_length"/>
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225 <param name="by_length" value="50K"/>
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226 </conditional>
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227 <output_collection name="outputs_files" type="list" count="10">
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228 <element name="seqkit_split2.part_001" ftype="fasta.gz">
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229 <assert_contents>
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230 <has_n_lines n="642"/>
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231 </assert_contents>
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232 </element>
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233 <element name="seqkit_split2.part_002" ftype="fasta.gz">
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234 <assert_contents>
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235 <has_n_lines n="589"/>
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236 </assert_contents>
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237 </element>
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238 </output_collection>
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239 </test>
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240 </tests>
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241 <help><![CDATA[
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242
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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243 **Seqkit Split2**
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244
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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245 This tool splits FASTA or FASTQ files (single-end or paired-end) into multiple files based on the number of parts, sequences per part, or sequence length. It supports low memory usage and fast processing.
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246
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247 **Input type**: Choose between single-end FASTA/FASTQ or paired-end FASTQ files.
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248
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249 **Split sequences by**:
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250 - **Number of parts**: Split into N parts using round-robin distribution.
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251 - **Number of sequences per part**: Split into parts with N sequences each.
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252 - **Length of sequences**: Split into chunks of >=N bases (supports K/M/G suffix, e.g., 10K, 1M).
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253
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254 **Outputs**
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255
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256 - A collection of split FASTA/FASTQ files
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257
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258 For more details, see the Seqkit Split2 documentation_
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259
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260 .. _documentation: https://bioinf.shenwei.me/seqkit/usage/#split2
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261
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262 ]]></help>
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263 <expand macro="citations"/>
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264 <creator>
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265 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12" identifier="https://orcid.org/0009-0003-9935-828X"/>
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266 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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267 </creator>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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268 </tool>