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"planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
author nml
date Tue, 28 Apr 2020 12:41:11 -0400
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0
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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1 <tool id="bamclipper" name="BAMClipper" version="@VERSION@+galaxy0">
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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2 <description> Remove gene-specific primer sequences from BAM alignments of PCR amplicons by soft-clipping with BEDPE file</description>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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3 <macros>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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4 <import>macros.xml</import>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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5 </macros>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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6 <expand macro="requirements" />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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7 <command detect_errors="exit_code"><![CDATA[
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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8 #import re
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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9
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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10 #set bamname = re.sub('[^\s\w-]', '_', str($input1.name))
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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11 ln -sf '$input1' '$bamname' &&
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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12 ln -sf '${input1.metadata.bam_index}' '${bamname}.bai' &&
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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13
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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14 bamclipper.sh -b '$bamname' -p '$primer_pairs' -n "\${GALAXY_SLOTS:-1}"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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15 #if $optional.upstream:
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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16 -u '$optional.upstream'
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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17 #end if
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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18 #if $optional.downstream:
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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19 -d '$optional.downstream'
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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20 #end if
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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21
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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22 ]]></command>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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23 <inputs>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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24 <param name="input1" type="data" format="bam"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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25 label="Input Bam file"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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26 argument="-b"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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27 />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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28 <param name="primer_pairs" type="data" format="bedpe, interval"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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29 label="BEDPE file of primer pair locations"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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30 argument="-p"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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31 />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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32 <section name="optional" title="Optional Parameters" expanded="false" >
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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33 <param name="upstream" type="integer" optional="true"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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34 label="Upstream"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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35 argument="-u"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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36 help="Number of nucleotides upstream of the 5' most nucleotide of the primer (in addition to 5' most nucleotide of primer) for assigning
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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37 alignments to primers based on the alignment starting position. Default 1"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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38 />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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39 <param name="downstream" type="integer" optional="true"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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40 label="Downstream"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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41 argument="-d"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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42 help="Number of nucleotides downstream to the 5' most nucleotide of primer (in addition to 5' most nucleotide of primer) for assigning
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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43 alignments to primers based on the alignment starting position. Default 5"
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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44 />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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45 </section>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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46 </inputs>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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47 <outputs>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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48 <data format_source="input1" from_work_dir="*.primerclipped.bam" name="output" label="${input1.name}.primerclipped" />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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49 </outputs>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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50 <tests>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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51 <test>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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52 <param name="input1" value="SRR2075598.bam" />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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53 <param name="primer_pairs" value="trusight_myeloid.bedpe" />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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54 <output name="output" file="SRR2075598.primerclipped.bam" ftype="bam" />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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55 </test>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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56 <test>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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57 <param name="input1" value="SRR2075598.bam" />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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58 <param name="primer_pairs" value="trusight_myeloid.bedpe" />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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59 <section name="optional">
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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60 <param name="upstream" value="1" />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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61 <param name="downstream" value="5" />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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62 </section>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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63 <output name="output" file="SRR2075598.primerclipped.bam" ftype="bam" />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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64 </test>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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65 </tests>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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66 <help><![CDATA[
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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67
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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68 Bamclipper
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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69 ----------
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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70
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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71 Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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72 to produce a new bam file called NAME.primerclipped.bam and its associated bam index (NAME.primerclipped.bam.bai)
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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73
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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74 Example primer pair BEDPE file lines:
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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75
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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76 ::
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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77
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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78 chr1 115256390 115256417 chr1 115256622 115256650
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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79 chr1 115258642 115258664 chr1 115258876 115258903
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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80 chr10 89692737 89692767 chr10 89692971 89692998
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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81 chr10 89692943 89692970 chr10 89693177 89693206
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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82 chr10 89717567 89717596 chr10 89717775 89717802
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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83
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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84
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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85 ]]></help>
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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86 <expand macro="citations" />
43437bfaee7d "planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
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87 </tool>