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annotate macros.xml @ 4:4e404acfafa6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
author iuc
date Thu, 27 Sep 2018 09:01:18 -0400
parents cc61ade70eb8
children fe34990e5ce7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
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5 <yield/>
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6 </requirements>
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7 </xml>
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4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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8 <token name="@TOOL_VERSION@">1.9</token>
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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10 <token name="@PREPARE_IDX@"><![CDATA[
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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11 ##prepare input and indices
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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12 ln -s '$input' infile &&
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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13 #if $input.is_of_type('bam'):
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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14 #if str( $input.metadata.bam_index ) != "None":
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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15 ln -s '${input.metadata.bam_index}' infile.bai &&
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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16 #else:
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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17 samtools index infile infile.bai &&
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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18 #end if
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19 #elif $input.is_of_type('cram'):
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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20 #if str( $input.metadata.cram_index ) != "None":
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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21 ln -s '${input.metadata.cram_index}' infile.crai &&
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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22 #else:
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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23 samtools index infile infile.crai &&
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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24 #end if
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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25 #end if
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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26 ]]></token>
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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27 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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28 ##prepare input and indices
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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29 #for $i, $bam in enumerate( $input_bams ):
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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30 ln -s '$bam' '${i}' &&
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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31 #if $bam.is_of_type('bam'):
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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32 #if str( $bam.metadata.bam_index ) != "None":
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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33 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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34 #else:
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35 samtools index '${i}' '${i}.bai' &&
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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36 #end if
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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37 #elif $bam.is_of_type('cram'):
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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38 #if str( $bam.metadata.cram_index ) != "None":
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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39 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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40 #else:
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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41 samtools index '${i}' '${i}.crai' &&
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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42 #end if
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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43 #end if
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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44 #end for
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45 ]]></token>
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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46 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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47 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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48 ##and sets the -t/-T parameters accordingly:
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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49 ##- in case of history a symbolic link is used because samtools (view) will generate
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50 ## the index which might not be possible in the directory containing the fasta file
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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51 ##- in case of cached the absolute path is used which allows to read the cram file
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52 ## without specifying the reference
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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53 #if $addref_cond.addref_select == "history":
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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54 ln -s '${addref_cond.ref}' reference.fa &&
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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55 samtools faidx reference.fa &&
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56 #set reffa="reference.fa"
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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57 #set reffai="reference.fa.fai"
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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58 #elif $addref_cond.addref_select == "cached":
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59 #set reffa=str($addref_cond.ref.fields.path)
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60 #set reffai=str($addref_cond.ref.fields.path)+".fai"
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61 #else
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62 #set reffa=None
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63 #set reffai=None
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64 #end if
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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65 ]]></token>
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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66 <token name="@ADDTHREADS@"><![CDATA[
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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67 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
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69 ]]></token>
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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70 <token name="@ADDMEMORY@"><![CDATA[
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71 ##compute the number of memory available to samtools sort (-m)
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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72 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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73 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
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74 ((addmemory=addmemory*75/100)) &&
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75 ]]></token>
4e404acfafa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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76 <xml name="seed_input">
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77 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
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78 </xml>
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79 <xml name="flag_options">
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80 <option value="1">read is paired</option>
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81 <option value="2">read is mapped in a proper pair</option>
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82 <option value="4">read is unmapped</option>
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83 <option value="8">mate is unmapped</option>
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84 <option value="16">read reverse strand</option>
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85 <option value="32">mate reverse strand</option>
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86 <option value="64">read is the first in a pair</option>
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87 <option value="128">read is the second in a pair</option>
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88 <option value="256">alignment or read is not primary</option>
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89 <option value="512">read fails platform/vendor quality checks</option>
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90 <option value="1024">read is a PCR or optical duplicate</option>
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91 <option value="2048">supplementary alignment</option>
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92 </xml>
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93
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94 <!-- region specification macros and tokens for tools that allow the specification
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95 of region by bed file / space separated list of regions -->
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96 <token name="@REGIONS_FILE@"><![CDATA[
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97 #if $cond_region.select_region == 'tab':
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98 -t '$cond_region.targetregions'
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99 #end if
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100 ]]></token>
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101 <token name="@REGIONS_MANUAL@"><![CDATA[
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102 #if $cond_region.select_region == 'text':
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103 #for $i, $x in enumerate($cond_region.regions_repeat):
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104 '${x.region}'
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105 #end for
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106 #end if
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107 ]]></token>
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108 <xml name="regions_macro">
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109 <conditional name="cond_region">
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110 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
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111 <option value="no" selected="True">No</option>
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112 <option value="text">Manualy specify regions</option>
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113 <option value="tab">Regions from tabular file</option>
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114 </param>
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115 <when value="no"/>
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116 <when value="text">
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117 <repeat name="regions_repeat" min="1" default="1" title="Regions">
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118 <param name="region" type="text" label="region" help="format chr:from-to">
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119 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
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120 </param>
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121 </repeat>
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122 </when>
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123 <when value="tab">
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124 <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />
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125 </when>
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126 </conditional>
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127 </xml>
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128
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129 <xml name="citations">
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130 <citations>
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131 <citation type="bibtex">
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132 @misc{SAM_def,
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133 title={Definition of SAM/BAM format},
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134 url = {https://samtools.github.io/hts-specs/},}
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135 </citation>
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136 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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137 <citation type="doi">10.1093/bioinformatics/btr076</citation>
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138 <citation type="doi">10.1093/bioinformatics/btr509</citation>
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139 <citation type="bibtex">
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140 @misc{Danecek_et_al,
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141 Author={Danecek, P., Schiffels, S., Durbin, R.},
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142 title={Multiallelic calling model in bcftools (-m)},
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143 url = {http://samtools.github.io/bcftools/call-m.pdf},}
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144 </citation>
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145 <citation type="bibtex">
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146 @misc{Durbin_VCQC,
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147 Author={Durbin, R.},
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148 title={Segregation based metric for variant call QC},
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149 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
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150 </citation>
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151 <citation type="bibtex">
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152 @misc{Li_SamMath,
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153 Author={Li, H.},
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154 title={Mathematical Notes on SAMtools Algorithms},
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155 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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156 </citation>
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157 <citation type="bibtex">
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158 @misc{SamTools_github,
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159 title={SAMTools GitHub page},
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160 url = {https://github.com/samtools/samtools},}
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161 </citation>
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162 </citations>
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163 </xml>
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164 <xml name="version_command">
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165 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
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166 </xml>
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167 <xml name="stdio">
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168 <stdio>
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169 <exit_code range="1:" level="fatal" description="Error" />
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170 </stdio>
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171 </xml>
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172 </macros>