Mercurial > repos > pimarin > bedtools
annotate macros.xml @ 0:4cacc5b8001b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
author | pimarin |
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date | Thu, 23 Feb 2023 09:50:24 +0000 |
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0
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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1 <macros> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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2 <xml name="requirements"> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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3 <requirements> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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4 <requirement type="package" version="@TOOL_VERSION@">bedtools</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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5 <yield/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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6 </requirements> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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7 </xml> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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8 <xml name="bio_tools"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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9 <xrefs> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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10 <xref type="bio.tools">bedtools</xref> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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11 </xrefs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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12 </xml> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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13 <token name="@TOOL_VERSION@">2.30.0</token> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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14 <token name="@SAMTOOLS_VERSION@">1.9</token> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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15 <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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16 <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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17 <token name="@PROFILE@">20.05</token> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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18 <xml name="stdio"> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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19 <stdio> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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20 <!-- Anything other than zero is an error --> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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21 <exit_code range="1:" /> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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22 <exit_code range=":-1" /> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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23 <!-- In case the return code has not been set propery check stderr too --> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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24 <regex match="Error:" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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25 <regex match="Exception:" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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26 </stdio> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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27 <version_command>bedtools --version</version_command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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28 </xml> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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29 <xml name="reciprocal"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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30 <param name="reciprocal" argument="-r" type="select" label="Require that the fraction of overlap be reciprocal for A and B" help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B."> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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31 <option value="" selected="true">No</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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32 <option value="-r">Yes</option> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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33 </param> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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34 </xml> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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35 <xml name="fraction" token_name="" token_argument="" token_label="" token_help="" > |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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36 <param name="@NAME@" argument="@ARGUMENT@" type="float" min="0" max="1" optional="true" label="@LABEL@" help="@HELP@" /> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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37 </xml> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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38 <xml name="overlap" token_name="overlap" token_argument="-f" token_fracof="A"> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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39 <expand macro="fraction" name="@NAME@" argument="@ARGUMENT@" label="Minimum overlap required as a fraction of @FRACOF@" help="Default is 1E-9, i.e. 1bp."/> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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40 </xml> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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41 <token name="@OVERLAP@"><![CDATA[ |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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42 #if str($overlap): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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43 -f $overlap |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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44 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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45 ]]></token> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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46 <xml name="strand2"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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47 <param name="strand" type="select" label="Calculation based on strandedness?"> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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48 <option value="" selected="true">Overlaps on either strand</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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49 <option value="-s">Only overlaps occurring on the **same** strand.</option> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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50 <option value="-S">Only overlaps occurring on the **opposite** strand.</option> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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51 </param> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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52 </xml> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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53 <xml name="seed"> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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54 <conditional name="seed"> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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55 <param name="seed_choose" type="select" label="Choose Seed?"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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56 <option value="False" selected="true">Random Shuffling</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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57 <option value="True">Choose fixed seed</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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58 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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59 <when value="True"> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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60 <param argument="-seed" type="integer" value="12345" label="Enter Seed" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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61 </when> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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62 <when value="False" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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63 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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64 </xml> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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65 <xml name="split"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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66 <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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67 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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68 help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." /> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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69 </xml> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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70 <xml name="input_conditional_genome_file" token_optional="false" token_help=""> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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71 <conditional name="genome_file_opts"> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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72 <param name="genome_file_opts_selector" type="select" label="Genome file" help="@HELP@"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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73 <option value="loc" selected="true">Locally installed Genome file</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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74 <option value="hist">Genome file from your history</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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75 </param> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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76 <when value="loc"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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77 <param name="genome" type="select" optional="@OPTIONAL@" multiple="false" label="Genome file"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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78 <options from_data_table="__dbkeys__" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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79 </param> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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80 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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81 <when value="hist"> |
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82 <param name="genome" type="data" optional="@OPTIONAL@" format="tabular" label="Genome file" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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83 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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84 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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85 </xml> |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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86 <token name="@GENOME_FILE@"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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87 #if $genome_file_opts.genome |
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88 -g |
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89 #if $genome_file_opts.genome_file_opts_selector == "loc": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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90 '$genome_file_opts.genome.fields.len_path' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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91 #elif $genome_file_opts.genome_file_opts_selector == "hist": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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92 '$genome_file_opts.genome' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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93 #end if |
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94 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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95 </token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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96 <token name="@GENOME_FILE_MAKEWINDOWS@"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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97 #if $type.type_select == "genome": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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98 #if $type.genome_file_opts.genome_file_opts_selector == "loc": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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99 -g '$type.genome_file_opts.genome.fields.len_path' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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100 #elif $type.genome_file_opts.genome_file_opts_selector == "hist": |
4cacc5b8001b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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101 -g '$type.genome_file_opts.genome' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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102 #end if |
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103 #end if |
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104 </token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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105 <token name="@GENOME_FILE_UNION@"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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106 #if $empty.empty_selector == "-empty": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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107 #if $empty.genome_file_opts.genome_file_opts_selector == "loc": |
