Mercurial > repos > iuc > read_it_and_keep

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 044b7c1696bf6fef1c8ebf5143c0a841831e92fa
author iuc
date Fri, 15 Mar 2024 16:14:58 +0000
parents 1563b58905f4
children
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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>
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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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5 </macros>
2
fa7086274673 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 044b7c1696bf6fef1c8ebf5143c0a841831e92fa
iuc
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6 <xrefs>
fa7086274673 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 044b7c1696bf6fef1c8ebf5143c0a841831e92fa
iuc
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7 <xref type="bio.tools">read_it_and_keep</xref>
fa7086274673 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 044b7c1696bf6fef1c8ebf5143c0a841831e92fa
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8 </xrefs>
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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9 <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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10 <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"
iuc
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11 <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"
iuc
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12 </requirements>
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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13 <version_command><![CDATA[readItAndKeep -V]]></version_command>
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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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14 <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"
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15 #if $ref_source.source == "history"
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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16 ln -s '$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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17 #elif $ref_source.source == "builtin"
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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18 ln -s '$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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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 $trim_reference
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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21 python '$__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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22 #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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23 #if $reads.read_type == "paired"
1
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24 #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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25 #set $ext_out2 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq'
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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26 ln -s '$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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27 ln -s '$reads.read2' read2 &&
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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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28 #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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29 #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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30 #set $ext_out2 = 'fasta' if $reads.paired_reads.reverse.ext in ['fasta', 'fasta.gz'] else 'fastq'
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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31 ln -s '$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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32 ln -s '$reads.paired_reads.reverse' read2 &&
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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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33 #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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34 #set $ext_out1 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq'
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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35 ln -s '$reads.read1' read1 &&
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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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36 #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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37 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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38 --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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39 --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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40 --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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41 --min_map_length_pc $adv.min_map_length_pc
1
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42 $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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43 --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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44 #if $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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45 --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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46 #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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47 -o output
1
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48 #if $reads.read_type == 'single':
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49 && mv output.reads.${ext_out1}.gz 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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50 #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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51 #if $reads.read_type == 'paired_collection':
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52 #if not $reads.paired_reads.forward.ext.endswith('.gz'):
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53 && gunzip ./output.reads_1.${ext_out1}.gz
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54 && gunzip ./output.reads_2.${ext_out2}.gz
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55 #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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56 #elif not $reads.read1.ext.endswith('.gz'):
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57 && gunzip ./output.reads_1.${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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58 #if $reads.read_type != 'single' and not $reads.read2.ext.endswith('.gz'):
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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59 && gunzip ./output.reads_2.${ext_out2}.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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60 #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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61 #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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62 ]]></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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63 <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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64 <conditional name="reads">
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65 <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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66 <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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67 <option value="paired_collection">Paired collection</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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68 <option value="single">Single ended</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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69 </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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70 <when value="paired">
1
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71 <param type="data" format="@INPUT_FORMATS@" name="read1" label="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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72 <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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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="paired_collection">
1
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75 <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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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 <when value="single">
1
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78 <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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79 </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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80 </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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81 <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:
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82 <param type="select" label="Reference genome source" name="source">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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83 <option value="history" selected="true">History</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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84 <option value="builtin">Built-in</option>
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85 </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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parents:
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86 <when 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
87 <param type="data" format="fasta" name="ref_fasta" label="Reference genome" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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88 </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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89 <when value="builtin">
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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90 <param type="select" name="ref_fasta_builtin" label="Reference genome">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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91 <options from_data_table="all_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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92 </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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93 </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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94 </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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95 <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)" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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96 <param type="select" argument="--tech" name="sequencing_tech" label="Sequencing technology">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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97 <option value="illumina">Illumina</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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98 <option value="ont">Oxford Nanopore</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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99 </param>
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100 <section name="adv" title="Advanced options">
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101 <param argument="--min_map_length" type="integer" min="0" value="50" label="Shortest match required to keep a read (in bp)" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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102 <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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parents: 0
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103 <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
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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104 </section>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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105 </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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106 <outputs>
1
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107 <data name="output_reads1" format_source="read1" label="Filtered reads ${on_string} - reads1" from_work_dir="output.reads_1.fast*">
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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108 <filter>reads["read_type"] == "single" or reads["read_type"] == "paired"</filter>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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109 </data>
1
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110 <data name="output_reads2" format_source="read2" label="Filtered reads ${on_string} - reads2" from_work_dir="output.reads_2.fast*">
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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111 <filter>reads["read_type"] == "paired"</filter>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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112 </data>
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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113 <collection type="paired" name="output_collection" format_source="paired_reads" label="Filtered reads ${on_string}">
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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114 <filter>reads["read_type"] == "paired_collection"</filter>
1
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115 <data name="forward" from_work_dir="output.reads_1.fast*" />
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116 <data name="reverse" from_work_dir="output.reads_2.fast*" />
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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117 </collection>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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118 </outputs>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
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119 <tests>
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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diff changeset
120 <!--Testing uncompressed fastq input-->
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121 <test expect_num_outputs="2">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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122 <conditional name="reads">
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diff changeset
123 <param name="read_type" value="paired" />
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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diff changeset
124 <param name="read1" value="test1.fastq.gz" ftype="fastqsanger" />
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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125 <param name="read2" value="test2.fastq.gz" 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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diff changeset
126 </conditional>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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127 <conditional name="ref_source">
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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128 <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"
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129 <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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130 </conditional>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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diff changeset
131 <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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parents: 0
