Mercurial > repos > iuc > samtools_view

annotate samtools_view.xml @ 2:02afb5ea2fce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
author iuc
date Thu, 27 Sep 2018 08:51:16 -0400
parents 6ade12d94f9a
children fdc58a0cc1d4
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00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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2 <description>reformat, filter, or subsample</description>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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3 <macros>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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4 <import>macros.xml</import>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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5 </macros>
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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6 <expand macro="requirements">
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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7 <requirement type="package">gawk</requirement>
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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8 </expand>
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00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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9 <expand macro="stdio"/>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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10 <expand macro="version_command"/>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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11 <command><![CDATA[
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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12 @ADDTHREADS@
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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13 ## prepare reference data
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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14 @PREPARE_FASTA_IDX@
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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15 @PREPARE_IDX@
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02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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16 #if $cond_subsample.select_subsample == 'target':
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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17 ##this must be done before the main command because we don't know the total # reads until execution time
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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18 #if str($cond_subsample.seed) == '':
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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19 #set seed_expr="int(rand() * 32768)"
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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20 #else
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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21 #set seed_expr=$cond_subsample.seed
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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22 #end if
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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23 #if $input.is_of_type('sam'):
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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24 sample_fragment=`samtools view -c infile | awk '{s=\$1} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s " $seed_expr+frac : "")}'` &&
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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25 #else
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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26 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s " $seed_expr+frac : "")}'` &&
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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27 #end if
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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28 #end if
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00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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29 ##call samtools view
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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30 samtools view
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31 -@ \$addthreads
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32
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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33 #if $outtype == 'count':
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34 -c
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35 #elif $outtype == 'bam':
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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36 -b
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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37 #elif $outtype == 'cram':
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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38 -C
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39 #end if
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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40
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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41 ## filter options (regions filter is the last parameter)
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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42 #if $cond_filter.select_filter == 'yes':
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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43 #if $cond_filter.cond_region.select_region == 'bed' and str( $cond_filter.cond_region.bedfile ) != 'None'
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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44 -L '$cond_filter.bedfile'
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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45 #end if
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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46 #if $cond_filter.cond_rg.select_rg == 'text':
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47 -r '$cond_filter.cond_rg.readgr'
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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48 #else if $cond_filter.cond_rg.select_rg == 'file':
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49 -R '$cond_filter.cond_rg.rgfile'
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50 #end if
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51 #if str($cond_filter.quality) != '' and int( $cond_filter.quality ) > 0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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52 -q $cond_filter.quality
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53 #end if
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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54 #if str( $cond_filter.library ) != ''
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55 -l '$cond_filter.library'
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56 #end if
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57 #if str( $cond_filter.cigarcons ) != ''
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58 -m $cond_filter.cigarcons
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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59 #end if
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60 #if str($cond_filter.inclusive_filter) != 'None':
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61 #set $filter = $cond_filter.inclusive_filter
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62 @FLAGS@
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63 -f $flags
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64 #end if
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65 #if str($cond_filter.exclusive_filter) != 'None':
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66 #set $filter = $cond_filter.exclusive_filter
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67 @FLAGS@
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68 -F $flags
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69 #end if
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70 #if str($cond_filter.exclusive_filter_all) != 'None':
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71 #set $filter = $cond_filter.exclusive_filter_all
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72 @FLAGS@
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73 -G $flags
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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74 #end if
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75 #for $i, $s in enumerate($cond_filter.readtags)
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76 -x '${s.readtag}'
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77 #end for
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78 #end if
2
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79 #if $cond_subsample.select_subsample != 'no':
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80 #if $cond_subsample.select_subsample == "target":
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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81 ##this is calculated at execution time before the main samtools command
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82 "\${sample_fragment}"
0
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83 #else
2
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84 #set fraction=str($cond_subsample.fraction).split('.')[1]
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85 #if str($cond_subsample.seed) == '':
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86 -s "\${RANDOM}".$fraction
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87 #else
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88 -s $cond_subsample.seed.$fraction
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89 #end if
