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1 <tool id="sum_fastqc" name="sum_fastqc" version="0.2">
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2 <requirements>
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3 </requirements>
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4 <command detect_errors="exit_code"><![CDATA[
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5
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6 #if $jobtype.select == "single"
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7 #set inname = $jobtype.file
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8 #set infile = $jobtype.file
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9 perl $__tool_directory__/sum_fastqc.pl "$inname" $qset.qscore $infile > sum_fastqc.tab
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10 #else if $jobtype.select == "col"
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11 #set inname = $jobtype.coll.name
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12 #set infile = $jobtype.coll.forward
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13 #set infile2 = $jobtype.coll.reverse
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14 perl $__tool_directory__/sum_fastqc.pl "$inname" $qset.qscore $infile $infile2 > sum_fastqc.tab;
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15 #end if
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16
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17 ]]></command>
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18 <inputs>
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19 <conditional name="jobtype">
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20 <param name="select" type="select" label="Select Input">
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21 <option value="single">Raw FASTQC output File</option>
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22 <option value="col">Pair of raw FASTQC Files</option>
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23 </param>
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24 <when value="single">
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25 <param name="file" type="data" format="txt" label="Raw FASTQC" />
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26 </when>
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27 <when value="col">
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28 <param name="coll" label="Raw FASTQC pair" type="data_collection" format="txt" collection_type="paired" />
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29 </when>
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30 </conditional>
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31 <conditional name="qset">
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32 <param name="selectq" type="select" label="Single or multiple Q scores">
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33 <option value="single">Single Q score</option>
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34 <option value="mul">Multiple Q scores</option>
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35 </param>
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36 <when value="single">
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37 <param name="qscore" type="integer" label="Q score threshold (i.e. reads >= Q score)" value="30">
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38 <validator type="in_range" message="Must be integer(0,40)." min="0" max="40"/>
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39 </param>
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40 </when>
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41 <when value="mul">
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42 <param name="qscore" type="text" label="Comma delimited Q score list (e.g. 25,30,35)" value="30"/>
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43 </when>
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44 </conditional>
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45 </inputs>
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46 <outputs>
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47 <data format="tabular" name="FASTQC Summary" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.tab"/>
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48 </outputs>
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49
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50 <help><![CDATA[
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51
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52 ]]></help>
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53 <citations>
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54 </citations>
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55 </tool>
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