Mercurial > repos > ebi-gxa > fastq_pair

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
author ebi-gxa
date Thu, 17 Mar 2022 01:46:15 +0000
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6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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1 <tool id="fastq_pair" name="Paired-end fastq pairer" profile="18.01" version="1.0+galaxy0">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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2 <description>Rewrite paired-end fastq files to make sure that all reads have a mate and to separate out singletons.</description>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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3 <requirements>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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4 <requirement type="package" version="1.0">fastq-pair</requirement>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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5 </requirements>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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6 <command detect_errors="exit_code"><![CDATA[
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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7
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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8 ## Unzip gzipped inputs
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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9 #if $fastq1.is_of_type("fastqsanger.gz"):
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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10 gzip -d -c '$fastq1' > 1.fq &&
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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11 #else:
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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12 mv '$fastq1' 1.fq &&
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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13 #end if
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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14
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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15 #if $fastq2.is_of_type("fastqsanger.gz"):
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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16 gzip -d -c '$fastq2' > 2.fq &&
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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17 #else:
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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18 mv '$fastq2' 2.fq &&
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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19 #end if
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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20
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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21
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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22 ## Run fastq_pair
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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23 fastq_pair
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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24
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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25 #if $table_size:
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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26 -t '$table_size'
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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27 #end if
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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28
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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29 #if $print_elements:
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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30 -p '$print_elements'
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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31 #end if
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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32
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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33 #if $verbose:
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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34 '$verbose'
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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35 #end if
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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36
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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37 1.fq 2.fq
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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38
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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39 ## Compress outputs
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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40 #if $compress == "yes":
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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41 ; gzip 1.fq.paired.fq
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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42 ; gzip 2.fq.paired.fq
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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43 ; gzip 1.fq.single.fq
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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44 ; gzip 2.fq.single.fq
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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45 #end if
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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46
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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47 ]]></command>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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48 <inputs>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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49 <param name="verbose" label="Verbose" optional="true" value="false" argument="-v" type="boolean" truevalue="-v" falsevalue="" checked="true" help="Verbose output. This is mainly for debugging." />
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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50 <param name="fastq1" label="FASTQ file 1" type="data" format="fastqsanger,fastqsanger.gz" optional="false" help="FASTQ file input, file 1 of pair" />
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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51 <param name="fastq2" label="FASTQ file 2" type="data" format="fastqsanger,fastqsanger.gz" optional="false" help="FASTQ file input, file 2 of pair" />
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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52 <param name="table_size" label="Table size" argument="-t" optional="true" value="100003" type="integer" help="Table size (default 100003)" />
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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53 <param name="print_elements" label="Number elements to print" argument="-p" type="integer" optional="true" help="Print this number of elements in each bucket in the table." />
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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54 <param name="compress" label="Compress outputs?" type="boolean" optional="true" value="true" truevalue="yes" falsevalue="no" checked="false" help="Check if outputs should be compressed (.gz)" />
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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55 </inputs>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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56 <outputs>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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57 <collection name="uncompressed" type="list" format="fastqsanger" label="${tool.name} on ${on_string}: Paired reads and singletons">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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58 <filter>compress == False</filter>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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59 <data name="fwd_paired" from_work_dir="1.fq.paired.fq"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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60 <data name="rev_paired" from_work_dir="2.fq.paired.fq"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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61 <data name="fwd_single" from_work_dir="1.fq.single.fq"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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62 <data name="rev_single" from_work_dir="2.fq.single.fq"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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63 </collection>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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64 <collection name="compressed" type="list" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Paired reads and singletons, compressed">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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65 <filter>compress</filter>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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66 <data name="fwd_paired_gz" from_work_dir="1.fq.paired.fq.gz"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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67 <data name="rev_paired_gz" from_work_dir="2.fq.paired.fq.gz"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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68 <data name="fwd_single_gz" from_work_dir="1.fq.single.fq.gz"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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69 <data name="rev_single_gz" from_work_dir="2.fq.single.fq.gz"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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70 </collection>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
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71 </outputs>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
72 <tests>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
73 <test>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
74 <param name="table_size" value="1000"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
75 <param name="fastq1" value="left.fastq"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
76 <param name="fastq2" value="right.fastq"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
77 <output_collection name="uncompressed" type="list" count="4">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
78 <element name="fwd_paired" ftype="fastqsanger">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
79 <assert_contents><has_line_matching expression="^@GFH7CG303GRT2I/1[ -~]+" /></assert_contents>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
80 </element>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
81 <element name="rev_paired" ftype="fastqsanger">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
82 <assert_contents><has_line_matching expression="^@GFH7CG303GRT2I/2[ -~]+" /></assert_contents>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
83 </element>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
84 <element name="fwd_single" ftype="fastqsanger">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
85 <assert_contents><has_line_matching expression="^@GFH7CG303GGIBL/1[ -~]+" /></assert_contents>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
86 </element>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
87 <element name="rev_single" ftype="fastqsanger">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
88 <assert_contents><has_line_matching expression="^@GFH7CG303GSASH/2[ -~]+" /></assert_contents>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
89 </element>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
90 </output_collection>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
91 </test>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
92 <test>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
93 <param name="table_size" value="1000"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
94 <param name="fastq1" value="left.fastq.gz"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
95 <param name="fastq2" value="right.fastq.gz"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
96 <param name="compress" value="true"/>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
97 <output_collection name="compressed" type="list" count="4">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
98 <element name="fwd_paired_gz" ftype="fastqsanger.gz">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
99 <assert_contents><has_size value="16000" delta="1600"/></assert_contents>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
100 </element>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
101 <element name="rev_paired_gz" ftype="fastqsanger.gz">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
102 <assert_contents><has_size value="16000" delta="1600"/></assert_contents>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
103 </element>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
104 <element name="fwd_single_gz" ftype="fastqsanger.gz">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
105 <assert_contents><has_size value="62000" delta="6200"/></assert_contents>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
106 </element>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
107 <element name="rev_single_gz" ftype="fastqsanger.gz">
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
108 <assert_contents><has_size value="8500" delta="850"/></assert_contents>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
109 </element>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
110 </output_collection>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
111 </test>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
112 </tests>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
113 <help><![CDATA[
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
114 =======================================================
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
115 Paired-end fastq pairer (fastq_pair)
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
116 =======================================================
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
117
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
118 Match up paired end fastq files quickly and efficiently.
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
119 This galaxy tool can accept gzipped fastq files.
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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diff changeset
120
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
121 OPTIONS
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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122 -t table size (default 100003)
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
123 -p print the number of elements in each bucket in the table
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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124 -v verbose output. This is mainly for debugging
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
125 ]]></help>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
126 <citations>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
127 <citation type="doi">10.1101/552885</citation>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
parents:
diff changeset
128 </citations>
6e13890afaef "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair commit e8517297f4bf2ab5afc544e6af7bb4c5f152dd3e"
ebi-gxa
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129 </tool>