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annotate macros.xml @ 10:3a0efe14891f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 84db51c96845854eb42c1a9949e4b79316b41925
author iuc
date Wed, 22 Jun 2022 07:48:55 +0000
parents 1cc79f49b8d5
children fed4aa48ba09
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>
3
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
0
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5 <yield/>
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6 </requirements>
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7 </xml>
8
e28839a4b932 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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8 <token name="@TOOL_VERSION@">1.13</token>
e28839a4b932 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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9 <token name="@PROFILE@">20.05</token>
e28839a4b932 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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10 <token name="@FLAGS@"><![CDATA[
e28839a4b932 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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11 #set $flags = 0
e28839a4b932 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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12 #if $filter
e28839a4b932 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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13 #set $flags = sum(map(int, str($filter).split(',')))
e28839a4b932 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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14 #end if
e28839a4b932 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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15 ]]></token>
3
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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16 <token name="@PREPARE_IDX@"><![CDATA[
8
e28839a4b932 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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17 ##prepare input and indices
3
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18 ln -s '$input' infile &&
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19 #if $input.is_of_type('bam'):
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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20 #if str( $input.metadata.bam_index ) != "None":
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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21 ln -s '${input.metadata.bam_index}' infile.bai &&
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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22 #else:
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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23 samtools index infile infile.bai &&
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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24 #end if
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25 #elif $input.is_of_type('cram'):
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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26 #if str( $input.metadata.cram_index ) != "None":
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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27 ln -s '${input.metadata.cram_index}' infile.crai &&
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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28 #else:
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29 samtools index infile infile.crai &&
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30 #end if
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31 #end if
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32 ]]></token>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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33 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
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e28839a4b932 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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34 ##prepare input and indices
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35 #for $i, $bam in enumerate( $input_bams ):
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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36 ln -s '$bam' '${i}' &&
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37 #if $bam.is_of_type('bam'):
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38 #if str( $bam.metadata.bam_index ) != "None":
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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39 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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40 #else:
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41 samtools index '${i}' '${i}.bai' &&
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42 #end if
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43 #elif $bam.is_of_type('cram'):
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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44 #if str( $bam.metadata.cram_index ) != "None":
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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45 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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46 #else:
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47 samtools index '${i}' '${i}.crai' &&
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48 #end if
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49 #end if
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50 #end for
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51 ]]></token>
95a7ddf617e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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52 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
9
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53 ## Make the user-selected reference genome, if any, accessible through
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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54 ## a shell variable $reffa, index the reference if necessary, and make
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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55 ## the fai-index file available through a shell variable $reffai.
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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56
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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57 ## For a cached genome simply sets the shell variables to point to the
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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58 ## genome file and its precalculated index.
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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59 ## For a genome from the user's history, if that genome is a plain
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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60 ## fasta file, the code creates a symlink in the pwd, creates the fai
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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61 ## index file next to it, then sets the shell variables to point to the
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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62 ## symlink and its index.
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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63 ## For a fasta.gz dataset from the user's history, it tries the same,
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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64 ## but this will only succeed if the file got compressed with bgzip.
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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65 ## For a regular gzipped file samtools faidx will fail, in which case
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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66 ## the code falls back to decompressing to plain fasta before
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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67 ## reattempting the indexing.
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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68 ## Indexing of a bgzipped file produces a regular fai index file *and*
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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69 ## a compressed gzi file. The former is identical to the fai index of
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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70 ## the uncompressed fasta.
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71
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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72 ## If the user has not selected a reference (it's an optional parameter
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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73 ## in some samtools wrappers), a cheetah boolean use_ref is set to
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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74 ## False to encode that fact.
