Mercurial > repos > iuc > seqkit_split2

annotate seqkit_split2.xml @ 1:911de3a36b31 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
author iuc
date Wed, 08 Oct 2025 20:26:20 +0000
parents c19015f577a5
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911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
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1 <tool id="seqkit_split2" name="Seqkit Split2" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
0
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>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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10 mkdir -p out &&
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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':
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16 #set paired = False
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17 #else:
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18 #set paired = True
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19 #end if
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21 #if $input_type == 'paired_collection'
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22 #set input_1 = $input_file_type.input_1.forward
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23 #set input_2 = $input_file_type.input_1.reverse
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24 #set read1 = re.sub('[^\w\-\s]', '_', str($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
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27 #set input_1 = $input_file_type.input_1
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28 #set read1 = re.sub('[^\w\-\s]', '_', str($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
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30
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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
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34 #set ext = ".fasta"
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35 #end if
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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
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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
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41
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42 #if $paired:
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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"
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45 #else
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46 #set ext2 = ".fasta"
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47 #end if
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48 #if $input_2.ext.endswith(".gz"):
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49 #set ext2=ext2+".gz"
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50 #end if
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51 #set read2 = $read2 + $ext2
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52 #end if
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53
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54 ## Link in the input files
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55 ln -fs '$input_1' '$read1' &&
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56 #if $paired:
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57 ln -fs '$input_2' '$read2' &&
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58 #end if
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59
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60 seqkit split2
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61 #if $paired:
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62 -1 '$read1'
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63 -2 '$read2'
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64 #else:
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65 '$read1'
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66 #end if
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67 #if str($split_type.split_selector) == 'by_part':
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68 -p $split_type.by_part
1
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69 #if $paired:
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70 --by-part-prefix "seqkit_split2_R{read}_"
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71 #end if
0
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72 #else if str($split_type.split_selector) == 'by_size':
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73 -s $split_type.by_size
1
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74 #if $paired:
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75 --by-size-prefix string "seqkit_split2_R{read}_"
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76 #end if
0
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77 #else if str($split_type.split_selector) == 'by_length':
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78 -l $split_type.by_length
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79 #end if
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80 -o seqkit_split2
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81 -O out
1
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82 -j "\${GALAXY_SLOTS:-4}"
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83 #if $paired:
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84 && (find out/ -type f -name "seqkit_split2_*.*" | while read -r file; do mv "\$file" "\$(echo \$file | sed -E 's/(seqkit_split2)_(R1|R2)_([0-9]+)(\..+)/\1_\3_\2\4/' | sed -E 's/_R1/_forward/; s/_R2/_reverse/')"; done)
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
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85 #end if
0
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86 ]]></command>
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87 <inputs>
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88 <conditional name="input_file_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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89 <param name="type" type="select" label="Single-end or Paired-end reads?">
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90 <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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91 <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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92 </param>
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93 <when value="single">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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94 <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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95 </when>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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96 <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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97 <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
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98 </when>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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99 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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100 <conditional name="split_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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101 <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
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102 <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
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103 <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
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104 <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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105 </param>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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106 <when value="by_part">
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107 <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
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108 </when>
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109 <when value="by_size">
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110 <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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111 </when>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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112 <when value="by_length">
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113 <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
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114 <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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115 </param>
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116 </when>
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117 </conditional>
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118 </inputs>
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119 <outputs>
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120 <collection name="outputs_files" type="list" label="${tool.name} on ${on_string}: Splitted files">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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121 <discover_datasets pattern="(?P&lt;designation&gt;seqkit_split2\.part_\d+)\.(?P&lt;ext&gt;.+)" directory="out"/>
1
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122 <filter>input_file_type['type'] == 'single' </filter>
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123 </collection>
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124 <collection name="outputs_paired_files" type="list:paired" label="${tool.name} on ${on_string}: Paired-End Splitted files">
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125 <filter>input_file_type['type'] == 'paired_collection' </filter>
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126 <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_(?P&lt;identifier_1&gt;forward|reverse)\.(?P&lt;ext&gt;.+)" directory="out"/>
0
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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127 </collection>
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128 </outputs>
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129 <tests>
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130 <!-- Test 01: for Seqkit Split with Single End FASTQ file; splitting by parts -->
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131 <test expect_num_outputs="1">
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132 <conditional name="input_file_type">
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133 <param name="type" value="single"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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134 <param name="input_1" value="reads_1.fq.gz"/>
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135 </conditional>
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136 <conditional name="split_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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137 <param name="split_selector" value="by_part"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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138 <param name="by_part" value="2"/>
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139 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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140 <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
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141 <element name="seqkit_split2.part_001" ftype="fastqsanger.gz">
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142 <assert_contents>
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143 <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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144 </assert_contents>
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145 </element>
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146 <element name="seqkit_split2.part_002" ftype="fastqsanger.gz">
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147 <assert_contents>
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148 <has_n_lines n="4949"/>
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149 </assert_contents>
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150 </element>
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151 </output_collection>
