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1 <tool id="ubu_sam2fastq" name="UBU sam2fastq" version="0.1.0">
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2 <description>Convert a SAM/BAM file to FASTQ</description>
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3
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4 <requirements>
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5 <requirement version="1.2">ubu</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10
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11 <command><![CDATA[
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12 java -Xmx1G -jar \$UBU_JAR sam2fastq --in $input --fastq1 paired1.fastq --fastq2 paired2.fastq --end1 '$end1' --end2 '$end2'
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13 ]]></command>
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14 <inputs>
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15 <param name="input" type="data" format="sam,bam" label="Sam or Bam file to convert" />
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16 <param name="end1" type="text" value="/1" label="Id suffix used to identify the first read in a pair." />
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17 <param name="end2" type="text" value="/2" label="Id suffix used to identify the second read in a pair." />
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18 </inputs>
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19 <outputs>
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20 <data name="fastq1" format="data" from_work_dir="paired1.fastq" />
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21 <data name="fastq2" format="data" from_work_dir="paired2.fastq" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input" value="sam2fastq_test.sam" />
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26 <output name="fastq1" file="sam2fastq_expected_paired1.fastq"/>
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27 <output name="fastq2" file="sam2fastq_expected_paired2.fastq"/>
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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31 input SAM/BAM file
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32 Option Description
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33 ------ -----------
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34 --in Required input sam or bam file
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35 --fastq1 Required output FASTQ file
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36 --fastq2 Second FASTQ file for paired end
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37 --end1 Id suffix used to identify the first
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38 read in a pair. i.e. /1 (omit this
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39 option to use bit flag)
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40 --end2 Id suffix used to identify the second
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41 read in a pair. i.e. /2 (omit this
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42 option to use bit flag)
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43
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44 ]]></help>
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45 </tool>
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