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annotate samtools_view.xml @ 14:5826298f6a73 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
author iuc
date Mon, 15 Aug 2022 09:19:43 +0000
parents 0dbf49c414ae
children 6be888be75f9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
5826298f6a73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
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parents: 13
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1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@REF_DATA@">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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6 ## additional reference data
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7 #if $use_ref:
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8 -T "\$reffa"
c370440f901e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c5ded4208dd70e88596ddc725795a2401773f02d"
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9 -t "\$reffai"
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10 #end if
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11 </token>
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12 <xml name="read_output_formatting">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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13 <yield />
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14 <section name="adv_output" title="Read Reformatting Options" expanded="false">
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15 <repeat name="readtags" title="Strip read tags from output">
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16 <param name="readtag" type="text" argument="-x" label="Read tag to strip" help="Read tag to exclude from output."/>
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17 </repeat>
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18 <param name="collapsecigar" type="boolean" argument="-B" truevalue="-B" falsevalue="" checked="false" label="Collapse backward CIGAR operation" help="Collapse the backward CIGAR operation." />
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19 </section>
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20 </xml>
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21 <xml name="output_format_selector">
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22 <conditional name="output_format">
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23 <param name="oformat" type="select" label="Output format"
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24 help="Note on BAM output format: The tool will generate coordinate-sorted BAM, i.e., may change the order of reads compared to the input. For BAM input, select 'Same as input' to produce BAM output with the read order retained.">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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25 <option value="input">Same as input</option>
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26 <option value="sam">SAM</option>
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27 <option value="bam" selected="True">BAM (-b)</option>
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28 <option value="cram">CRAM (-C)</option>
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29 </param>
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30 <when value="input" />
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31 <when value="sam">
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32 <yield />
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33 </when>
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34 <when value="bam" />
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35 <when value="cram" />
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36 </conditional>
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37 </xml>
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38 </macros>
2
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39 <expand macro="requirements">
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40 <requirement type="package" version="5.1.0">gawk</requirement>
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41 </expand>
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42 <expand macro="stdio"/>
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43 <expand macro="version_command"/>
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44 <command><![CDATA[
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45 @ADDTHREADS@
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46 @ADDMEMORY@
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47 ## prepare reference data
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48 @PREPARE_FASTA_IDX@
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49 @PREPARE_IDX@
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50
8
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51 ## determine the output format flag to pass to samtools view
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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52 ## -c for count mode
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53 ## -b to produce BAM-formatted output
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54 ## -C to produce CRAM-formatted output
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55 ## SAM is the default ouput format
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56 #set $fmtopt = ''
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57 #if str($mode.output_options.reads_report_type) == 'count':
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58 #set $fmtopt = '-c'
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59 #else:
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60 #if str($mode.output_options.output_format.oformat) == 'bam':
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61 #set $fmtopt = '-b'
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62 #elif str($mode.output_options.output_format.oformat) == 'cram':
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63 #set $fmtopt = '-C'
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64 #elif str($mode.output_options.output_format.oformat) == 'input':
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65 #if $input.is_of_type('bam'):
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66 #set $fmtopt = '-b'
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67 #elif $input.is_of_type('cram'):
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68 #set $fmtopt = '-C'
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69 #else:
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70 ## input in SAM format, make sure to keep header if present
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71 #set $fmtopt = '-h'
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72 #end if
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73 #end if
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74 #end if
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75
7
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76 #if str($mode.outtype) == 'header':
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77 ## call samtools view and be done
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78 samtools view
8
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79 -H $fmtopt -o outfile
7
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80 @REF_DATA@
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81 infile
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82 #else:
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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83 ## are filtering and/or subsampling in effect?
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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84 #set $with_filtering = False
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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85 #set $with_subsampling = False
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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86 #if str($mode.outtype) == 'selected_reads':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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87 #set $with_filtering = True
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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88 #if str($mode.subsample_config.subsampling_mode.select_subsample) != 'fraction' or $mode.subsample_config.subsampling_mode.factor > 1:
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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89 #set $with_subsampling = True
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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90 #end if
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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91 #end if
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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92
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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93 ## are we producing one or two outputs?
