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1 <tool id="pathoscope_map" name="Pathoscope Map" version="0.1.0">
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2 <description> Pathoscope Map </description>
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3 <requirements>
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4 <requirement type="package" version="2.0.6"> pathoscope </requirement>
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5 </requirements>
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6 <command> <![CDATA[
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7 pathoscope MAP
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8 #if str($library.type) == "single"
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9 -U $fastqU
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10 #elif str($library.type) == "paired"
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11 -1 $fastq1
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12 -2 $fastq2
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13 #end if
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14 -indexDir $targetAlignPrefixes.fields.path
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15 -targetAlignPrefixes $targetAlignPrefixes
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16 -filterAlignPrefixes $filterAlignPrefixes
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17 ]]>
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18 </command>
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19 <inputs>
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20 <conditional name="library">
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21 <param name="type" type="select" label="Is this single or paired library" help="">
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22 <option value="single">Single-end</option>
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23 <option value="paired">Paired-end</option>
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24 </param>
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25 <when value="single">
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26 <param name="fastqU" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
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27 </when>
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28 <when value="paired">
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29 <param name="fastq1" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
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30 <param name="fastq2" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
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31 </when>
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32 </conditional>
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33 <param name="targetAlignPrefixes" type="select" label="targetAlignPrefixes" help="Target Index Prefixes">
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34 <options from_data_table="pathoscope_indexes">
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35 <column name="value" index="0"/>
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36 <column name="name" index="0"/>
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37 <column name="path" index="0"/>
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38 </options>
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39 </param>
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40 <param name="filterAlignPrefixes" type="select" label="filterAlignPrefixes" help="Filter Alignment Files Prefixes">
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41 <options from_data_table="pathoscope_indexes">
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42 <column name="value" index="0"/>
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43 <column name="name" index="0"/>
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44 <column name="path" index="0"/>
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45 </options>
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46 </param>
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47 </inputs>
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48 <outputs>
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49 </outputs>
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50 <help>
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51 This module will take your reads and map them against a target library. Then it will map the mapping reads
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52 against a filter library. All the reads that map to the filter library with a score equal or greater than the mapping
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53 score to the target library will be discarded. The reads mapping with a better score to the target library will be
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54 used downstream by the PathoID module.
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55 </help>
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56 <citations>
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57 <citation type="doi">10.1101/gr.150151.112</citation>
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58 <citation type="doi">10.1186/2049-2618-2-33</citation>
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59 <citation type="doi">10.1186/1471-2105-15-262</citation>
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60 <citation type="doi">10.4137/CIN.S13890</citation>
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61 </citations>
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62 </tool>
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