Mercurial > repos > iuc > bam_to_scidx

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit cadf726e05de4dfc4f2cf708674fcd2828e4c319
author iuc
date Mon, 03 Jul 2017 10:09:42 -0400
parents b737f6d83f48
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1 <tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.1">
0
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2 <description></description>
1
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3 <requirements>
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4 <requirement type="package" version="8.0.112">openjdk</requirement>
1
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5 </requirements>
5
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6 <command detect_errors="exit_code"><![CDATA[
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7 ln -s '${input_bam}' localbam.bam &&
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8 ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
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9 java -jar '$__tool_directory__/BAMtoscIDX.jar'
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10 -b localbam.bam
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11 -i localbam.bam.bai
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12 -p $require_proper_mate_pairing
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13 -r $read
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14 #if str($min_insert_size):
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15 -m $min_insert_size
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16 #end if
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17 #if str($max_insert_size):
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18 -M $max_insert_size
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19 #end if
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20 -o '$output'
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21 1>/dev/null
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22 ]]></command>
0
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23 <inputs>
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24 <param name="input_bam" type="data" format="bam" label="BAM file" />
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25 <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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26 <option value="1" selected="True">Yes</option>
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27 <option value="0">No</option>
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28 </param>
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29 <param name="read" type="select" label="Read to output">
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30 <option value="0" selected="True">Read1</option>
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31 <option value="1">Read2</option>
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32 <option value="2">Combined</option>
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33 </param>
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34 <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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35 <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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36 </inputs>
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37 <outputs>
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38 <data name="output" format="scidx" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input_bam" value="input.bam" ftype="bam" />
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43 <param name="require_proper_mate_pairing" value="1" />
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44 <param name="read" value="0" />
1
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45 <output name="output" file="output.scidx" lines_diff="1" ftype="scidx" compare="contains" />
0
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46 </test>
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47 </tests>
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48 <help>
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49
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50 **What it does**
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51
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52 Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by tools within
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53 the Chip-exo Galaxy flavor. ScIdx files are 1-based. The format consists of 5 columns: the chromosome,
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54 the position of the genomic coordinate, the number of tags on the forward strand, the number of tags on
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55 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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56 READ1 will be used to create the ScIdx data file. Tools that use this format include GeneTrack and MultiGPS.
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57
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58 -----
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59
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60 **Options**
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61
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62 * **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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63 * **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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64 * **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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65
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66 </help>
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67 <citations>
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68 <citation type="bibtex">
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69 @unpublished{None,
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70 author = {Lai, William},
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71 title = {None},
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72 year = {None},
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73 eprint = {None},
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74 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
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75 }</citation>
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76 </citations>
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77 </tool>