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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94 #if str($mode.outtype) == 'selected_reads' and str($mode.output_options.reads_report_type) != 'count' and str($mode.output_options.complementary_output) == 'yes':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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95 #set $with_non_selected_reads_output = True
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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96 #else:
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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97 #set $with_non_selected_reads_output = False
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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98 #end if
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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99
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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100 #set $std_filters = ''
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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101 #set $reg_filters = ''
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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102 #if $with_filtering:
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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103 ## build string of all user-configured filter options
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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104 #if str($mode.filter_config.cond_region.select_region) == 'bed':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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105 #set std_filters = $std_filters + " -L '%s'" % str($mode.filter_config.cond_region.bedfile)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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106 #elif str($mode.filter_config.cond_region.select_region) == 'text':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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107 #set $reg_filters = "'%s'" % str($mode.filter_config.cond_region.regions).strip()
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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108 #end if
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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109
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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110 #if $mode.filter_config.cond_rg.select_rg == 'text':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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111 #set $std_filters = $std_filters + " -r '%s'" % str($mode.filter_config.cond_rg.readgr)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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112 #else if $mode.filter_config.cond_rg.select_rg == 'file':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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113 #set $std_filters = $std_filters + " -R '%s'" % str($mode.filter_config.cond_rg.rgfile)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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114 #end if
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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115 #if str($mode.filter_config.quality) != '' and int($mode.filter_config.quality) > 0:
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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116 #set $std_filters = $std_filters + " -q %s" % str($mode.filter_config.quality)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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117 #end if
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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118 #if str($mode.filter_config.library):
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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119 #set $std_filters = $std_filters + " -l '%s'" % str($mode.filter_config.library)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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120 #end if
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121 #if str($mode.filter_config.cigarcons):
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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122 #set $std_filters = $std_filters + " -m %s" % str($mode.filter_config.cigarcons)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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123 #end if
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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124 #set $filter = $mode.filter_config.inclusive_filter
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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125 @FLAGS@
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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126 #set $std_filters = $std_filters + " -f %s" % str($flags)
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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127 #set $filter = $mode.filter_config.exclusive_filter
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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128 @FLAGS@
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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129 #set $std_filters = $std_filters + " -F %s" % str($flags)
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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130 #set $filter = $mode.filter_config.exclusive_filter_all
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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131 @FLAGS@
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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132 #set $std_filters = $std_filters + " -G %s" % str($flags)
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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133 #if $mode.filter_config.tag:
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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134 #set $std_filters = $std_filters + " --tag '%s'" % $mode.filter_config.tag
7
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135 #end if
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136 #if $mode.filter_config.qname_file:
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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137 #set std_filters = $std_filters + " --qname-file '%s'" % $mode.filter_config.qname_file
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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138 #end if
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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139 #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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140
7
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141 #if $with_subsampling:
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142 ## handle seed and fraction calculation for subsampling
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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143 #import random
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144 #if str($mode.subsample_config.subsampling_mode.seed):
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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145 #set $seed = int($mode.subsample_config.subsampling_mode.seed)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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146 #else:
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147 #set $seed = random.randrange(32768)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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148 #end if
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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149
7
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150 #if $mode.subsample_config.subsampling_mode.select_subsample == 'target':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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151 ##this must be done before the main command because we don't know the total # reads until execution time
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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152 #if $input.is_of_type('sam') or $std_filters or $reg_filters:
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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153 ## There is no index or we cannot use it because we are
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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154 ## not dealing with all of the reads in the indexed
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155 ## file. We have to do an extra pass over the input to
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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156 ## count the reads to subsample.
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157 sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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158 #else:
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159 ## We can get the count of reads to subsample using
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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160 ## an inexpensive call to idxstats.
