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annotate chimerascan.xml @ 0:d85dea371064 draft

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author bioitcore
date Thu, 07 Sep 2017 17:55:18 -0400
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1 <tool id="chimerascan" name="ChimeraScan">
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2 <description>A tool for identifying chimeric transcription in sequencing data.</description>
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3 <command detect_errors="exit_code" interpreter="python">
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4 $__tool_directory__/chimerascan_run.py -p 8 $__tool_directory__/myindex
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5 #if $input_type_conditional.chimerascan_input_type == "paired"
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6 $input_type_conditional.input_1 $input_type_conditional.input_2
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7 #else
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8 $input_type_conditional.input.forward $input_type_conditional.input.reverse
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9 #end if
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10 $galaxy_output
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11 </command>
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12 <inputs>
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13 <conditional name="input_type_conditional">
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14 <param name="chimerascan_input_type" type="select" label="Input Type" help="Select between paired and paired collection">
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15 <option value="paired" selected="true">Paired</option>
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16 <option value="paired_collection">Paired Collection</option>
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17 </param>
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18 <when value="paired">
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19 <param format='fastq' name='input_1' type='data' label='FASTQ file, forward reads' />
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20 <param format='fastq' name='input_2' type='data' label='FASTQ file, reverse reads' />
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21 </when>
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22 <when value="paired_collection">
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23 <param format="fastq" name='input' type="data_collection" collection_type="paired" label="Select a paired collection" help="Specify paired dataset collection containing paired reads"/>
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24 </when>
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25 </conditional>
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26 </inputs>
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27 <outputs>
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28 <data name="galaxy_output" format="bed" />
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29 </outputs>
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30
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31 <tests>
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32 <test>
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33 <param name="input1" value="input1.fastq"/>
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34 <param name="input2" value="input2.fastq"/>
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35 <output name="galaxy_output" file="outputfile.bed" ftype="bed"/>
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36 </test>
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37 <test>
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38 <param name="fastq_input">
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39 <collection type="paired">
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40 <element name="forward" value="input1.fastq" />
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41 <element name="reverse" value="input2.fastq" />
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42 </collection>
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43 </param>
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44 <param name="input_type" value="paired_collection" />
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45 <output name="galaxy_output" file="outputfile.bed" ftype="bed"/>
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46 </test>
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47 </tests>
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48
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49 <help>
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50 Bowtie index files must be placed inside 'myindex folder'
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51 A tool for identifying chimeric transcription in sequencing data.
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52 </help>
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53
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54 </tool>