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annotate macros.xml @ 5:c147e3a10573 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:12:02 +0000
parents e65c2cd0964c
children 92ec40abcdcf
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
2
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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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>
5
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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8 <token name="@TOOL_VERSION@">1.13</token>
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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9 <token name="@PROFILE@">20.05</token>
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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10 <token name="@FLAGS@"><![CDATA[
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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11 #set $flags = 0
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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12 #if $filter
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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13 #set $flags = sum(map(int, str($filter).split(',')))
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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14 #end if
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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15 ]]></token>
2
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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16 <token name="@PREPARE_IDX@"><![CDATA[
5
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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17 ##prepare input and indices
2
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18 ln -s '$input' infile &&
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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19 #if $input.is_of_type('bam'):
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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20 #if str( $input.metadata.bam_index ) != "None":
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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21 ln -s '${input.metadata.bam_index}' infile.bai &&
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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22 #else:
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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23 samtools index infile infile.bai &&
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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24 #end if
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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25 #elif $input.is_of_type('cram'):
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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26 #if str( $input.metadata.cram_index ) != "None":
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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27 ln -s '${input.metadata.cram_index}' infile.crai &&
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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28 #else:
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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29 samtools index infile infile.crai &&
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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30 #end if
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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31 #end if
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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32 ]]></token>
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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33 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
5
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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34 ##prepare input and indices
2
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35 #for $i, $bam in enumerate( $input_bams ):
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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36 ln -s '$bam' '${i}' &&
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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37 #if $bam.is_of_type('bam'):
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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38 #if str( $bam.metadata.bam_index ) != "None":
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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39 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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40 #else:
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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41 samtools index '${i}' '${i}.bai' &&
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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42 #end if
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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43 #elif $bam.is_of_type('cram'):
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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44 #if str( $bam.metadata.cram_index ) != "None":
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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45 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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46 #else:
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47 samtools index '${i}' '${i}.crai' &&
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48 #end if
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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49 #end if
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50 #end for
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51 ]]></token>
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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52 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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53 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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54 ##and sets the -t/-T parameters accordingly:
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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55 ##- in case of history a symbolic link is used because samtools (view) will generate
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56 ## the index which might not be possible in the directory containing the fasta file
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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57 ##- in case of cached the absolute path is used which allows to read the cram file
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58 ## without specifying the reference
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59 #if $addref_cond.addref_select == "history":
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60 ln -s '${addref_cond.ref}' reference.fa &&
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61 samtools faidx reference.fa &&
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62 #set reffa="reference.fa"
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63 #set reffai="reference.fa.fai"
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64 #elif $addref_cond.addref_select == "cached":
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65 #set reffa=str($addref_cond.ref.fields.path)
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66 #set reffai=str($addref_cond.ref.fields.path)+".fai"
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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67 #else
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68 #set reffa=None
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69 #set reffai=None
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70 #end if
e65c2cd0964c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c
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71 ]]></token>
5
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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72
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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73 <xml name="optional_reference">
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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74 <conditional name="addref_cond">
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75 <param name="addref_select" type="select" label="Use a reference sequence">
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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76 <help>@HELP@</help>
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77 <option value="no">No</option>
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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78 <option value="history">Use a genome/index from the history</option>
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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79 <option value="cached">Use a built-in genome</option>
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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80 </param>
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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81 <when value="no"/>
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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82 <when value="history">
c147e3a10573 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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83 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
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84 </when>
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85 <when value="cached">
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86 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
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87 <options from_data_table="fasta_indexes">
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88 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
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89 </options>
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90 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
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91 </param>
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92 </when>
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93 </conditional>
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94 </xml>
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95 <xml name="mandatory_reference" token_help="" token_argument="">
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96 <conditional name="addref_cond">
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97 <param name="addref_select" type="select" label="Use a reference sequence">
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98 <help>@HELP@</help>
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99 <option value="history">Use a genome/index from the history</option>