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161 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
7
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162 #end if
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163 #end if
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164 #end if
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165
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166 ## call samtools view
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167 samtools view
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168 -@ \$addthreads
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169 $fmtopt
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170
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171 ## filter options (except regions filter, which is the last parameter)
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172 $std_filters
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173
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174 #if $with_subsampling:
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175 #if str($mode.subsample_config.subsampling_mode.select_subsample) == "target":
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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176 ##this is calculated at execution time before the main samtools command
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177 -s \${sample_fragment}
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178 #else:
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179 #set $fraction = $seed + 1 / float($mode.subsample_config.subsampling_mode.factor)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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180 -s $fraction
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181 #end if
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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182 #end if
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183
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184 ## output options
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185 #if str($mode.output_options.reads_report_type) == 'count':
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186 -o outfile
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187 #else:
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188 ## output options
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189 #if str($mode.output_options.output_format.oformat) == 'sam':
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190 ${mode.output_options.output_format.with_header}
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191 #end if
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192 ${mode.output_options.adv_output.collapsecigar}
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193 #for $s in $mode.output_options.adv_output.readtags:
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194 -x '${s.readtag}'
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195 #end for
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196 #if str($mode.output_options.reads_report_type) == 'retained'
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197 -o outfile
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198 #if $with_non_selected_reads_output:
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199 -U inv_outfile
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200 #end if
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201 #else:
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202 -U outfile
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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203 #if $with_non_selected_reads_output:
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204 -o inv_outfile
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205 #else:
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206 -o /dev/null
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207 #end if
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208 #end if
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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209
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210 ##currently reference based CRAM is disabled (see https://github.com/galaxyproject/tools-iuc/pull/1963)
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211 #if $mode.output_options.output_format.oformat == 'cram':
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212 --output-fmt-option no_ref
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213 #end if
0
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214 #end if
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215
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216 @REF_DATA@
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217
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218 infile
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219
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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220 ## region filter needs to be at the end
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221 $reg_filters
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222
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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223 #if str($mode.output_options.reads_report_type) != 'count':
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224 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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225 ## then sort the output by coordinate,
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226 #if not $input.is_of_type('bam') and str($mode.output_options.output_format.oformat) == 'bam':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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227 && samtools sort
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228 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
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229 -O bam
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230 -o tmpsam
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231 outfile
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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232 && mv tmpsam outfile
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233 #if $with_non_selected_reads_output:
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234 && samtools sort
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235 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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236 -O bam
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237 -o tmpsam
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238 inv_outfile
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239 && mv tmpsam inv_outfile
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240 #end if
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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241 #end if
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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242 #end if
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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243
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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244 ##end of reads and count-specific section
0
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245 #end if
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246 ]]></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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247 <inputs>
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248 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
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249 <param name="input" format="sam,unsorted.bam,cram" type="data" label="SAM/BAM/CRAM data set" />
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250 <conditional name="mode">
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251 <param name="outtype" type="select" label="What would you like to look at?">
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252 <option value="all_reads">All reads in the input dataset</option>
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253 <option value="selected_reads">A filtered/subsampled selection of reads</option>
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254 <option value="header">Just the input header (-H)</option>
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255 </param>
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256 <when value="all_reads">
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257 <conditional name="output_options">
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258 <param name="reads_report_type" type="select" label="What would you like to have reported?">
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259 <option value="retained">The actual reads</option>
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260 <option value="count">The count of reads (-c)</option>
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261 </param>
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262 <when value="retained">
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263 <expand macro="read_output_formatting" />
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264 <expand macro="output_format_selector">
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265 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True"
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266 label="Include SAM header in the output?" />
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267 </expand>
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268 </when>
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269 <when value="count" />
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270 </conditional>
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271 </when>
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272 <when value="selected_reads">
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273 <section name="filter_config" title="Configure filters" expanded="false">
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274 <conditional name="cond_region">
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275 <param name="select_region" type="select" label="Filter by regions">
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276 <option value="no" selected="True">No</option>
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277 <option value="text">Manualy specify regions</option>
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278 <option value="bed">Regions from BED file</option>
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279 </param>
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280 <when value="no"/>
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281 <when value="text">
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282 <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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283 </when>
