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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 #from os import listdir
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8 #set path=$targetIndexPrefixes.fields.path.split(',')[0]
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9 #set prefixes=[f for f in listdir(path) if f.endswith(".3.bt2")]
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10 #set targetRefs=str($targetIndexPrefixes)
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11 #set targetR=targetRefs.split(',')
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12 #set p=[]
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13 #for $f in prefixes
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14 #for $t in targetR
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15 #if $t in f
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16 #set p = p + [f[:-6]]
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17 #end if
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18 #end for
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19 #end for
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20 #set target=','.join(p)
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21 pathoscope MAP
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22 #if str($reads.type) == "single"
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23 -U $fastqU
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24 #elif str($reads.type) == "paired"
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25 -1 $fastq1
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26 -2 $fastq2
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27 #end if
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28 -indexDir $path
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29 -targetIndexPrefixes $target
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30 -filterIndexPrefixes $filterIndexPrefixes 2>&1
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31 && mv outalign.sam "$outalign"
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32 && mv pathomap-appendAlign.fq "$pathomap_appendAlign"
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33 ]]>
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34 </command>
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35 <inputs>
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36 <conditional name="reads">
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37 <param name="type" type="select" label="Is this single or paired reads" help="">
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38 <option value="single">Single-end</option>
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39 <option value="paired">Paired-end</option>
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40 </param>
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41 <when value="single">
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42 <param name="fastqU" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
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43 </when>
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44 <when value="paired">
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45 <param name="fastq1" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
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46 <param name="fastq2" format="fastqsanger" type="data" label="FASTQ file" help="Input Read Fastq File (Unpaired/Single-end)" />
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47 </when>
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48 </conditional>
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49 <param name="targetIndexPrefixes" multiple="true" type="select" label="targetIndexPrefixes" help="Target Index Prefixes">
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50 <options from_data_table="pathoscope_indexes">
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51 <filter type="sort_by" column="2"/>
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52 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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53 </options>
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54 </param>
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55 <param name="filterIndexPrefixes" multiple="true" type="select" label="filterIndexPrefixes" help="Filter Index Prefixes">
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56 <options from_data_table="pathoscope_indexes">
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57 <filter type="sort_by" column="2"/>
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58 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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59 </options>
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60 </param>
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61 </inputs>
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62 <outputs>
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63 <data format="sam" name="outalign" label="outalign.sam" />
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64 <data format="fastqsanger" name="pathomap_appendAlign" label="pathomap_appendAlign.fastq" />
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65 </outputs>
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66
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67 <help>
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68 IMPORTANT: The name and the path of the reference database (with bowtie indexed)
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69 should be added to the pathoscope.loc entry.
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70 </help>
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71 <citations>
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72 <citation type="doi">10.1101/gr.150151.112</citation>
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73 <citation type="doi">10.1186/2049-2618-2-33</citation>
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74 <citation type="doi">10.1186/1471-2105-15-262</citation>
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75 <citation type="doi">10.4137/CIN.S13890</citation>
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76 </citations>
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77 </tool>
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