0
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90 #end if
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91 #end if
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92
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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93 ## output options
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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94 $adv_output.header
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95 $adv_output.collapsecigar
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96 #if $adv_output.outputpassing == 'yes'
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97 -U inv_outfile
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98 #end if
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99 -o outfile
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100
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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101 ## additional reference data
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102 #if $reffa!=None:
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103 -T '$reffa'
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104 -t '$reffai'
1
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105 #end if
6ade12d94f9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
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106
6ade12d94f9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
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107 ##currently reference based CRAM is disabled (see https://github.com/galaxyproject/tools-iuc/pull/1963)
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108 #if $outtype=='cram':
0
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109 --output-fmt-option no_ref
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110 #end if
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111
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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112 infile
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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113
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114 ## region filter need to be at the end
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115 #if $cond_filter.select_filter == 'yes' and $cond_filter.cond_region.select_region == 'text':
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116 '$cond_filter.cond_region.regions'
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117 #end if
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118
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119 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
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120 ## then sort the output by coordinate,
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121 #if not $input.is_of_type('bam') and $outtype == 'bam':
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122 && samtools sort
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123 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
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124 -O bam
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125 -o 'tmpsam'
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126 outfile
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127 && mv tmpsam outfile
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128 #if $adv_output.outputpassing == 'yes':
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129 && samtools sort
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130 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
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131 -O bam
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132 -o 'tmpsam'
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133 inv_outfile
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134 && mv tmpsam inv_outfile
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135 #end if
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136 #end if
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137 ]]></command>
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138 <inputs>
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139 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
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140 <param name="input" format="sam,unsorted.bam,cram" type="data" label="SAM/BAM/CRAM data set" />
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141 <param name="outtype" type="select" argument="-b/-C/-c" label="Output type">
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142 <help>Select output type. In case of counts only the total number of alignments is returned. All filters are taken into account</help>
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143 <option value="sam">SAM</option>
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144 <option value="bam">BAM (-b)</option>
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145 <option value="cram">CRAM (-C)</option>
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146 <option value="count">Count of alignments (-c)</option>
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147 </param>
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148 <conditional name="cond_filter">
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149 <param name="select_filter" type="select" label="Filter alignment">
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150 <option value="yes">Yes</option>
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151 <option value="no" selected="True">No</option>
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152 </param>
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153 <when value="yes">
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154 <conditional name="cond_region">
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155 <param name="select_region" type="select" label="Filter by regions">
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156 <option value="no" selected="True">No</option>
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157 <option value="text">Manualy specify regions</option>
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158 <option value="bed">Regions from BED file</option>
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159 </param>
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160 <when value="no"/>
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161 <when value="text">
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162 <param name="regions" type="text" optional="false" label="Filter by regions" help="One or more space-separated region specifications to restrict output to only those alignments which overlap the specified region(s)."/>
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163 </when>
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164 <when value="bed">
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165 <param name="bedfile" format="bed" argument="-L" optional="false" type="data" label="Filter by intervals in a bed file" help="Only output alignments overlapping the intervals in the input bed file." />
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166 </when>
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167 </conditional>
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168 <conditional name="cond_rg">
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169 <param name="select_rg" type="select" label="Filter by readgroup">
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170 <option value="no" selected="True">No</option>
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171 <option value="text">Single read group </option>
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172 <option value="file">Read groups from file</option>
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173 </param>
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174 <when value="no"/>
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175 <when value="text">
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176 <param name="readgr" type="text" argument="-r" label="Filter by read group" help="Only output alignments in read group." />
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177 </when>
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178 <when value="file">
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179 <param name="rgfile" type="data" format="tabular" argument="-R" label="Filter by read groups in file" help="Output alignments in read groups listed in FILE." />
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180 </when>
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181 </conditional>
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182 <param name="quality" type="integer" argument="-q" optional="true" min="0" label="Filter by quality" help="Skip alignments with MAPQ smaller than INT." />
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183 <param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" />
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184 <param name="cigarcons" type="integer" argument="-m" optional="true" min="0" label="Filter by number of CIGAR bases consuming query sequence" help="Only output alignments with number of CIGAR bases consuming query sequence greater than or equal INT." />
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185 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
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186 <expand macro="flag_options" />
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187 </param>
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188 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
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189 <expand macro="flag_options" />
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190 </param>
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191 <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set">
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192 <expand macro="flag_options" />
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193 </param>