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284 <when value="bed">
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285 <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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286 </when>
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287 </conditional>
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288 <conditional name="cond_rg">
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289 <param name="select_rg" type="select" label="Filter by readgroup">
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290 <option value="no" selected="True">No</option>
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291 <option value="text">Single read group </option>
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292 <option value="file">Read groups from file</option>
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293 </param>
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294 <when value="no"/>
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295 <when value="text">
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296 <param name="readgr" type="text" argument="-r" label="Filter by read group" help="Only output alignments in read group." />
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297 </when>
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298 <when value="file">
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299 <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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300 </when>
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301 </conditional>
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302 <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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303 <param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" />
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304 <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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305 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
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306 <expand macro="flag_options" />
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307 </param>
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308 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
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309 <expand macro="flag_options" />
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310 </param>
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311 <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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312 <expand macro="flag_options" />
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313 </param>
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314 <param argument="--tag" type="text" optional="true" label="Filter by tag" help="Only include reads with tag STR1 and associated value STR2. Write in the format STR1:STR2 (see help for more details)." />
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315 <!-- TODO implement -D -->
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316 <param argument="--qname-file" format="txt" optional="true" type="data" label="Filter by readnames" help="Only output alignments with readnames that are listed in this file." />
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317 </section>
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318 <section name="subsample_config" title="Configure subsampling" expanded="false">
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319 <conditional name="subsampling_mode">
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320 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment">
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321 <option value="fraction">Specify a downsampling factor</option>
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322 <option value="target">Specify a target # of reads</option>
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323 </param>
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324 <when value="fraction">
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325 <param name="factor" type="float" optional="False" value="1" min="1" label="Downsampling factor" help="The factor by which to downsample the input reads. A fraction of approx. 1/factor of the reads will be kept (default: 1 = no downsampling)." />
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326 <expand macro="seed_input" />
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327 </when>
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328 <when value="target">
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329 <param name="target" type="integer" optional="False" min="1" value="" label="Target # of reads" help="Sets the approx. target number of reads to subsample." />
7
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330 <expand macro="seed_input" />
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331 </when>
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332 </conditional>
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333 </section>
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334 <conditional name="output_options">
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335 <param name="reads_report_type" type="select"
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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336 label="What would you like to have reported?"
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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337 help="Hint: To invert all of the filtering/subsampling logic configured above, choose 'Reads dropped during filtering and subsampling'.">
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338 <option value="retained">All reads retained after filtering and subsampling</option>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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339 <option value="dropped">Reads dropped during filtering and subsampling</option>
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340 <option value="count">The count of retained reads (-c)</option>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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341 </param>
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342 <when value="retained">
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343 <expand macro="read_output_formatting">
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344 <param name="complementary_output" type="boolean" truevalue="yes" falsevalue="no" checked="false"
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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345 label="Produce extra dataset with dropped reads?" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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346 </expand>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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347 <expand macro="output_format_selector">
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348 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True"
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349 label="Include SAM header in the output?" />
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350 </expand>
0
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351 </when>
7
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352 <when value="dropped">
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353 <expand macro="read_output_formatting">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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354 <param name="complementary_output" type="boolean" truevalue="yes" falsevalue="no" checked="false"
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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355 label="Produce extra dataset with retained reads?" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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356 </expand>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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357 <expand macro="output_format_selector">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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358 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True"
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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359 label="Include SAM header in the output?" />
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360 </expand>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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361 </when>
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362 <when value="count" />
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363 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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364 </when>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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365 <when value="header">
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366 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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367 <param name="reads_report_type" type="select" label="What would you like to have reported?">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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368 <option value="">The header in ...</option>
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369 </param>
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370 <when value="">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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371 <expand macro="output_format_selector" />
0
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372 </when>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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373 </conditional>
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374 </when>
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375 </conditional>
10
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376 <expand macro="optional_reference" argument="-t" help="Reference data as fasta(.gz). Required for SAM input without @SQ headers and useful/required for writing CRAM output (see help)."/>
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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377 </inputs>
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378 <outputs>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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379 <!-- TODO do I need an action for dbkey? -->
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380 <data name="outputsam" format_source="input" from_work_dir="outfile" label="${tool.name} on ${on_string}: filtered alignments">
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381 <filter>mode['outtype'] == 'header' or mode['output_options']['reads_report_type'] != 'count'</filter>