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108 -g '$empty.genome_file_opts.genome.fields.len_path' |
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109 #elif $empty.genome_file_opts.genome_file_opts_selector == "hist": |
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110 -g '$empty.genome_file_opts.genome' |
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111 #end if |
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112 #end if |
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113 </token> |
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114 <token name="@GENOME_FILE_COVERAGE@"> |
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115 #if $input_type.input_type_select == "bam": |
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116 -ibam '$input_type.input' |
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117 #else: |
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118 -i '$input_type.input' |
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119 #if $input_type.genome_file_opts.genome_file_opts_selector == "loc": |
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120 -g '$input_type.genome_file_opts.genome.fields.len_path' |
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121 #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist": |
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122 -g '$input_type.genome_file_opts.genome' |
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123 #end if |
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124 #end if |
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125 </token> |
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126 <xml name="closest_D_option"> |
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127 <param argument="-iu" type="boolean" truevalue="-iu" falsevalue="" checked="false" |
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128 label="Ignore features in B that are upstream of features in A" |
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129 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" /> |
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130 |
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131 <param argument="-id" type="boolean" truevalue="-id" falsevalue="" checked="false" |
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132 label="Ignore features in B that are downstream of features in A" |
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133 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" /> |
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134 |
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135 <param argument="-fu" type="boolean" truevalue="-fu" falsevalue="" checked="false" |
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136 label="Choose first from features in B that are upstream of features in A" |
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137 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" /> |
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138 |
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139 <param argument="-fd" type="boolean" truevalue="-fd" falsevalue="" checked="false" |
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140 label="Choose first from features in B that are downstream of features in A" |
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141 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" /> |
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142 </xml> |
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143 <xml name="addition"> |
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144 <conditional name="addition"> |
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145 <param name="addition_select" type="select" label="Choose what you want to do"> |
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146 <option value="b" selected="true">Increase the @STD_BEDTOOLS_INPUT_LABEL@ entry by the same number base pairs in each direction.</option> |
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147 <option value="lr">Increase by Start Coordinate and End Coordinate</option> |
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148 </param> |
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149 <when value="b"> |
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150 <param name="b" value="1" label="Number of base pairs" type="integer" /> |
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151 </when> |
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152 <when value="lr"> |
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153 <param name="l" type="integer" value="0" label="The number of base pairs to subtract from the start coordinate" /> |
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154 <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" /> |
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155 </when> |
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156 </conditional> |
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157 </xml> |
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158 <xml name="print_header"> |
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159 <param argument="-header" type="boolean" truevalue="-header" falsevalue="" checked="false" |
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160 label="Print the header from the A file prior to results" /> |
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161 </xml> |
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162 <!-- TODO this is currently not used, but we should make use of it --> |
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163 <xml name="genome_validator"> |
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164 <validator type="unspecified_build" /> |
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165 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> |
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166 </xml> |
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167 |
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168 <!-- ToDo column_picker --> |
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169 <xml name="choose_columns"> |
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170 <param name="cols" argument="-c" type="text" value="" |
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171 label="Specify the column(s) that should be summarized" |
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172 help="Comma separated"> |
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173 <sanitizer invalid_char=""> |
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174 <valid initial="string.digits"><add value=","/></valid> |
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175 </sanitizer> |
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176 </param> |
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177 </xml> |
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178 |
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179 <token name="@C_AND_O_ARGUMENT@"> |
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180 #set $col = list() |
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181 #set $op = list() |
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182 #for $item in $c_and_o_argument_repeat: |
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183 #silent $col.append( str($item.col) ) |
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184 #silent $op.append( str($item.operation) ) |
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185 #end for |
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186 #if $col: |
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187 -c #echo ','.join($col)# |
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188 -o #echo ','.join($op)# |
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189 #end if |
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190 </token> |
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191 |
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192 <xml name="c_and_o_argument"> |
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193 <repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0"> |
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194 <yield /> |
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195 <expand macro="choose_operations"> |
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196 <expand macro="math_options" /> |
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197 <expand macro="additional_math_options" /> |
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198 </expand> |
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199 </repeat> |
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200 </xml> |
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201 |
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202 <xml name="choose_operations"> |
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203 <param name="operation" type="select" label="Specify the operation"> |
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204 <yield /> |
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205 </param> |
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206 </xml> |
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207 |
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208 <xml name="math_options"> |
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209 <option value="sum" selected="true">Sum - numeric only</option> |
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210 <option value="min">Min - numeric only</option> |
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211 <option value="max">Max - numeric only</option> |
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212 <option value="absmin">AbsMin - numeric only</option> |
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213 <option value="absmax">AbsMax - numeric only</option> |
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214 <option value="mean">Mean - numeric only</option> |
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215 <option value="median">Median - numeric only</option> |
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216 <option value="mode">Mode - numeric only</option> |
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217 <option value="antimode">Antimode - numeric only</option> |
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218 <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option> |
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219 </xml> |
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220 <xml name="additional_math_options"> |
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221 <option value="count">Count - numeric or text</option> |
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222 <option value="count_disctinct">Count Distinct - numeric or text</option> |
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223 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option> |
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224 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option> |
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225 </xml> |
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226 <xml name="sorted"> |
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227 <!-- -sorted -g --> |
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228 <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false" |
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229 label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/> |
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230 </xml> |
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231 <token name="@SORTED@"> |
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232 <![CDATA[ |
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233 $sorted |
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234 #if str($sorted) != '': |
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235 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'): |
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236 -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5) |
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237 #else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'): |
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238 -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5) |
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239 #end if |
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240 #end if |
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241 ]]> |
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242 </token> |
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243 <token name="@REFERENCES@"> |
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244 <![CDATA[ |
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245 ------ |
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246 |
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247 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_. |
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248 |
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249 .. _bedtools package: https://github.com/arq5x/bedtools2 |
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250 .. _Quinlan laboratory: http://quinlanlab.org |
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251 |
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252 |
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253 **Citation** |
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254 |
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255 If you use this tool in Galaxy, please cite: |
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256 |
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257 Bjoern A. Gruening (2014), `Galaxy wrapper <https://github.com/bgruening/galaxytools>`_ |
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258 ]]> |
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259 </token> |
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260 <xml name="citations"> |
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261 <citations> |
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262 <citation type="doi">10.1093/bioinformatics/btq033</citation> |
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263 <yield /> |
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264 </citations> |
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265 </xml> |
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266 </macros> |