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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
author mvdbeek
date Tue, 25 Sep 2018 04:09:34 -0400
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12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
mvdbeek
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1 <macros>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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2 <xml name="requirements">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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3 <requirements>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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5 <yield/>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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6 </requirements>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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7 </xml>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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8 <token name="@TOOL_VERSION@">1.9</token>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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10 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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11 ##prepare input and indices
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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12 #for $i, $bam in enumerate( $input_bams ):
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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13 ln -s '$bam' '${i}' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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14 #if $bam.is_of_type('bam'):
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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15 #if str( $bam.metadata.bam_index ) != "None":
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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16 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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17 #else:
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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18 samtools index '${i}' '${i}.bai' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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19 #end if
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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20 #elif $bam.is_of_type('cram'):
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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21 #if str( $bam.metadata.cram_index ) != "None":
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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22 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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23 #else:
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24 samtools index '${i}' '${i}.crai' &&
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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25 #end if
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26 #end if
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27 #end for
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28 ]]></token>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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29 <xml name="flag_options">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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30 <option value="1">read is paired</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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31 <option value="2">read is mapped in a proper pair</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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32 <option value="4">read is unmapped</option>
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33 <option value="8">mate is unmapped</option>
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34 <option value="16">read reverse strand</option>
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35 <option value="32">mate reverse strand</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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36 <option value="64">read is the first in a pair</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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37 <option value="128">read is the second in a pair</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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38 <option value="256">alignment or read is not primary</option>
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39 <option value="512">read fails platform/vendor quality checks</option>
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40 <option value="1024">read is a PCR or optical duplicate</option>
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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41 <option value="2048">supplementary alignment</option>
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42 </xml>
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43 <xml name="citations">
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44 <citations>
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45 <citation type="bibtex">
12bc610792b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 22e524ec4416170792a8f8eb1bb283789fff2f61-dirty
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46 @misc{SAM_def,
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47 title={Definition of SAM/BAM format},
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48 url = {https://samtools.github.io/hts-specs/},}
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49 </citation>
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50 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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51 <citation type="doi">10.1093/bioinformatics/btr076</citation>
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52 <citation type="doi">10.1093/bioinformatics/btr509</citation>
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53 <citation type="bibtex">
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54 @misc{Danecek_et_al,
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55 Author={Danecek, P., Schiffels, S., Durbin, R.},
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56 title={Multiallelic calling model in bcftools (-m)},
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57 url = {http://samtools.github.io/bcftools/call-m.pdf},}
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58 </citation>
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59 <citation type="bibtex">
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60 @misc{Durbin_VCQC,
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61 Author={Durbin, R.},
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62 title={Segregation based metric for variant call QC},
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63 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
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64 </citation>
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65 <citation type="bibtex">
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66 @misc{Li_SamMath,
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67 Author={Li, H.},
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68 title={Mathematical Notes on SAMtools Algorithms},
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69 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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70 </citation>
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71 <citation type="bibtex">
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72 @misc{SamTools_github,
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73 title={SAMTools GitHub page},
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74 url = {https://github.com/samtools/samtools},}
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75 </citation>
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76 </citations>
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77 </xml>
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78 <xml name="version_command">
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79 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
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80 </xml>
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81 <xml name="stdio">
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82 <stdio>
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83 <exit_code range="1:" level="fatal" description="Error" />
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84 </stdio>
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85 </xml>
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86 <token name="@no-chrom-options@">
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87 -----
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88
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89 .. class:: warningmark
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90
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91 **No options available? How to re-detect metadata**
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92
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93 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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94
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95 1. Click on the **pencil** icon adjacent to the dataset in the history
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96 2. A new menu will appear in the center pane of the interface
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97 3. Click **Datatype** tab
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98 4. Set **New Type** to **BAM**
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99 5. Click **Save**
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100
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101 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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102 </token>
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103 </macros>