Mercurial > repos > iuc > samtools_ampliconclip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:21:59 +0000
parents d90472d5f10a
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b5f87b4cfda6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
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1 <tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>clip primer bases from bam files</description>
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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3 <macros>
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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4 <import>macros.xml</import>
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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5 </macros>
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @ADDTHREADS@
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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11 samtools ampliconclip
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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12 $hard_clip_mode
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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13 #if $min_length:
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14 --fail-len $min_length
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15 #end if
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16 --tolerance $tolerance
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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17 $strand
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18 -b '${input_bed}'
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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19 -u
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20 $both_ends
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21 $no_excluded
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22 -@ \$addthreads
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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23 '${input_bam}'
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24 | samtools collate -@ \$addthreads -O -u -
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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25 | samtools fixmate -@ \$addthreads -u - -
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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26 | samtools sort -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" -o '${output_bam}'
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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27 ]]></command>
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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28 <inputs>
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29 <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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30 <param name="input_bam" type="data" format="bam" label="BAM file" />
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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31 <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchekced = default soft-clipping" />
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32 <param argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
b5f87b4cfda6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
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33 <param argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
b5f87b4cfda6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
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34 <param argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
0
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35 <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" />
2
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36 <param argument="--tolerance" type="integer" value="5" min="0" label="Tolerance" help="match region within this number of bases, default 5." />
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37
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38 </inputs>
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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39 <outputs>
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40 <data name="output_bam" format="bam" />
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41 </outputs>
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42 <tests>
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43 <!-- 1) -->
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44 <test>
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45 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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46 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
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47 <output name="output_bam" file="eboVir3.clipped.bam" ftype="bam" lines_diff="22" />
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48 </test>
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49 <!-- 2) testing strand -->
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50 <test>
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51 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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52 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
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53 <param name="strand" value="--strand" />
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54 <output name="output_bam" file="eboVir3.clipped.strand.bam" ftype="bam" lines_diff="16" />
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55 </test>
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56 <!-- 3) testing hard clip-->
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57 <test>
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58 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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59 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
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60 <param name="hard_clip_mode" value="--hard-clip" />
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61 <output name="output_bam" file="eboVir3.hardclipped.bam" ftype="bam" lines_diff="14" />
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62 </test>
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63 <!-- 4) testing strand and min length-->
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64 <test>
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65 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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66 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
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67 <param name="min_length" value="30" />
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68 <param name="strand" value="--strand" />
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69 <param name="tolerance" value="6" />
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70 <param name="both_ends" value="--both-ends" />
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71 <param name="no_excluded" value="--no-excluded" />
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72 <output name="output_bam" file="eboVir3.clipped.strand_gt30.bam" ftype="bam" lines_diff="13" />
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73 </test>
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74
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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75 </tests>
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76 <help>
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77 **What it does**
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78 Clips read alignments where they match BED file defined regions (e.g. for amplicon sequencing).
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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79
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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80 samtools ampliconclip -b [INPUT BED] [INPUT BAM1] -o [OUTPUT]
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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81 </help>
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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82 <expand macro="citations"/>
65b88f67edf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
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83 </tool>