0
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382 <change_format>
7
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383 <when input="mode.output_options.output_format.oformat" value="sam" format="sam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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384 <when input="mode.output_options.output_format.oformat" value="bam" format="bam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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385 <when input="mode.output_options.output_format.oformat" value="cram" format="cram" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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386 </change_format>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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387 </data>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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388 <data name="invoutputsam" format_source="input" from_work_dir="inv_outfile" label="${tool.name} on ${on_string}: unfiltered alignments">
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389 <filter>mode['outtype'] == 'selected_reads' and mode['output_options']['reads_report_type'] != 'count' and mode['output_options']['complementary_output']</filter>
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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390 <change_format>
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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391 <when input="mode.output_options.output_format.oformat" value="sam" format="sam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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392 <when input="mode.output_options.output_format.oformat" value="bam" format="bam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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393 <when input="mode.output_options.output_format.oformat" value="cram" format="cram" />
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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394 </change_format>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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395 </data>
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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396 <data name="outputcnt" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts">
7
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397 <filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter>
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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398 </data>
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399 </outputs>
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400 <tests>
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401 <!-- 1) sam to bam (copied from the sam_to_bam tool) -->
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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402 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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403 <param name="input" ftype="sam" value="in_test_1.sam" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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404 <output name="outputsam" ftype="bam" file="test_1.bam" lines_diff="4" />
0
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405 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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406 <!-- 2) -->
0
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407 <test>
10
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parents: 9
diff changeset
408 <param name="input" ftype="sam" dbkey="equCab2" value="in_test_1.sam" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
409 <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
410 <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
411 <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
412 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
413 <output name="outputsam" ftype="bam" file="test_2.bam" lines_diff="4" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
414 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
415 <!-- 3) -->
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
416 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
417 <param name="input" ftype="sam" value="in_test_3.sam" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
418 <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
419 <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
420 <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
421 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
422 <output name="outputsam" ftype="bam" file="test_3.bam" lines_diff="4" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
423 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
424 <!-- 4) cram to bam -->
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
425 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
426 <param name="input" value="in_test_4.cram" ftype="cram" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
427 <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
428 <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
429 <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
430 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
431 <output name="outputsam" file="test_4.bam" ftype="bam" lines_diff="4" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
432 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
433 <!-- 5) within bam operations expected to result in sorting or not -->
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
434 <test >
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
435 <!-- sorted bam should always result in unmodifed output -->
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
436 <param name="input" ftype="bam" value="in_test_5.bam" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
437 <assert_command>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
438 <not_has_text text="samtools sort" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
439 </assert_command>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
440 <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/>
4
fdc58a0cc1d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
iuc
parents: 2
diff changeset
441 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
442 <!-- 6) -->
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
443 <test>
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
444 <!-- sorted bam should always result in unmodifed output -->
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
445 <param name="input" ftype="bam" value="in_test_5.bam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
446 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
447 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
448 <conditional name="output_format">
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
449 <param name="oformat" value="input" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
450 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
451 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
452 </conditional>
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
453 <assert_command>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
454 <not_has_text text="samtools sort" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
455 </assert_command>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
456 <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/>
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
457 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
458 <!-- 7) -->
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
459 <test>
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
460 <!-- qname_sorted.bam should get sorted during "conversion" to bam ... -->
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
461 <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
462 <assert_command>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
463 <has_text text="samtools sort" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
464 </assert_command>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
465 <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
466 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
467 <!-- 8) -->
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
468 <test>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
469 <!-- ... but should be emitted unmodifed when using input format -->
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
470 <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
471 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
472 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
473 <conditional name="output_format">
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
474 <param name="oformat" value="input" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
475 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
476 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
477 </conditional>
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
478 <assert_command>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
479 <not_has_text text="samtools sort" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
480 </assert_command>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
481 <output name="outputsam" ftype="qname_sorted.bam" file="test_8.bam" lines_diff="2"/>
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
482 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
483 <!-- 9) -->
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
484 <test>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
485 <!-- unsorted.bam should get sorted during "conversion" to bam ... -->
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
486 <param name="input" ftype="unsorted.bam" value="in_test_7.bam" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
487 <assert_command>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
488 <has_text text="samtools sort" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
489 </assert_command>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
490 <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
491 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
492 <!-- 10) -->
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
493 <test>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
494 <!-- ... ... but should be emitted unmodifed when using input format -->
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
495 <param name="input" ftype="unsorted.bam" value="in_test_7.bam" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
496 <conditional name="mode">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
497 <conditional name="output_options">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
498 <conditional name="output_format">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
499 <param name="oformat" value="input" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
500 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
