Mercurial > repos > iuc > read_it_and_keep

annotate read-it-and-keep.xml @ 1:1563b58905f4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
author iuc
date Thu, 17 Mar 2022 11:12:09 +0000
parents 554aa2a63f04
children fa7086274673
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554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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1 <tool id="read_it_and_keep" name="Read It and Keep" version="@TOOL_VERSION@+galaxy0" profile="20.09">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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2 <macros>
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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3 <token name="@INPUT_FORMATS@">fasta,fastq,fasta.gz,fastq.gz</token>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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4 <token name="@TOOL_VERSION@">0.2.2</token>
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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5 </macros>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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6 <requirements>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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7 <requirement type="package" version="@TOOL_VERSION@">read-it-and-keep</requirement>
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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8 <requirement type="package" version="3.10">python</requirement>
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554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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9 </requirements>
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
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10 <version_command><![CDATA[readItAndKeep -V]]></version_command>
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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11 <command detect_errors="exit_code"><![CDATA[
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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12 #if $ref_source.source == "history"
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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13 ln -s '$ref_source.ref_fasta' ref${trim_reference}.fasta &&
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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14 #elif $ref_source.source == "builtin"
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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15 ln -s '$ref_source.ref_fasta_builtin.path' ref${trim_reference}.fasta &&
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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16 #end if
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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17 #if $trim_reference
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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18 python '$__tool_directory__/trim_reference.py' ref${trim_reference}.fasta ref.fasta &&
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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19 #end if
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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20 #if $reads.read_type == "paired"
1
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21 #set $ext_out1 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq'
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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22 #set $ext_out2 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq'
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
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23 ln -s '$reads.read1' read1 &&
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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24 ln -s '$reads.read2' read2 &&
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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25 #elif $reads.read_type == 'paired_collection'
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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26 #set $ext_out1 = 'fasta' if $reads.paired_reads.forward.ext in ['fasta', 'fasta.gz'] else 'fastq'
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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27 #set $ext_out2 = 'fasta' if $reads.paired_reads.reverse.ext in ['fasta', 'fasta.gz'] else 'fastq'
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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28 ln -s '$reads.paired_reads.forward' read1 &&
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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29 ln -s '$reads.paired_reads.reverse' read2 &&
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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30 #elif $reads.read_type == 'single'
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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31 #set $ext_out1 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq'
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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32 ln -s '$reads.read1' read1 &&
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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33 #end if
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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34 readItAndKeep
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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35 --tech $sequencing_tech
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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36 --ref_fasta ref.fasta
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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37 --min_map_length $adv.min_map_length
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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38 --min_map_length_pc $adv.min_map_length_pc
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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39 $adv.enumerate_names
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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40 --reads1 read1
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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41 #if $reads.read_type != "single"
1
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42 --reads2 read2
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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43 #end if
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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44 -o output
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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45 #if $reads.read_type == 'single':
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46 && mv output.reads.${ext_out1}.gz output.reads_1.${ext_out1}.gz
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47 #end if
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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48 #if $reads.read_type == 'paired_collection':
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49 #if not $reads.paired_reads.forward.ext.endswith('.gz'):
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50 && gunzip ./output.reads_1.${ext_out1}.gz
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51 && gunzip ./output.reads_2.${ext_out2}.gz
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52 #end if
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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53 #elif not $reads.read1.ext.endswith('.gz'):
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54 && gunzip ./output.reads_1.${ext_out1}.gz
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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55 #if $reads.read_type != 'single' and not $reads.read2.ext.endswith('.gz'):
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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56 && gunzip ./output.reads_2.${ext_out2}.gz
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57 #end if
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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58 #end if
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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59 ]]></command>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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60 <inputs>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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61 <conditional name="reads">
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62 <param type="select" label="Read type" name="read_type">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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63 <option value="paired" selected="true">Paired end</option>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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64 <option value="paired_collection">Paired collection</option>
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65 <option value="single">Single ended</option>
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66 </param>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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67 <when value="paired">
1
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68 <param type="data" format="@INPUT_FORMATS@" name="read1" label="Read1" />
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69 <param type="data" format="@INPUT_FORMATS@" name="read2" label="Read2" />
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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70 </when>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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71 <when value="paired_collection">
1
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72 <param type="data_collection" collection_type="paired" format="@INPUT_FORMATS@" name="paired_reads" label="Reads" />
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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73 </when>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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74 <when value="single">
1
