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1 <tool id="FeaturesParser" name="Parse GFF3 features" version="0.9.1">
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2 <description>in sRbowtie alignment</description>
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3 <requirements><requirement type='package'>bowtie-inspect</requirement></requirements>
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4 <parallelism method="basic"></parallelism>
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5 <command interpreter="python">
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6 FeaturesParser.py
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7 #if $refGenomeSource.genomeSource == "history":
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8 $refGenomeSource.ownFile ## index source ## 1
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9 --do_not_extract_index ## 2
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10 #else:
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11 #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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12 $reference ## index source ## 1
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13 --extract_index ## 2
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14 #end if
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15 $output ## 3
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16 $gff3 ## 4
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17 #for $i in $refGenomeSource.input_list
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18 $i $i.ext "$i.name"
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19 #end for
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20
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21 </command>
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22 <inputs>
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23 <conditional name="refGenomeSource">
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24 <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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25 <option value="indexed">Use a built-in index</option>
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26 <option value="history">Use one from the history</option>
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27 </param>
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28 <when value="indexed">
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29 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true">
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30 <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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31 </param>
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32 </when>
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33 <when value="history">
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34 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" />
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35 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/>
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36 </when>
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37 </conditional> <!-- refGenomeSource -->
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38 <param name="gff3" type="data" format="gff3" label="A GFF3 with features' coordinates"/>
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39 </inputs>
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40 <outputs>
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41 <data format="tabular" name="output" label="Feature Counts Lists"/>
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42 </outputs>
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43 <help>
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44
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45 **What it does**
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46
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47 Parses Features Counts from one or several sRBowtie alignments (in tabular, Sam or Bam format).
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48
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49 Both sense and antisense alignments are counted
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50
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51 The library labels are infered from the input dataset names in the galaxy history.
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52
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53 **It is thus essential that input datasets are appropriately renamed**
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54
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55 **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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56
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57
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58
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59 </help>
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60 </tool>
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61
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