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1 <tool id="rtg_format_fastq" name="Format FASTQ">
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2 <description>to SDF with rtg format</description>
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3 <command interpreter="bash">galaxy-rtg-wrapper.sh format
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4 -f fastq
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5 #if $paired.sPaired == "paired":
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6 -l $paired.input1
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7 -r $paired.input2
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8 #else:
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9 $paired.input1
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10 #end if
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11 #if str($protein) == "true":
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12 -p
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13 #end if
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14 -q $quality_format
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15 -o ${output.extra_files_path} >$output</command>
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16 <inputs>
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17 <conditional name="paired">
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18 <param name="sPaired" type="select" label="Are you formatting paired-end reads?">
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19 <option value="single">Non-read data or single-end</option>
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20 <option value="paired">Paired-end</option>
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21 </param>
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22 <when value="single">
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23 <param name="input1" type="data" format="fastq" label="Source FASTQ file"/>
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24 </when>
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25 <when value="paired">
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26 <param name="input1" type="data" format="fastq" label="First of pair FASTA file"/>
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27 <param name="input2" type="data" format="fastq" label="Second of pair FASTA file"/>
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28 </when>
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29 </conditional>
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30 <param name="quality_format" type="select" label="Quality format">
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31 <option value="sanger" selected="true">Sanger</option>
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32 <option value="solexa">Solexa</option>
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33 <option value="illumina">Illumina</option>
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34 </param>
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35 <param name="protein" type="select" label="Input consists of protein">
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36 <option value="false" selected="true">False</option>
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37 <option value="true">True</option>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data format="rtg_sdf" name="output" />
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42 </outputs>
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43
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44 <help>
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45 This tool formats a FASTQ file to RTG SDF.
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46 </help>
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47
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48 </tool>
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