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75 <param type="data" format="@INPUT_FORMATS@" name="read1" label="Read1" />
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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76 </when>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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77 </conditional>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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78 <conditional name="ref_source">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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79 <param type="select" label="Reference genome source" name="source">
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80 <option value="history" selected="true">History</option>
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81 <option value="builtin">Built-in</option>
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82 </param>
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83 <when value="history">
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84 <param type="data" format="fasta" name="ref_fasta" label="Reference genome" />
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85 </when>
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86 <when value="builtin">
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87 <param type="select" name="ref_fasta_builtin" label="Reference genome">
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88 <options from_data_table="all_fasta" />
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89 </param>
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90 </when>
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91 </conditional>
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92 <param type="boolean" name="trim_reference" label="Trim trailing As from the reference sequence" checked="true" truevalue="_untrimmed" falsevalue="" help="Remove all As at the end of the reference sequence to ensure that the reference has no poly-A tail (see Note in the general help section below)" />
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93 <param type="select" argument="--tech" name="sequencing_tech" label="Sequencing technology">
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94 <option value="illumina">Illumina</option>
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95 <option value="ont">Oxford Nanopore</option>
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96 </param>
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97 <section name="adv" title="Advanced options">
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98 <param argument="--min_map_length" type="integer" min="0" value="50" label="Shortest match required to keep a read (in bp)" />
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99 <param argument="--min_map_length_pc" type="float" min="0.0" max="100.0" value="50.0" label="Minimum length of match required to keep a read (as percentage of read length" />
1
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100 <param name="enumerate_names" type="boolean" truevalue="--enumerate_names" falsevalue="" label="Rename the reads 1,2,3,... (for paired reads, will also add /1 or /2 to the end of names)" />
0
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101 </section>
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102 </inputs>
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103 <outputs>
1
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104 <data name="output_reads1" format_source="read1" label="Filtered reads ${on_string} - reads1" from_work_dir="output.reads_1.fast*">
0
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105 <filter>reads["read_type"] == "single" or reads["read_type"] == "paired"</filter>
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106 </data>
1
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107 <data name="output_reads2" format_source="read2" label="Filtered reads ${on_string} - reads2" from_work_dir="output.reads_2.fast*">
0
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108 <filter>reads["read_type"] == "paired"</filter>
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109 </data>
1
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110 <collection type="paired" name="output_collection" format_source="paired_reads" label="Filtered reads ${on_string}">
0
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111 <filter>reads["read_type"] == "paired_collection"</filter>
1
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112 <data name="forward" from_work_dir="output.reads_1.fast*" />
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113 <data name="reverse" from_work_dir="output.reads_2.fast*" />
0
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114 </collection>
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115 </outputs>
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116 <tests>
1
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117 <!--Testing uncompressed fastq input-->
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118 <test expect_num_outputs="2">
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119 <conditional name="reads">
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120 <param name="read_type" value="paired" />
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121 <param name="read1" value="test1.fastq.gz" ftype="fastqsanger" />
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122 <param name="read2" value="test2.fastq.gz" ftype="fastqsanger" />
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123 </conditional>
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124 <conditional name="ref_source">
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125 <param name="source" value="history" />
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126 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
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127 </conditional>
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128 <param name="sequencing_tech" value="illumina" />
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129 <output name="output_reads1" file="output.test1.reads_1.fastq" ftype="fastqsanger"/>
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130 <output name="output_reads2" file="output.test1.reads_2.fastq" ftype="fastqsanger"/>
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131 </test>
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132 <test expect_num_outputs="3">
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133 <conditional name="reads">
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134 <param name="read_type" value="paired_collection" />
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135 <param name="paired_reads">
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136 <collection type="paired">
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137 <element name="forward" value="test1.fastq.gz" ftype="fastqsanger" />
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138 <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger" />
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139 </collection>
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140 </param>
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141 </conditional>
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142 <conditional name="ref_source">
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143 <param name="source" value="history" />
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144 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
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145 </conditional>
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146 <param name="sequencing_tech" value="illumina" />
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147 <output_collection name="output_collection" type="paired">
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148 <element name="forward" file="output.test1.reads_1.fastq" ftype="fastqsanger"/>
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149 <element name="reverse" file="output.test1.reads_2.fastq" ftype="fastqsanger"/>
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150 </output_collection>
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151 </test>
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152 <test expect_num_outputs="1">
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153 <conditional name="reads">
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154 <param name="read_type" value="single" />
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155 <param name="read1" value="test3.fastq.gz" ftype="fastqsanger"/>
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156 </conditional>
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157 <conditional name="ref_source">
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158 <param name="source" value="history" />
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159 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
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160 </conditional>
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iuc
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161 <param name="sequencing_tech" value="ont" />
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162 <param name="enumerate_names" value="True" />
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iuc
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163 <output name="output_reads1" file="output.test3.reads_1.fastq" ftype="fastqsanger"/>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
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164 </test>
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165 <!--Testing uncompressed fasta input-->
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iuc
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166 <test expect_num_outputs="2">
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iuc
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167 <conditional name="reads">
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iuc
parents: 0
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168 <param name="read_type" value="paired" />
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iuc
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169 <param name="read1" value="test1.fasta.gz" ftype="fasta" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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170 <param name="read2" value="test2.fasta.gz" ftype="fasta" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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171 </conditional>