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100 <option value="cached">Use a built-in genome</option>
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101 </param>
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102 <when value="history">
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103 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
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104 </when>
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105 <when value="cached">
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106 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
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107 <options from_data_table="fasta_indexes">
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108 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
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109 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
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110 </options>
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111 </param>
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112 </when>
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113 </conditional>
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114 </xml>
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115
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116
2
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117 <token name="@ADDTHREADS@"><![CDATA[
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118 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
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119 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
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120 ]]></token>
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121 <token name="@ADDMEMORY@"><![CDATA[
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122 ##compute the number of memory available to samtools sort (-m)
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123 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
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124 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
2
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125 ((addmemory=addmemory*75/100)) &&
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126 ]]></token>
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127 <xml name="seed_input">
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128 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
2
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129 </xml>
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130 <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
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131 <option value="1" selected="@S1@">Read is paired</option>
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132 <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
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133 <option value="4" selected="@S4@">Read is unmapped</option>
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134 <option value="8" selected="@S8@">Mate is unmapped</option>
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135 <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>
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136 <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>
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137 <option value="64" selected="@S64@">Read is the first in a pair</option>
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138 <option value="128" selected="@S128@">Read is the second in a pair</option>
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139 <option value="256" selected="@S256@">Alignment of the read is not primary</option>
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140 <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>
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141 <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>
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142 <option value="2048" selected="@S2048@">Alignment is supplementary</option>
2
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143 </xml>
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144
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145 <!-- region specification macros and tokens for tools that allow the specification
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146 of region by bed file / space separated list of regions -->
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147 <token name="@REGIONS_FILE@"><![CDATA[
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148 #if $cond_region.select_region == 'tab':
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149 -t '$cond_region.targetregions'
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150 #end if
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151 ]]></token>
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152 <token name="@REGIONS_MANUAL@"><![CDATA[
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153 #if $cond_region.select_region == 'text':
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154 #for $i, $x in enumerate($cond_region.regions_repeat):
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155 '${x.region}'
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156 #end for
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157 #end if
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158 ]]></token>
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159 <xml name="regions_macro">
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160 <conditional name="cond_region">
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161 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
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162 <option value="no" selected="True">No</option>
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163 <option value="text">Manualy specify regions</option>
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164 <option value="tab">Regions from tabular file</option>
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165 </param>
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166 <when value="no"/>
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167 <when value="text">
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168 <repeat name="regions_repeat" min="1" default="1" title="Regions">
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169 <param name="region" type="text" label="region" help="format chr:from-to">
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170 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
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171 </param>
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172 </repeat>
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173 </when>
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174 <when value="tab">
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175 <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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176 </when>
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177 </conditional>
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178 </xml>
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179
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180 <xml name="citations">
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181 <citations>
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182 <citation type="bibtex">
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183 @misc{SAM_def,
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184 title={Definition of SAM/BAM format},
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185 url = {https://samtools.github.io/hts-specs/},}
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186 </citation>
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187 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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188 <citation type="doi">10.1093/bioinformatics/btr076</citation>
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189 <citation type="doi">10.1093/bioinformatics/btr509</citation>
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190 <citation type="bibtex">
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191 @misc{Danecek_et_al,
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192 Author={Danecek, P., Schiffels, S., Durbin, R.},
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193 title={Multiallelic calling model in bcftools (-m)},
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194 url = {http://samtools.github.io/bcftools/call-m.pdf},}
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195 </citation>
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196 <citation type="bibtex">
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197 @misc{Durbin_VCQC,
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198 Author={Durbin, R.},
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199 title={Segregation based metric for variant call QC},
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200 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
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201 </citation>
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202 <citation type="bibtex">
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203 @misc{Li_SamMath,
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204 Author={Li, H.},
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205 title={Mathematical Notes on SAMtools Algorithms},
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206 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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207 </citation>
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208 <citation type="bibtex">
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209 @misc{SamTools_github,
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210 title={SAMTools GitHub page},
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211 url = {https://github.com/samtools/samtools},}
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212 </citation>
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213 </citations>
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214 </xml>
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215 <xml name="version_command">
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216 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
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217 </xml>
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218 <xml name="stdio">
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219 <stdio>
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220 <exit_code range="1:" level="fatal" description="Error" />
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221 </stdio>
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222 </xml>
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223 </macros>