diff changeset
132 <output name="output_reads1" file="output.test1.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"
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133 <output name="output_reads2" file="output.test1.reads_2.fastq" ftype="fastqsanger"/>
1563b58905f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
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134 </test>
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135 <test expect_num_outputs="3">
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
diff changeset
136 <conditional name="reads">
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iuc
parents: 0
diff changeset
137 <param name="read_type" value="paired_collection" />
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
diff changeset
138 <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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139 <collection type="paired">
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iuc
parents: 0
diff changeset
140 <element name="forward" value="test1.fastq.gz" ftype="fastqsanger" />
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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141 <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger" />
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142 </collection>
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143 </param>
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144 </conditional>
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145 <conditional name="ref_source">
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parents: 0
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146 <param name="source" value="history" />
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147 <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
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148 </conditional>
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149 <param name="sequencing_tech" value="illumina" />
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150 <output_collection name="output_collection" type="paired">
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151 <element name="forward" file="output.test1.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"
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parents: 0
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152 <element name="reverse" file="output.test1.reads_2.fastq" ftype="fastqsanger"/>
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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153 </output_collection>
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iuc
parents: 0
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154 </test>
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iuc
parents: 0
diff changeset
155 <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"
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parents: 0
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156 <conditional name="reads">
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parents: 0
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157 <param name="read_type" value="single" />
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parents: 0
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158 <param name="read1" value="test3.fastq.gz" ftype="fastqsanger"/>
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parents: 0
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159 </conditional>
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iuc
parents: 0
diff changeset
160 <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
161 <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
162 <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
163 </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
164 <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
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165 <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
166 <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
parents: 0
diff changeset
167 </test>
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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168 <!--Testing uncompressed fasta input-->
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iuc
parents: 0
diff changeset
169 <test expect_num_outputs="2">
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
170 <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
171 <param name="read_type" value="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
172 <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"
iuc
parents: 0
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173 <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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174 </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
175 <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
176 <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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177 <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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178 </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
179 <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
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180 <output name="output_reads1" 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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181 <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"
iuc
parents: 0
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182 </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
183 <test expect_num_outputs="3">
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
184 <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
185 <param name="read_type" value="paired_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
186 <param name="paired_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
187 <collection type="paired">
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iuc
parents: 0
diff changeset
188 <element name="forward" 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"
iuc
parents: 0
diff changeset
189 <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"
iuc
parents: 0
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190 </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
191 </param>
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iuc
parents: 0
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192 </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
193 <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
194 <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
195 <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
196 </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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197 <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
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198 <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
199 <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
diff changeset
200 <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"
iuc
parents: 0
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201 </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
202 </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
203 <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
204 <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
205 <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
206 <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
diff changeset
207 </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
208 <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
209 <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
210 <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
211 </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
212 <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
213 <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
214 <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"
iuc
parents: 0
diff changeset
215 </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
216 <!--Testing compressed fasta input-->
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
217 <test expect_num_outputs="2">
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
218 <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
219 <param name="read_type" value="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
220 <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
diff changeset
221 <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"
iuc
parents: 0
diff changeset
222 </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
223 <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
224 <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
225 <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
226 </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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227 <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
228 <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"
iuc
parents: 0
diff changeset
229 <output name="output_reads2" decompress="true" file="output.test1.reads_2.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
230 </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
231 <test expect_num_outputs="3">
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
232 <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
233 <param name="read_type" value="paired_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
234 <param name="paired_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
235 <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
236 <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
diff changeset
237 <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
diff changeset
238 </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
239 </param>
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
240 </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
241 <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
242 <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
243 <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
244 </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
245 <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
246 <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
247 <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
248 <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
249 <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
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 </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
252 <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
253 <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
254 <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
255 </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
256 </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
257 </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
258 </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
259 <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
260 <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
261 <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
262 <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
263 </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
264 <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
265 <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
266 <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
267 </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
268 <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
269 <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
270 <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
271 </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
272 <!--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
273 <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
274 <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
275 <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
276 <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
277 <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
278 </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
279 <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
280 <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
281 <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
282 </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
283 <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
284 <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
285 <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
286 </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
287 <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
288 <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
289 <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
290 <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
291 <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
292 <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
293 <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
294 </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
295 </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
296 </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
297 <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
298 <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
299 <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
300 </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
301 <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
302 <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
303 <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
304 <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
305 <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
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 </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
308 <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
309 <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
310 <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
311 </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
312 </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
313 </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
314 </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
315 <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
316 <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
317 <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
318 <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
319 </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
320 <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
321 <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
322 <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
323 </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
324 <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
325 <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
326 <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
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327 </test>
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 </tests>
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 <help><![CDATA[
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
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 -------------
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
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 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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334 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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335 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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336
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 **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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338 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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339 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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340
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 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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342 ]]></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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343 <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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344 <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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345 </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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346 </tool>