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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75
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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76 #set use_ref=True
3
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77 #if $addref_cond.addref_select == "history":
9
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78 #if $addref_cond.ref.is_of_type('fasta'):
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79 reffa="reference.fa" &&
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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80 ln -s '${addref_cond.ref}' \$reffa &&
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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81 samtools faidx \$reffa &&
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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82 #else:
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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83 reffa="reference.fa.gz" &&
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84 ln -s '${addref_cond.ref}' \$reffa &&
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85 {
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86 samtools faidx \$reffa ||
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87 {
1cc79f49b8d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c5ded4208dd70e88596ddc725795a2401773f02d"
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88 echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 &&
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89 gzip -dc \$reffa > reference.fa &&
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90 reffa="reference.fa" &&
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91 samtools faidx \$reffa;
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92 }
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93 } &&
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94 #end if
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95 reffai=\$reffa.fai &&
3
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96 #elif $addref_cond.addref_select == "cached":
9
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97 ## in case of cached the absolute path is used which allows to read
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98 ## a cram file without specifying the reference
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99 reffa='${addref_cond.ref.fields.path}' &&
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100 reffai=\$reffa.fai &&
3
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101 #else
9
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102 #set use_ref=False
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103 #end if
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104 ]]></token>
8
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105
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106 <xml name="optional_reference">
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107 <conditional name="addref_cond">
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108 <param name="addref_select" type="select" label="Use a reference sequence">
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109 <help>@HELP@</help>
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110 <option value="no">No</option>
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111 <option value="history">Use a genome/index from the history</option>
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112 <option value="cached">Use a built-in genome</option>
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113 </param>
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114 <when value="no"/>
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115 <when value="history">
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116 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
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117 </when>
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118 <when value="cached">
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119 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
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120 <options from_data_table="fasta_indexes">
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121 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
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122 </options>
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123 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
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124 </param>
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125 </when>
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126 </conditional>
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127 </xml>
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128 <xml name="mandatory_reference" token_help="" token_argument="">
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129 <conditional name="addref_cond">
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130 <param name="addref_select" type="select" label="Use a reference sequence">
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131 <help>@HELP@</help>
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132 <option value="history">Use a genome/index from the history</option>
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133 <option value="cached">Use a built-in genome</option>
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134 </param>
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135 <when value="history">
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136 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
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137 </when>
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138 <when value="cached">
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139 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
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140 <options from_data_table="fasta_indexes">
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141 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
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142 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
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143 </options>
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144 </param>
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145 </when>
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146 </conditional>
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147 </xml>
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148
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149
3
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150 <token name="@ADDTHREADS@"><![CDATA[
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151 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
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152 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
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153 ]]></token>
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154 <token name="@ADDMEMORY@"><![CDATA[
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155 ##compute the number of memory available to samtools sort (-m)
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156 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
8
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157 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
3
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158 ((addmemory=addmemory*75/100)) &&
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159 ]]></token>
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160 <xml name="seed_input">
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161 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
3
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162 </xml>
8
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163 <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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164 <option value="1" selected="@S1@">Read is paired</option>
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165 <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
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166 <option value="4" selected="@S4@">Read is unmapped</option>
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167 <option value="8" selected="@S8@">Mate is unmapped</option>
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168 <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>
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169 <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>
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170 <option value="64" selected="@S64@">Read is the first in a pair</option>
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171 <option value="128" selected="@S128@">Read is the second in a pair</option>
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172 <option value="256" selected="@S256@">Alignment of the read is not primary</option>
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173 <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>
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174 <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>
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175 <option value="2048" selected="@S2048@">Alignment is supplementary</option>
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176 </xml>
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177
8
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178 <!-- region specification macros and tokens for tools that allow the specification
3
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179 of region by bed file / space separated list of regions -->
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180 <token name="@REGIONS_FILE@"><![CDATA[
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181 #if $cond_region.select_region == 'tab':
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182 -t '$cond_region.targetregions'
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183 #end if
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184 ]]></token>
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185 <token name="@REGIONS_MANUAL@"><![CDATA[
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186 #if $cond_region.select_region == 'text':
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187 #for $i, $x in enumerate($cond_region.regions_repeat):
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188 '${x.region}'
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189 #end for
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190 #end if
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191 ]]></token>
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192 <xml name="regions_macro">
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193 <conditional name="cond_region">
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194 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
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195 <option value="no" selected="True">No</option>
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196 <option value="text">Manualy specify regions</option>
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197 <option value="tab">Regions from tabular file</option>
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198 </param>
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199 <when value="no"/>
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200 <when value="text">
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201 <repeat name="regions_repeat" min="1" default="1" title="Regions">
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202 <param name="region" type="text" label="region" help="format chr:from-to">
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203 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
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204 </param>
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205 </repeat>
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206 </when>
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207 <when value="tab">
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208 <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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209 </when>
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210 </conditional>
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211 </xml>
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212
0
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213 <xml name="citations">
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214 <citations>
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215 <citation type="bibtex">
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216 @misc{SAM_def,
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217 title={Definition of SAM/BAM format},
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218 url = {https://samtools.github.io/hts-specs/},}
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219 </citation>
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220 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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221 <citation type="doi">10.1093/bioinformatics/btr076</citation>
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222 <citation type="doi">10.1093/bioinformatics/btr509</citation>
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223 <citation type="bibtex">
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224 @misc{Danecek_et_al,
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225 Author={Danecek, P., Schiffels, S., Durbin, R.},
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226 title={Multiallelic calling model in bcftools (-m)},
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227 url = {http://samtools.github.io/bcftools/call-m.pdf},}
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228 </citation>
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229 <citation type="bibtex">
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230 @misc{Durbin_VCQC,
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231 Author={Durbin, R.},
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232 title={Segregation based metric for variant call QC},
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233 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
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234 </citation>
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235 <citation type="bibtex">
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236 @misc{Li_SamMath,
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237 Author={Li, H.},
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238 title={Mathematical Notes on SAMtools Algorithms},
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239 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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240 </citation>
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241 <citation type="bibtex">
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242 @misc{SamTools_github,
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243 title={SAMTools GitHub page},
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244 url = {https://github.com/samtools/samtools},}
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245 </citation>
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246 </citations>
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247 </xml>
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248 <xml name="version_command">
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249 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
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250 </xml>
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251 <xml name="stdio">
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252 <stdio>
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253 <exit_code range="1:" level="fatal" description="Error" />
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254 </stdio>
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255 </xml>
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256 </macros>