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1 <tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0">
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2 <description></description>
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3 <command>
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4 <![CDATA[
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5 python $__tool_directory__/bam_to_scidx.py
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6 -j $__tool_directory__/BAMtoIDX.jar
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7 -b "$input_bam"
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8 -i "${input_bam.metadata.bam_index}"
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9 -r $read
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10 -o "$output"
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11 ]]>
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12 </command>
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13 <inputs>
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14 <param name="input_bam" type="data" format="bam" label="BAM file" help="BAM file must be sorted and indexed" />
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15 <param name="read" type="select" label="Read to output">
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16 <option value="0" selected="True">Read1</option>
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17 <option value="1">Read2</option>
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18 <option value="2">Combined</option>
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19 </param>
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20 </inputs>
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21 <outputs>
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22 <data name="output" format="scidx" label="${tool.name} on ${on_string}" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" value="input.bam" ftype="bam" />
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27 <param name="read" value="0" />
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28 <output name="output" file="output.scidx" lines_diff="1" />
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29 </test>
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30 </tests>
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31 <help>
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32
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33 **What it does**
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34
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35 Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by tools within
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36 the Chip-exo Galaxy flavor. ScIdx files are 1-based. The format consists of 5 columns: the chromosome,
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37 the position of the genomic coordinate, the number of tags on the forward strand, the number of tags on
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38 the reverse strand and the number of total tags on the position. With pair-end reads, only the 5’ end of
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39 READ1 will be used to create the ScIdx data file. Tools that use this format include GeneTrack and MultiGPS.
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40
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41 </help>
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42 <citations>
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43 <citation type="bibtex">
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44 @unpublished{None,
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45 author = {None},
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46 title = {None},
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47 year = {None},
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48 eprint = {None},
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49 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
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50 }</citation>
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51 </citations>
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52 </tool>
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