Mercurial > repos > drosofff > msp_sr_bowtie_parser

annotate sRbowtieParser.xml @ 1:ca3845fb0b31 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09
author drosofff
date Mon, 18 Apr 2016 10:09:08 -0400
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ca3845fb0b31 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09
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1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.6">
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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="0.7.7">pysam</requirement>
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6 <requirement type="package" version="1.9">numpy</requirement>
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7 </requirements>
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8 <command>
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9 python $__tool_directory__/sRbowtieParser.py
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10 #if $refGenomeSource.genomeSource == "history":
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11 --IndexSource $refGenomeSource.ownFile
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12 --ExtractDirective fastaSource
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13 #else:
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14 #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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15 --IndexSource $reference
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16 --ExtractDirective bowtieIndex
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17 #end if
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18 --output $output
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19 --polarity $polarity
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20 --alignmentSource
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21 #for $i in $refGenomeSource.input_list
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22 $i
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23 #end for
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24 --alignmentFormat
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25 #for $i in $refGenomeSource.input_list
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26 $i.ext
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27 #end for
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28 --alignmentLabel
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29 #for $i in $refGenomeSource.input_list
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30 "$i.element_identifier"
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31 #end for
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32
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33 </command>
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34 <inputs>
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35 <conditional name="refGenomeSource">
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36 <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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37 <option value="indexed">Use a built-in index</option>
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38 <option value="history">Use one from the history</option>
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39 </param>
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40 <when value="indexed">
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41 <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true">
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42 <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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43 </param>
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44 </when>
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45 <when value="history">
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46 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" />
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ca3845fb0b31 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09
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47 <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true"/>
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48 </when>
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49 </conditional> <!-- refGenomeSource -->
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50 <param name="polarity" type="select" label="how to count sense and antisense reads">
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51 <option value="both">count both sense and antisense reads</option>
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52 <option value="forward">count only sense reads</option>
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53 <option value="reverse">count only antisense reads</option>
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54 </param>
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55 </inputs>
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56 <outputs>
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57 <data format="tabular" name="output" label="Read Count Lists"/>
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58 </outputs>
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59 <help>
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60
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61 **What it does**
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62
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63 Parses read counts from one or several sRBowtie alignments (in tabular, Sam or Bam format).
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64 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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65
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66 Sense, antisense or both sense and antisense alignments can be counted
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67
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68 The library labels are infered from the input dataset names in the galaxy history.
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69
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70 **It is thus essential that input datasets are appropriately renamed**
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71
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72 **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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73
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74 </help>
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75 <tests>
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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" file="Read_Count_Lists.tab" />
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82 </test>
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83 </tests>
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84 </tool>
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85