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iuc
parents: 0
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172 <conditional name="ref_source">
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iuc
parents: 0
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173 <param name="source" value="history" />
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iuc
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174 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
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iuc
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175 </conditional>
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176 <param name="sequencing_tech" value="illumina" />
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iuc
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177 <output name="output_reads1" file="output.test1.reads_1.fasta" ftype="fasta"/>
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178 <output name="output_reads2" file="output.test1.reads_2.fasta" ftype="fasta"/>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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179 </test>
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iuc
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180 <test expect_num_outputs="3">
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iuc
parents: 0
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181 <conditional name="reads">
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iuc
parents: 0
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182 <param name="read_type" value="paired_collection" />
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iuc
parents: 0
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183 <param name="paired_reads">
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iuc
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184 <collection type="paired">
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iuc
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185 <element name="forward" value="test1.fasta.gz" ftype="fasta" />
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iuc
parents: 0
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186 <element name="reverse" value="test2.fasta.gz" ftype="fasta" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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187 </collection>
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188 </param>
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iuc
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189 </conditional>
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iuc
parents: 0
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190 <conditional name="ref_source">
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parents: 0
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191 <param name="source" value="history" />
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iuc
parents: 0
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192 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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193 </conditional>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
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194 <param name="sequencing_tech" value="illumina" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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195 <output_collection name="output_collection" type="paired">
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iuc
parents: 0
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196 <element name="forward" file="output.test1.reads_1.fasta" ftype="fasta"/>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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197 <element name="reverse" file="output.test1.reads_2.fasta" ftype="fasta"/>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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198 </output_collection>
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iuc
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199 </test>
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iuc
parents: 0
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200 <test expect_num_outputs="1">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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201 <conditional name="reads">
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iuc
parents: 0
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202 <param name="read_type" value="single" />
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iuc
parents: 0
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203 <param name="read1" value="test3.fasta.gz" ftype="fasta"/>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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204 </conditional>
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iuc
parents: 0
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205 <conditional name="ref_source">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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206 <param name="source" value="history" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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207 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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208 </conditional>
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iuc
parents: 0
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209 <param name="sequencing_tech" value="ont" />
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parents: 0
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210 <param name="enumerate_names" value="True" />
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iuc
parents: 0
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211 <output name="output_reads1" file="output.test3.reads_1.fasta" ftype="fasta"/>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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parents: 0
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212 </test>
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iuc
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213 <!--Testing compressed fasta input-->
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iuc
parents: 0
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214 <test expect_num_outputs="2">
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iuc
parents: 0
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215 <conditional name="reads">
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iuc
parents: 0
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216 <param name="read_type" value="paired" />
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iuc
parents: 0
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217 <param name="read1" value="test1.fasta.gz" ftype="fasta.gz" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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218 <param name="read2" value="test2.fasta.gz" ftype="fasta.gz" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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219 </conditional>
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iuc
parents: 0
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220 <conditional name="ref_source">
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iuc
parents: 0
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221 <param name="source" value="history" />
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iuc
parents: 0
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222 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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parents: 0
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223 </conditional>
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224 <param name="sequencing_tech" value="illumina" />
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parents: 0
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225 <output name="output_reads1" decompress="true" file="output.test1.reads_1.fasta" ftype="fasta.gz"/>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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parents: 0
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226 <output name="output_reads2" decompress="true" file="output.test1.reads_2.fasta" ftype="fasta.gz"/>
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227 </test>
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parents: 0
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228 <test expect_num_outputs="3">
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iuc
parents: 0
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229 <conditional name="reads">
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iuc
parents: 0
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230 <param name="read_type" value="paired_collection" />
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iuc
parents: 0
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231 <param name="paired_reads">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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parents: 0
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232 <collection type="paired">
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iuc
parents: 0
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233 <element name="forward" value="test1.fasta.gz" ftype="fasta.gz" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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234 <element name="reverse" value="test2.fasta.gz" ftype="fasta.gz" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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235 </collection>
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iuc
parents: 0
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236 </param>
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iuc
parents: 0