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194 <!-- TODO could also make this a text field (comma/space separated) -->
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195 <repeat name="readtags" title="Filter by read tags">
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196 <param name="readtag" type="text" argument="-x" label="Filter by read tag" help="Read tag to exclude from output."/>
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197 </repeat>
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198 </when>
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199 <when value="no"/>
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200 </conditional>
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201 <conditional name="cond_subsample">
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202 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment">
2
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203 <option value="fraction">Specify a fraction to keep</option>
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204 <option value="target">Specify a target # of reads</option>
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205 <option value="no" selected="True">No downsampling</option>
0
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206 </param>
2
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207 <when value="fraction">
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208 <param name="fraction" type="float" optional="False" value="0.5" min="0" max="1" label="Subsampling fraction" help="sets the fraction of templates/pairs to subsample." />
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209 <expand macro="seed_input" />
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210 </when>
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211 <when value='target'>
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212 <param name="target" type="integer" optional="False" value="" min="0" label="Target # of reads" help="sets the target number of reads to subsample." />
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213 <expand macro="seed_input" />
0
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214 </when>
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215 <when value="no"/>
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216 </conditional>
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217 <conditional name="addref_cond">
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218 <param name="addref_select" type="select" label="Reference data">
1
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219 <help>Reference data as fasta(.gz). Required for SAM input without @SQ headers and useful/required for writing CRAM output (see help).</help>
0
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220 <option value="no" selected="True">No, see help (-output-fmt-option no_ref)</option>
1
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221 <option value="history">Use a genome/index from the history (-t/-T)</option>
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222 <option value="cached">Use a built-in genome (-t/-T)</option>
0
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223 </param>
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224 <when value="no"/>
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225 <when value="history">
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226 <param name="ref" format="fasta,fasta.gz" optional="true" type="data" label="Reference file"/>
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227 </when>
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228 <when value="cached">
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229 <param name="ref" type="select" label="Using reference genome">
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230 <options from_data_table="fasta_indexes">
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231 <filter column="1" key="dbkey" ref="input" type="data_meta" />
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232 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
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233 </options>
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234 </param>
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235 </when>
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236 </conditional>
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237 <section name="adv_output" title="Output Options" expanded="false">
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238 <param name="header" type="select" argument="-h/-H" label="Header options">
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239 <option value="-h" selected="True">Include header in SAM output (-h)</option>
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240 <option value="-H">Return header only (-H)</option>
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241 <option value="">Exclude header</option>
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242 </param>
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243 <param name="outputpassing" type="boolean" argument="-U" truevalue="yes" falsevalue="no" checked="false" label="Output alignments not passing the filter" help="Write alignments that are not selected by the various filter options to an extra data set. When this option is used, all alignments (or all alignments intersecting the regions specified) are written to either the output data set or this extra output data set, but never both." />
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244 <param name="collapsecigar" type="boolean" argument="-B" truevalue="-B" falsevalue="" checked="false" label="Collapse backward CIGAR operation" help="Collapse the backward CIGAR operation." />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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diff changeset
245 </section>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
246 </inputs>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
247 <outputs>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
248 <!-- TODO do I need an action for dbkey? -->
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
249 <data name="outputsam" format_source="input" from_work_dir="outfile" label="${tool.name} on ${on_string}: filtered alignments">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
250 <filter>outtype != 'count'</filter>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
251 <!-- TODO is change_format deprecated? how can I modify the type for the different bam types? -->
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
252 <change_format>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
253 <when input="outtype" value="sam" format="sam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
254 <when input="outtype" value="bam" format="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
255 <when input="outtype" value="cram" format="cram" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
256 </change_format>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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257 </data>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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258 <data name="invoutputsam" format_source="input" from_work_dir="inv_outfile" label="${tool.name} on ${on_string}: unfiltered alignments">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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259 <filter>adv_output['outputpassing'] == 'yes' and outtype != 'count'</filter>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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260 <change_format>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
261 <when input="outtype" value="sam" format="sam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
262 <when input="outtype" value="bam" format="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
263 <when input="outtype" value="cram" format="cram" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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264 </change_format>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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265 </data>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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266 <data name="outputcnt" format="txt" from_work_dir="sam" label="${tool.name} on ${on_string}: Counts">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
267 <filter>outtype == 'count'</filter>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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268 </data>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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269 </outputs>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
270 <tests>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
271 <!-- sam to bam (copied from the sam_to_bam tool) -->
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
272 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
273 <param name="input" ftype="sam" value="sam_to_bam_in1.sam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
274 <param name="outtype" value="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
275 <conditional name="addref_cond">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
276 <param name="addref_select" value="history" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
277 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
278 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
279 <output name="outputsam" ftype="bam" file="sam_to_bam_out1.bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
280 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
281 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
282 <param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
283 <param name="outtype" value="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
284 <conditional name="addref_cond">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
285 <param name="addref_select" value="cached" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
286 <param name="ref" value="equCab2chrM" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
