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1 <tool id="merged_paired_reads_wrapper" version="1.0" name="Merge paired reads">
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2 <requirements>
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3 <requirement type='package' version="1.7">sortmerna</requirement>
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4 </requirements>
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5 <description>Merges two fastq paired-reads files into one file.</description>
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6 <command>
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7 merge-paired-reads.sh $input_reads1 $input_reads2 output_file.txt
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8 </command>
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9 <inputs>
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10 <param format="fastq" name="input_reads1" type="data"
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11 label="First reads file (fastq)" help=""/>
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12 <param format="fastq" name="input_reads2" type="data"
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13 label="Second reads file (fastq)" help=""/>
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14 </inputs>
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15 <outputs>
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16 <data format="fastq" name="output" from_work_dir="output_file.txt"
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17 label="Merged reads from ${on_string} (fastq)">
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18 </data>
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19 </outputs>
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20 <stdio>
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21 <exit_code range="2" level="fatal"
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22 description="Too few or two many arguments provided" />
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23 </stdio>
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24 <tests>
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25 <test>
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26 <param name="input_reads1" value="sortmerna_wrapper_accept1.fastq" />
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27 <param name="input_reads2" value="sortmerna_wrapper_other1.fastq" />
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28 <output name="output" file="merged-paired-reads_output.fastq" />
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29 </test>
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30 </tests>
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31 <help>
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32 Merges two fastq paired-reads files into one file.
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33
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34 To run merge-paired-reads::
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35
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36 bash merge-paired-reads.sh file1.fastq file2.fastq outputfile.fastq
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37 </help>
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38 </tool> |