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237 </conditional>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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238 <conditional name="ref_source">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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239 <param name="source" value="history" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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240 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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241 </conditional>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
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242 <param name="sequencing_tech" value="illumina" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
243 <output_collection name="output_collection" type="paired">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
244 <element name="forward" ftype="fasta.gz">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
245 <assert_contents>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
246 <has_size value="680" delta="50" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
247 </assert_contents>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
248 </element>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
249 <element name="reverse" ftype="fasta.gz">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
250 <assert_contents>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
251 <has_size value="670" delta="50" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
252 </assert_contents>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
253 </element>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
254 </output_collection>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
255 </test>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
256 <test expect_num_outputs="1">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
257 <conditional name="reads">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
258 <param name="read_type" value="single" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
259 <param name="read1" value="test3.fasta.gz" ftype="fasta.gz"/>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
260 </conditional>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
261 <conditional name="ref_source">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
262 <param name="source" value="history" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
263 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
264 </conditional>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
265 <param name="sequencing_tech" value="ont" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
266 <param name="enumerate_names" value="True" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
267 <output name="output_reads1" decompress="true" file="output.test3.reads_1.fasta" ftype="fasta.gz"/>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
268 </test>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
269 <!--Testing compressed fastq input-->
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
270 <test expect_num_outputs="2">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
271 <conditional name="reads">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
272 <param name="read_type" value="paired" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
273 <param name="read1" value="test1.fastq.gz" ftype="fastqsanger.gz" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
274 <param name="read2" value="test2.fastq.gz" ftype="fastqsanger.gz" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
275 </conditional>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
276 <conditional name="ref_source">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
277 <param name="source" value="history" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
278 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
279 </conditional>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
280 <param name="sequencing_tech" value="illumina" />
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
281 <output name="output_reads1" decompress="true" file="output.test1.reads_1.fastq" ftype="fastqsanger.gz"/>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
282 <output name="output_reads2" decompress="true" file="output.test1.reads_2.fastq" ftype="fastqsanger.gz"/>
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
283 </test>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
284 <test expect_num_outputs="3">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
285 <conditional name="reads">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
286 <param name="read_type" value="paired_collection" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
287 <param name="paired_reads">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
288 <collection type="paired">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
289 <element name="forward" value="test1.fastq.gz" ftype="fastqsanger.gz" />
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
290 <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger.gz" />
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
291 </collection>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
292 </param>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
293 </conditional>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
294 <conditional name="ref_source">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
295 <param name="source" value="history" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
296 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
297 </conditional>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
298 <param name="sequencing_tech" value="illumina" />
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
299 <output_collection name="output_collection" type="paired">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
300 <element name="forward" ftype="fastqsanger.gz">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
301 <assert_contents>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
302 <has_size value="995" delta="50" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
303 </assert_contents>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
304 </element>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
305 <element name="reverse" ftype="fastqsanger.gz">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
306 <assert_contents>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
307 <has_size value="960" delta="50" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
308 </assert_contents>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
309 </element>
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
310 </output_collection>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
311 </test>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
312 <test expect_num_outputs="1">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
313 <conditional name="reads">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
314 <param name="read_type" value="single" />
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
315 <param name="read1" value="test3.fastq.gz" ftype="fastqsanger.gz"/>
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
316 </conditional>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
317 <conditional name="ref_source">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
318 <param name="source" value="history" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
319 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
320 </conditional>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
321 <param name="sequencing_tech" value="ont" />
1
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
322 <param name="enumerate_names" value="True" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
iuc
parents: 0
diff changeset
323 <output name="output_reads1" decompress="true" file="output.test3.reads_1.fastq" ftype="fastqsanger.gz"/>
0
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
324 </test>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
325 </tests>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
326 <help><![CDATA[
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
327 ReadItAndKeep
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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328 -------------
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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329
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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330 ReadItAndKeep is a tool for filtering viral sequence data to remove host reads, developed for cleaning
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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331 SARS-CoV-2 sequencing data. It maps reads against the SARS-CoV-2 viral genome (with the poly-A tail removed)
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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332 and only keeps those that map well.
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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333
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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334 **Note**: If the reference genome supplied contains a poly-A tail, reads that contain part of a poly-A tail will map
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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335 to the refence, no matter what species they originate from. If you are not sure if the reference you are using has had
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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336 trailing A's trimmed, enable the `Trim trailing As` option.
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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337
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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338 Input can be either Illumina or Oxford Nanopore reads.
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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339 ]]></help>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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340 <citations>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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341 <citation type="doi">10.1101/2022.01.21.477194</citation>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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342 </citations>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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343 </tool>