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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
author iuc
date Sat, 12 Dec 2015 15:46:03 -0500
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741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
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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 ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" &&
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
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6 java -jar $__tool_directory__/BAMtoscIDX.jar -b "$input_bam" -i "${input_bam}.bai" -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
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7 ]]>
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8 </command>
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9 <inputs>
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10 <param name="input_bam" type="data" format="bam" label="BAM file" />
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11 <param name="require_proper_mate_pairing" type="select" label="Require proper mate-pairing?" help="Required if filtering by insert size for single-end Reqd 1 (below)." >
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12 <option value="1" selected="True">Yes</option>
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13 <option value="0">No</option>
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14 </param>
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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 <param name="min_insert_size" type="integer" value="" optional="True" min="0" label="Minimum insert size to output" help="Will not filter out single-end Read 1 unless proper mate-pairing is required (above)."/>
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21 <param name="max_insert_size" type="integer" value="" optional="True" min="0" label="Maximum insert size to output" help="Will not filter out single-end Read 1 unless proper mate-pairing is required (above)." />
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22 </inputs>
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23 <outputs>
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24 <data name="output" format="scidx" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input_bam" value="input.bam" ftype="bam" />
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
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29 <param name="require_proper_mate_pairing" value="1" />
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30 <param name="read" value="0" />
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31 <output name="output" file="output.scidx" lines_diff="1" ftype="scidx" />
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32 </test>
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33 </tests>
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34 <help>
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35
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36 **What it does**
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37
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38 Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by tools within
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
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39 the Chip-exo Galaxy flavor. ScIdx files are 1-based. The format consists of 5 columns: the chromosome,
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40 the position of the genomic coordinate, the number of tags on the forward strand, the number of tags on
741b8af6386c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit dfaab7cbfdee82c9fe4ff34ce02b42fc456b9db9
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41 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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42 READ1 will be used to create the ScIdx data file. Tools that use this format include GeneTrack and MultiGPS.
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43
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44 -----
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45
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46 **Options**
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47
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48 * **Require proper mate-pairing?** - Select **Yes** to require proper mate paring. Filtering by insert size parameters will not filter out single-end Read 1 unless proper mate-pairing is required.
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49 * **Minimum insert size to output** - Insert size below the minimum will be filtered from the results, but single-end Read 1 will not be filtered unless proper mate-pairing is required.
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50 * **Maximum insert size to output** - Insert size above the maximum will be filtered from the results, but single-end Read 1 will not be filtered unless proper mate-pairing is required.
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51
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52 </help>
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53 <citations>
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54 <citation type="bibtex">
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55 @unpublished{None,
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56 author = {Lai, William},
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57 title = {None},
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58 year = {None},
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59 eprint = {None},
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60 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
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61 }</citation>
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62 </citations>
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63 </tool>