287 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
288 <output name="outputsam" ftype="bam" file="sam_to_bam_out2.bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
289 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
290 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
291 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
292 <param name="outtype" value="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
293 <conditional name="addref_cond">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
294 <param name="addref_select" value="history" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
295 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
296 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
297 <output name="outputsam" ftype="bam" file="sam_to_bam_out3.bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
298 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
299 <!-- bam to cram + region filter (adapted from bam_to_cram tool)-->
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
300 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
301 <param name="input" value="test.bam" ftype="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
302 <param name="outtype" value="cram" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
303 <conditional name="addref_cond">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
304 <param name="addref_select" value="history" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
305 <param name="ref" value="test.fa" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
306 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
307 <conditional name="cond_filter">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
308 <param name="select_filter" value="yes" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
309 <conditional name="cond_region">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
310 <param name="select_region" value="no"/>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
311 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
312 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
313 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
314 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
315 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
316 <param name="input" value="test.sam" ftype="sam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
317 <param name="outtype" value="cram" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
318 <conditional name="addref_cond">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
319 <param name="addref_select" value="history" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
320 <param name="ref" value="test.fa" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
321 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
322 <conditional name="cond_filter">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
323 <param name="select_filter" value="yes" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
324 <conditional name="cond_region">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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diff changeset
325 <param name="select_region" value="no"/>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
326 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
327 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
328 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
329 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
330 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
331 <param name="input" value="test.bam" ftype="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
332 <param name="outtype" value="cram" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
333 <conditional name="addref_cond">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
334 <param name="addref_select" value="history" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
335 <param name="ref" value="test.fa" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
336 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
337 <conditional name="cond_filter">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
338 <param name="select_filter" value="yes" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
339 <conditional name="cond_region">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
340 <param name="select_region" value="text"/>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
341 <param name="regions" value="CHROMOSOME_I" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
342 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
343 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
344 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
345 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
346 <!-- bam to sam + header options (adapted from bam_to_sam tool)-->
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
347 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
348 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
349 <param name="outtype" value="sam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
350 <param name="header" value="-h" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
351 <output file="bam_to_sam_out1.sam" ftype="sam" name="outputsam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
352 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
353 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
354 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
355 <param name="outtype" value="sam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
356 <param name="header" value="-H" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
357 <output file="bam_to_sam_out2.sam" ftype="sam" name="outputsam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
358 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
359 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
360 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
361 <param name="outtype" value="sam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
362 <param name="header" value="" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
363 <output file="bam_to_sam_out3.sam" ftype="sam" name="outputsam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
364 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
365 <!-- cram to bam + region (adapted from cram_to_bam tool)-->
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
366 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
367 <param name="input" value="test.cram" ftype="cram" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
368 <param name="outtype" value="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
369 <conditional name="addref_cond">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
370 <param name="addref_select" value="history" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
371 <param name="ref" value="test.fa" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
372 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
373 <output name="outputsam" file="test.bam" ftype="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
374 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
375 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
376 <param name="input" value="test.cram" ftype="cram" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
377 <param name="outtype" value="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
378 <conditional name="addref_cond">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
379 <param name="addref_select" value="history" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
380 <param name="ref" value="test.fa" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
381 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
382 <param name="target_region" value="region" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
383 <param name="region_string" value="CHROMOSOME_I" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
384 <output name="outputsam" file="test.bam" ftype="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
385 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
386 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
387 <param name="input" value="test.cram" ftype="cram" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
388 <param name="outtype" value="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
389 <conditional name="addref_cond">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
390 <param name="addref_select" value="history" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
391 <param name="ref" value="test.fa" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
392 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
393 <param name="target_region" value="regions_bed_file" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
394 <param name="regions_bed_file" value="test.bed" ftype="bed" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
395
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
396 <output name="outputsam" file="test.bam" ftype="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
397 </test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
398 <test>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
399 <param name="input" value="test2.cram" dbkey="equCab2" ftype="cram" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
400 <param name="outtype" value="bam" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
401 <conditional name="addref_cond">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
402 <param name="addref_select" value="cached" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
403 <param name="ref" value="equCab2chrM" />
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
404 </conditional>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
405 <conditional name="cond_region">
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
406 <param name="select_region" value="no"/>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
407 </conditional>
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408 <output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" />
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409 </test>
2