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152 </test>
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153
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
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154 <!-- Test 02: for Seqkit Split with Paired FASTQ Collection; splitting by parts -->
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155 <test expect_num_outputs="1">
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156 <conditional name="input_file_type">
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157 <param name="type" value="paired_collection"/>
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158 <param name="input_1">
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159 <collection type="paired">
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160 <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
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161 <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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162 </collection>
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163 </param>
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164 </conditional>
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165 <conditional name="split_type">
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166 <param name="split_selector" value="by_part"/>
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167 <param name="by_part" value="2"/>
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168 </conditional>
1
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169 <output_collection name="outputs_paired_files" type="list:paired" count="2">
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170 <element name="seqkit_split2_001">
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171 <element name="forward" ftype="fastqsanger.gz">
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172 <assert_contents>
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173 <has_n_lines n="4958"/>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
174 </assert_contents>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
175 </element>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
176 <element name="reverse" ftype="fastqsanger.gz">
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
177 <assert_contents>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
178 <has_n_lines n="3792"/>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
179 </assert_contents>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
180 </element>
0
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
181 </element>
1
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
182 <element name="seqkit_split2_002">
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
183 <element name="forward" ftype="fastqsanger.gz">
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
184 <assert_contents>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
185 <has_n_lines n="4949"/>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
186 </assert_contents>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
187 </element>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
188 <element name="reverse" ftype="fastqsanger.gz">
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
189 <assert_contents>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
190 <has_n_lines n="3657"/>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
191 </assert_contents>
911de3a36b31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0
iuc
parents: 0
diff changeset
192 </element>
0
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
193 </element>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
194 </output_collection>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
195 </test>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
196
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
197 <!-- 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
iuc
parents:
diff changeset
198 <test expect_num_outputs="1">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
199 <conditional name="input_file_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
200 <param name="type" value="single"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
201 <param name="input_1" value="hairpin.fa.gz"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
202 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
203 <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
204 <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
parents:
diff changeset
205 <param name="by_part" value="2"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
206 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
207 <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
parents:
diff changeset
208 <element name="seqkit_split2.part_001" ftype="fasta.gz">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
209 <assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
210 <has_n_lines n="2988"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
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211 </assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
212 </element>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
213 <element name="seqkit_split2.part_002" ftype="fasta.gz">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
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214 <assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
215 <has_n_lines n="2987"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
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216 </assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
217 </element>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
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218 </output_collection>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
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219 </test>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
220
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
221 <!-- Test 04: for Seqkit Split with Single End FASTA file; splitting by size -->
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
222 <test expect_num_outputs="1">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
223 <conditional name="input_file_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
224 <param name="type" value="single"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
225 <param name="input_1" value="hairpin.fa.gz"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
226 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
227 <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
228 <param name="split_selector" value="by_size"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
229 <param name="by_size" value="200"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
230 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
231 <output_collection name="outputs_files" type="list" count="25">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
232 <element name="seqkit_split2.part_001" ftype="fasta.gz">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
233 <assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
234 <has_n_lines n="224"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
235 </assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
236 </element>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
237 <element name="seqkit_split2.part_002" ftype="fasta.gz">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
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238 <assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
239 <has_n_lines n="281"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
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240 </assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
241 </element>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
242 </output_collection>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
243 </test>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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244
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
245 <!-- Test 05: for Seqkit Split with Single End FASTA file; splitting by length -->
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
246 <test expect_num_outputs="1">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
247 <conditional name="input_file_type">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
248 <param name="type" value="single"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
249 <param name="input_1" value="hairpin.fa.gz"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
250 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
251 <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
252 <param name="split_selector" value="by_length"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
253 <param name="by_length" value="50K"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
254 </conditional>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
255 <output_collection name="outputs_files" type="list" count="10">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
256 <element name="seqkit_split2.part_001" ftype="fasta.gz">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
257 <assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
258 <has_n_lines n="642"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
259 </assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
260 </element>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
261 <element name="seqkit_split2.part_002" ftype="fasta.gz">
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
262 <assert_contents>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
parents:
diff changeset
263 <has_n_lines n="589"/>
c19015f577a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
iuc
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264 </assert_contents>
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265 </element>
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266 </output_collection>
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267 </test>
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268 </tests>
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269 <help><![CDATA[
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270
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271 **Seqkit Split2**
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272
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273 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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274
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275 **Input type**: Choose between single-end FASTA/FASTQ or paired-end FASTQ files.
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276
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277 **Split sequences by**:
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278 - **Number of parts**: Split into N parts using round-robin distribution.
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279 - **Number of sequences per part**: Split into parts with N sequences each.
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280 - **Length of sequences**: Split into chunks of >=N bases (supports K/M/G suffix, e.g., 10K, 1M).
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281
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282 **Outputs**
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283
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284 - A collection of split FASTA/FASTQ files
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285
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286 For more details, see the Seqkit Split2 documentation_
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287
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288 .. _documentation: https://bioinf.shenwei.me/seqkit/usage/#split2
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289
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290 ]]></help>
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291 <expand macro="citations"/>
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292 <creator>
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293 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12" identifier="https://orcid.org/0009-0003-9935-828X"/>
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294 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
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295 </creator>
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296 </tool>