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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author iuc
date Mon, 29 Jul 2019 08:40:14 -0400
parents c2549832fb33
children
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="1.3.1">samtools</requirement>
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5 <yield/>
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6 </requirements>
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7 </xml>
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c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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8 <token name="@TOOL_VERSION@">1.3.1</token>
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9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
49ed010c7eef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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10 <xml name="filter_options">
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11 <option value="1">Read is paired</option>
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12 <option value="2">Read is mapped in a proper pair</option>
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13 <option value="4">The read is unmapped</option>
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14 <option value="8">The mate is unmapped</option>
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15 <option value="16">Read strand</option>
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16 <option value="32">Mate strand</option>
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17 <option value="48">Read is the first in a pair</option>
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18 <option value="64">Read is the second in a pair</option>
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19 <option value="256">The alignment or this read is not primary</option>
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20 <option value="512">The read fails platform/vendor quality checks</option>
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21 <option value="768">The read is a PCR or optical duplicate</option>
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22 <option value="1024">Supplementary alignment</option>
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23 </xml>
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24 <xml name="citations">
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25 <citations>
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26 <citation type="bibtex">
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27 @misc{SAM_def,
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28 title={Definition of SAM/BAM format},
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29 url = {https://samtools.github.io/hts-specs/},}
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30 </citation>
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31 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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32 <citation type="doi">10.1093/bioinformatics/btr076</citation>
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33 <citation type="doi">10.1093/bioinformatics/btr509</citation>
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34 <citation type="bibtex">
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35 @misc{Danecek_et_al,
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36 Author={Danecek, P., Schiffels, S., Durbin, R.},
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37 title={Multiallelic calling model in bcftools (-m)},
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38 url = {http://samtools.github.io/bcftools/call-m.pdf},}
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39 </citation>
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40 <citation type="bibtex">
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41 @misc{Durbin_VCQC,
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42 Author={Durbin, R.},
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43 title={Segregation based metric for variant call QC},
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44 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
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45 </citation>
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46 <citation type="bibtex">
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47 @misc{Li_SamMath,
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48 Author={Li, H.},
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49 title={Mathematical Notes on SAMtools Algorithms},
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50 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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51 </citation>
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52 <citation type="bibtex">
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53 @misc{SamTools_github,
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54 title={SAMTools GitHub page},
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55 url = {https://github.com/samtools/samtools},}
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56 </citation>
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57 </citations>
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58 </xml>
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59 <xml name="version_command">
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60 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
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61 </xml>
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62 <xml name="stdio">
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63 <stdio>
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64 <exit_code range="1:" level="fatal" description="Error" />
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65 </stdio>
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66 </xml>
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67 <token name="@no-chrom-options@">
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68 -----
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69
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70 .. class:: warningmark
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71
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72 **No options available? How to re-detect metadata**
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73
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74 If you see a &quot;No options available&quot; within the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
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75
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76 1. Click on the **pencil** icon adjacent to the dataset in the history
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77 2. A new menu will appear in the center pane of the interface
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78 3. Click **Datatype** tab
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79 4. Set **New Type** to **BAM**
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80 5. Click **Save**
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81
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82 The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
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83 </token>
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84 </macros>