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410 <!-- sampling options-->
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411 <test>
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412 <param name="input" value="test.sam" ftype="sam" />
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413 <param name="outtype" value="sam" />
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414 <conditional name="cond_subsample">
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415 <param name="select_subsample" value="target" />
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416 <param name="target" value="2" />
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417 </conditional>
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418 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" />
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419 </test>
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420 <test>
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421 <param name="input" value="test.sam" ftype="sam" />
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422 <param name="outtype" value="sam" />
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423 <conditional name="cond_subsample">
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424 <param name="select_subsample" value="target" />
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425 <param name="seed" value="7" />
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426 <param name="target" value="2" />
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427 </conditional>
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428 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="4" />
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429 </test>
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430 <test>
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431 <param name="input" value="test.bam" ftype="bam" />
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432 <param name="outtype" value="bam" />
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433 <conditional name="cond_subsample">
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434 <param name="select_subsample" value="target" />
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435 <param name="seed" value="7" />
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436 <param name="target" value="2" />
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437 </conditional>
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438 <output name="outputsam" file="test_ds.bam" ftype="bam" />
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439 </test>
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440 <test>
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441 <param name="input" value="test.bam" ftype="bam" />
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442 <param name="outtype" value="bam" />
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443 <conditional name="cond_subsample">
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444 <param name="select_subsample" value="fraction" />
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445 <param name="seed" value="7" />
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446 <param name="fraction" value=".2" />
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447 </conditional>
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448 <output name="outputsam" file="test_ds.bam" ftype="bam" />
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449 </test>
0
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450 </tests>
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451 <help>
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452 **What it does**
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453
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454 Samtools view can:
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455
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456 1. filter alignments according to various criteria
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457 2. convert between alignment formats (SAM, BAM, CRAM)
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458
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459 With no options or regions specified, prints all alignments in the specified input alignment file (in SAM, BAM, or CRAM format) to standard output in SAM format (with no header).
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460
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461 **Alignment format conversion**
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462
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463 Inputs of type SAM, BAM, and CRAM are accepted and can be converted to each of these formats (alternatively alignment counts can be computed) by selecting the appropriate "Output type".
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464
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465 .. class:: infomark
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466
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467 samtools view allows to specify a reference sequence. This is required for SAM input with missing @SQ headers (which include sequence names, length, md5, etc) and useful (and sometimes necessary) for CRAM input and output. In the following the use of reference sequence in the CRAM format is detailed.
1
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468 CRAM is (intended as a primarily) a reference-based compressed format, i.e. only differences between the stored sequences and the reference are stored. As a consequence the reference that was used to generate the alignemnts is always needed in order to interpret the alignments (a checksum stored in the CRAM file is used to verify that the only the correct sequence can be used), i.e. the CRAM file on its own is not useful per default. This allows for a more space efficient storage compared to BAM.
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469 But it is also possible to use CRAM without a reference with the disadvantage that the reference is stored explicitely (as in SAM and BAM).
0
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470
1
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471 The Galaxy tool **currently generates only CRAM without reference sequence**.
0
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472
1
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473 For reference based CRAM input the correct refernce sequence needs to be specified.
0
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474
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475 **Filtering alignments**
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476
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477 samtools view allows to filter alignements based on various criteria, i.e. the output will contain only alignemnts matching all criteria (an additional output containing the remaining alignments can be created additionally, see "Output alignments not passing the filter" in "output options"): e.g. by regions (see below), alignment quality (see below), and tags or flags set in the alignments.
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478
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479
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480
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481 **Filtering by regions**
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482
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483 You may specify one or more space-separated region specifications after the input filename to restrict output to only those alignments which overlap the specified region(s). Use of region specifications requires a coordinate-sorted and indexed input file (in BAM or CRAM format).
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484
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485 Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based.
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486
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487 Important note: when multiple regions are given, some alignments may be output multiple times if they overlap more than one of the specified regions.
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488
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489 Examples of region specifications:
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490
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491 - chr1 Output all alignments mapped to the reference sequence named 'chr1' (i.e. @SQ SN:chr1).
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492 - chr2:1000000 The region on chr2 beginning at base position 1,000,000 and ending at the end of the chromosome.
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493 - chr3:1000-2000 The 1001bp region on chr3 beginning at base position 1,000 and ending at base position 2,000 (including both end positions).
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494 - '*' Output the unmapped reads at the end of the file. (This does not include any unmapped reads placed on a reference sequence alongside their mapped mates.)
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495 - . Output all alignments. (Mostly unnecessary as not specifying a region at all has the same effect.)
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496
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497 **Filtering by quality**
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498
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499 This filters based on the MAPQ column of the SAM format which gives an estimate about the correct placement of the alignemnt. Note that aligners do not follow a consistent definition.
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500
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501 The -x, -B, and -s options modify the data which is contained in each alignment.
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502 </help>
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503 <expand macro="citations"/>
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504 </tool>