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1 <tool id="mapper" name="Mapping to reference">
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2 <description>Mapping using a bowtie index</description>
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3
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4 <requirements>
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5 <requirement type="perl-module">mapper_wrapper.pl</requirement>
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6 </requirements>
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7
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8 <command interpreter="perl">
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9 ./mapper_wrapper.pl $bowtie_index_name $output_arf $bowtie_index_name.extra_files_path $reads
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10
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11 #if $reads.extension.startswith("fastq"):
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12 -e
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13 #end if
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14
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15 #if $reads.extension.startswith("fasta"):
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16 -c
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17 #end if
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18
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19 #if str($convert_rna) == "convert_rna_true":
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20 -i
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21 #end if
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22
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23 #if str($remove_non_atcgun) == "remove_non_atcgun_true":
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24 -j
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25 #end if
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26
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27 #if str($adapter_seq) != "":
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28 -k $adapter_seq
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29 #end if
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30
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31 #if str($discard_short_reads) != "":
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32 -l $discard_short_reads
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33 #end if
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34
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35 #if str($collapse_reads) == "Collapsed Reads Fasta":
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36 -m
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37 #end if
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38
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39 #if str($map_mismatch) == "map_mismatch_false":
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40 -q
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41 #end if
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42
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43 #if str($map_threshold) != "":
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44 -r $map_threshold
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45 #end if
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46
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47 -h -s $output_fasta -n
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48 </command>
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49
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50 <inputs>
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51 <param format="fastq, fasta" name="reads" type="data" optional="false" label="Reads" help="Reads in fastq or fasta format"/>
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52 <param format="bowtie_html_index" name="bowtie_index_name" type="data" optional="false" label="Bowtie indexed reference" help="Select the bowtie-build run, NOT the fasta reference file you indexed."/>
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53
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54 <param name="convert_rna" type="boolean" truevalue="convert_rna_true" falsevalue="convert_rna_false" checked="false" label="Convert RNA to DNA alphabet (to map against genome)"/>
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55
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56 <param name="remove_non_atcgun" type="boolean" truevalue="remove_non_atcgun_true" falsevalue="remove_non_atcgun_false" checked="false" label="Remove reads with non-standard nucleotides" help="Remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N"/>
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57
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58 <param name="adapter_seq" value="" type="text" optional="true" label="Clip 3' Adapter Sequence (optional)" help="Adapter Sequence can only contain a,c,g,t,u,n,A,C,G,T,U,N">
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59 <validator type="regex" message="Adapter can ONLY contain a,c,g,t,u,n,A,C,G,T,U,N">^[ACGTUacgtu]+$</validator>
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60 </param>
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61
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62 <param name="discard_short_reads" value="17" type="integer" optional="false" label="Discard reads shorter than this length (0 for keeping all reads)" help="Note that miRDeep2 requires no reads under 17 in length">
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63 <validator type="in_range" min="0" message="Minimum value is 0"/>
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64 </param>
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65
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66 <param name="collapse_reads" type="boolean" truevalue="Collapsed Reads Fasta" falsevalue="Fasta" checked="true" label="Collapse identical reads into one read with count information in sequence header (default)"/>
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67
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68 <param name="map_mismatch" type="boolean" truevalue="map_mismatch_true" falsevalue="map_mismatch_false" checked="false" label="Map with one mismatch in the seed (mapping takes longer)"/>
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69
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70 <param name="map_threshold" value="5" type="integer" optional="false" label="A read is allowed to map up to this number of positions in the genome">
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71 <validator type="in_range" min="1" message="Minimum value is 1"/>
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72 </param>
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73 </inputs>
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74
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75 <outputs>
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76 <data format="fasta" name="output_fasta" label="$collapse_reads of ${tool.name} on ${on_string}"/>
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77 <data format="arf" name="output_arf" label="Mapping output of ${tool.name} on ${on_string} in ARF format"/>
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78 </outputs>
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79 </tool>
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80
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