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1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.1">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.12.7">bowtie</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 <requirement type="package" version="0.7.7">pysam</requirement>
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7 </requirements>
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8 <parallelism method="basic"></parallelism>
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9 <command interpreter="python">
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10 sRbowtieParser.py
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11 #if $refGenomeSource.genomeSource == "history":
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12 --IndexSource $refGenomeSource.ownFile
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13 --ExtractDirective fastaSource
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14 #else:
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15 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
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16 --IndexSource $reference
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17 --ExtractDirective bowtieIndex
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18 #end if
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19 --output $output
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20 --polarity $polarity
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21 --alignmentSource
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22 #for $i in $refGenomeSource.input_list
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23 $i
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24 #end for
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25 --alignmentFormat
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26 #for $i in $refGenomeSource.input_list
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27 $i.ext
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28 #end for
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29 --alignmentLabel
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30 #for $i in $refGenomeSource.input_list
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31 "$i.name"
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32 #end for
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33
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34 </command>
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35 <inputs>
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36 <conditional name="refGenomeSource">
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37 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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38 <option value="indexed">Use a built-in index</option>
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39 <option value="history">Use one from the history</option>
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40 </param>
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41 <when value="indexed">
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42 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true">
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43 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
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44 </param>
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45 </when>
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46 <when value="history">
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47 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" />
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48 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/>
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49 </when>
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50 </conditional> <!-- refGenomeSource -->
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51 <param name="polarity" type="select" label="how to count sense and antisense reads">
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52 <option value="both">count both sense and antisense reads</option>
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53 <option value="forward">count only sense reads</option>
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54 <option value="reverse">count only antisense reads</option>
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55 </param>
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56 </inputs>
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57 <outputs>
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58 <data format="tabular" name="output" label="Read Count Lists"/>
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59 </outputs>
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60 <help>
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61
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62 **What it does**
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63
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64 Parses read counts from one or several sRBowtie alignments (in tabular, Sam or Bam format).
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65 Here a bowtie match done against an index composed of a set of items is parsed and expressed as a hit list of the corresponding items
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66
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67 Sense, antisense or both sense and antisense alignments can be counted
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68
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69 The library labels are infered from the input dataset names in the galaxy history.
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70
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71 **It is thus essential that input datasets are appropriately renamed**
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72
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73 **it is preferable that you do not put any space in this input dataset names. You may edit these names in the history**
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74
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75 </help>
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76 <test>
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77 <param name="genomeSource" value="history" />
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78 <param name="ownFile" value ="dme-mir-v20" ftype="fasta" />
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79 <param name="input_list" value="matchedSample_1, matchedSample_2" ftype="tabular" />
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80 <param name="polarity" value="forward" />
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81 <output name="output" ftype="tabular" value="Read_Count_Lists.tab" />
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82 </test>
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83
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84 </tool>
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85
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