Mercurial > repos > iuc > read_it_and_keep

annotate read-it-and-keep.xml @ 0:554aa2a63f04 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
author iuc
date Fri, 28 Jan 2022 18:47:34 +0000
parents
children 1563b58905f4
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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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diff changeset
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>
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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3 <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
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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4 <token name="@TOOL_VERSION@">0.1.0</token>
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"
iuc
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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"
iuc
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7 <requirement type="package" version="@TOOL_VERSION@">read-it-and-keep</requirement>
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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8 <requirement type="package">python</requirement>
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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9 </requirements>
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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10 <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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11 #if $ref_source.source == "history"
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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12 ln -s '$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"
iuc
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13 #elif $ref_source.source == "builtin"
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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14 ln -s '$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"
iuc
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15 #end if
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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16 #if $trim_reference
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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17 python '$__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"
iuc
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18 #end if
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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19 #if $reads.read_type == "paired"
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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20 ln -s '$reads.read1' read1.fastq &&
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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21 ln -s '$reads.read2' read2.fastq &&
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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22 #elif $reads.read_type == 'paired_collection'
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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23 ln -s '$reads.paired_reads.forward' read1.fastq &&
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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24 ln -s '$reads.paired_reads.reverse' read2.fastq &&
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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25 #elif $reads.read_type == 'single'
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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26 ln -s '$reads.single_read1' read1.fastq &&
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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27 #end if
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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28 readItAndKeep
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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29 --tech $sequencing_tech
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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30 --ref_fasta ref.fasta
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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31 --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"
iuc
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32 --min_map_length_pc $adv.min_map_length_pc
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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33 --reads1 read1.fastq
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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34 #if $reads.read_type != "single"
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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35 --reads2 read2.fastq
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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36 #end if
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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37 -o output
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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38 #if $reads.read_type == 'single'
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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39 && mv output.reads.fastq.gz output.reads_1.fastq.gz
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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40 #end if
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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41 ]]></command>
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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42 <inputs>
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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43 <conditional name="reads">
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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44 <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"
iuc
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45 <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"
iuc
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46 <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"
iuc
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47 <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"
iuc
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48 </param>
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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49 <when value="paired">
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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50 <param type="data" format="@FASTQ_FORMATS@" name="read1" label="Read1" />
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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51 <param type="data" format="@FASTQ_FORMATS@" name="read2" label="Read2" />
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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52 </when>
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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53 <when value="paired_collection">
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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54 <param type="data_collection" collection_type="paired" format="@FASTQ_FORMATS@" name="paired_reads" label="Reads" />
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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55 </when>
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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56 <when value="single">
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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57 <param type="data" format="@FASTQ_FORMATS@" name="single_read1" label="Read1" />
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 </when>
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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59 </conditional>
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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60 <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
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61 <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
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62 <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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63 <option value="builtin">Built-in</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 </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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65 <when value="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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66 <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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67 </when>
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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68 <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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69 <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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70 <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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71 </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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72 </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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73 </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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74 <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"
iuc
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75 <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"
iuc
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76 <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"
iuc
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77 <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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78 </param>
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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79 <section name="adv" title="Advanced options">
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 <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"
iuc
parents:
diff changeset
81 <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" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
82 </section>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
83 </inputs>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
84 <outputs>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
85 <data name="output_reads1" format="fastqsanger.gz" label="Filtered reads ${on_string} - reads1" from_work_dir="output.reads_1.fastq.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
86 <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"
iuc
parents:
diff changeset
87 </data>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
88 <data name="output_reads2" format="fastqsanger.gz" label="Filtered reads ${on_string} - reads2" from_work_dir="output.reads_2.fastq.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
89 <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"
iuc
parents:
diff changeset
90 </data>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
91 <collection type="paired" format="fastqsanger.gz" name="output_collection" label="Filtered reads ${on_string}">
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
92 <filter>reads["read_type"] == "paired_collection"</filter>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
93 <data name="forward" format="fastqsanger.gz" from_work_dir="output.reads_1.fastq.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
94 <data name="reverse" format="fastqsanger.gz" from_work_dir="output.reads_2.fastq.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
95 </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
96 </outputs>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
97 <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
98 <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
99 <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
100 <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
101 <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
102 <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
103 </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
104 <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
105 <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
106 <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
107 </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
108 <param name="sequencing_tech" value="illumina" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
109 <output name="output_reads1" value="output_test1.fastq.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
110 <output name="output_reads2" value="output_test2.fastq.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
111 </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
112 <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
113 <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
114 <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
115 <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
116 <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
117 <element name="forward" 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
118 <element name="reverse" 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
119 </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
120 </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
121 </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
122 <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
123 <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
124 <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
125 </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
126 <param name="sequencing_tech" value="illumina" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
127 <output_collection name="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
128 <element name="forward" value="output_test1.fastq.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
129 <element name="reverse" value="output_test2.fastq.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
130 </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
131 </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
132 <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
133 <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
134 <param name="read_type" value="single" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
135 <param name="single_read1" value="test3.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
136 </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
137 <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
138 <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
139 <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
140 </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
141 <param name="sequencing_tech" value="ont" />
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
142 <output name="output_reads1" value="output_test3.fastq.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
143 </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
144 </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
145 <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
146 ReadItAndKeep
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
147 -------------
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
148
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
149 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"
iuc
parents:
diff changeset
150 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"
iuc
parents:
diff changeset
151 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"
iuc
parents:
diff changeset
152
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
153 **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"
iuc
parents:
diff changeset
154 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"
iuc
parents:
diff changeset
155 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"
iuc
parents:
diff changeset
156
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
157 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"
iuc
parents:
diff changeset
158 ]]></help>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
159 <citations>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
160 <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"
iuc
parents:
diff changeset
161 </citations>
554aa2a63f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
162 </tool>