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1 <tool id="VarAmpliCNV_Count" name="Count Aligned Amplicons" version="0.1.0" >
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2 <requirements>
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3 <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 ##prepare input and indices
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7 ln -s '$bam' infile &&
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8 #if $bam.is_of_type('bam'):
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9 #if str( $bam.metadata.bam_index ) != "None":
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10 ln -s '${bam.metadata.bam_index}' infile.bai &&
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11 #else:
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12 samtools index infile infile.bai &&
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13 #end if
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14 #elif $bam.is_of_type('cram'):
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15 #if str( $bam.metadata.cram_index ) != "None":
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16 ln -s '${bam.metadata.cram_index}' infile.crai &&
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17 #else:
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18 samtools index infile infile.crai &&
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19 #end if
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20 #end if
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21
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22 ## Run Counter.
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23 parseBAM.py '$bed' 'infile' '$counts' '$unmapped' '$stats'
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24
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25 ]]></command>
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26 <inputs>
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27 <param name="bed" type="data" format="BED" optional="false" label="Unique Amplicons (BED)" help="This file is created by the VarAmpliCNV 'Annotate Amplicons' tool." />
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28 <param name="bam" type="data" format="bam" optional="false" label="BAM file" help="Sequencing data file" />
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29 </inputs>
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30 <outputs>
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31 <data name="counts" format="tabular" label="VarAmpliCNV on ${on_string}: Counts" />
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32 <data name="unmapped" format="bam" label="VarAmpliCNV on ${on_string}: UnMapped Reads" />
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33 <data name="stats" format="txt" label="VarAmpliCNV on ${on_string}: Statistics" />
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34 </outputs>
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35 <help>
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36 **VarAmpliCNV : Counting**
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37
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38 BAM files are parsed for readpairs exactly matching specified amplicons, based on start and end position.
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39
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40 **Parameters are :**
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41
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42 * Amplicon Design File (BED) : The de-duplicated amplicon list, generated by "varAmpliCNV Annotate".
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43 * Sample Data (BAM) : The sample read data, provided as a single BAM file, or a collection of BAM files.
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44
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45 **Output files :**
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46
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47 * Count file (txt): the amplicon-read table.
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48 * Unmapped (BAM) : Reads not matching amplicons. This bam file can be used to investigate issues.
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49 * Stats (txt): Overview of the matching performance. Use it to investigate issues.
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50
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51 In case a collection of BAM files is provided, the output files will be grouped in collections as well.
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52
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53 </help>
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54 </tool>
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