501 </conditional>
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
502 </conditional>
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
503 <assert_command>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
504 <not_has_text text="samtools sort" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
505 </assert_command>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
506 <output name="outputsam" ftype="unsorted.bam" file="test_8.bam" lines_diff="2" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
507 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
508 <!-- 11) bam to sam + header options (adapted from bam_to_sam tool)-->
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
509 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
510 <param ftype="bam" name="input" value="in_test_11.bam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
511 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
512 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
513 <conditional name="output_format">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
514 <param name="oformat" value="sam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
515 <param name="with_header" value="true" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
516 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
517 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
518 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
519 <output file="test_11.sam" ftype="sam" name="outputsam" lines_diff="2" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
520 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
521 <!-- 12) -->
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
522 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
523 <param ftype="bam" name="input" value="in_test_11.bam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
524 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
525 <param name="outtype" value="header" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
526 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
527 <conditional name="output_format">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
528 <param name="oformat" value="sam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
529 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
530 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
531 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
532 <output file="test_12.sam" ftype="sam" name="outputsam" lines_diff="2" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
533 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
534 <!-- 13) -->
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
535 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
536 <param ftype="bam" name="input" value="in_test_11.bam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
537 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
538 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
539 <conditional name="output_format">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
540 <param name="oformat" value="sam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
541 <param name="with_header" value="false" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
542 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
543 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
544 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
545 <output file="test_13.sam" ftype="sam" name="outputsam" lines_diff="2" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
546 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
547 <!-- 14) count alignments -->
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
548 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
549 <param name="input" value="in_test_14.bam" ftype="bam" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
550 <conditional name="mode">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
551 <param name="outtype" value="all_reads" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
552 <conditional name="output_options">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
553 <param name="reads_report_type" value="count" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
554 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
555 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
556 <output name="outputcnt" file="test_14.tab" ftype="tabular" lines_diff="2" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
557 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
558 <!-- 15) region filters -->
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
559 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
560 <param name="input" value="in_test_15.sam" ftype="sam" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
561 <conditional name="mode">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
562 <param name="outtype" value="selected_reads" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
563 <section name="filter_config">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
564 <conditional name="cond_region">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
565 <param name="select_region" value="no"/>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
566 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
567 </section>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
568 <conditional name="output_options">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
569 <conditional name="output_format">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
570 <param name="oformat" value="cram" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
571 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
572 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
573 </conditional>
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
574 <conditional name="addref_cond">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
575 <param name="addref_select" value="history" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
576 <param name="ref" value="test.fa" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
577 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
578 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
579 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
580 <!-- 16) -->
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
581 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
582 <param name="input" value="in_test_14.bam" ftype="bam" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
583 <conditional name="mode">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
584 <param name="outtype" value="selected_reads" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
585 <section name="filter_config">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
586 <conditional name="cond_region">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
587 <param name="select_region" value="no"/>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
588 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
589 </section>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
590 <conditional name="output_options">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
591 <conditional name="output_format">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
592 <param name="oformat" value="cram" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
593 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
594 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
595 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
596 <conditional name="addref_cond">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
597 <param name="addref_select" value="history" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
598 <param name="ref" value="test.fa" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
599 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
600 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
601 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
602 <!-- 17) -->
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
603 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
604 <param name="input" value="in_test_17.cram" dbkey="equCab2" ftype="cram" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
605 <conditional name="mode">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
606 <param name="outtype" value="selected_reads" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
607 <section name="filter_config">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
608 <conditional name="cond_region">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
609 <param name="select_region" value="no"/>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
610 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
611 </section>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
612 <conditional name="output_options">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
613 <conditional name="output_format">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
614 <param name="oformat" value="bam" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
615 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
616 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
617 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
618 <conditional name="addref_cond">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
619 <param name="addref_select" value="cached" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
620 <param name="ref" value="equCab2chrM" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
621 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
622 <output name="outputsam" file="test_17.bam" ftype="bam" lines_diff="4" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
623 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
624 <!-- 18) -->
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
625 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
626 <param name="input" value="in_test_14.bam" ftype="bam" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
627 <conditional name="mode">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
628 <param name="outtype" value="selected_reads" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
629 <section name="filter_config">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
630 <conditional name="cond_region">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
631 <param name="select_region" value="text"/>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
632 <param name="regions" value="CHROMOSOME_I" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
633 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
634 </section>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
635 <conditional name="output_options">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
636 <conditional name="output_format">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
637 <param name="oformat" value="cram" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
638 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
639 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
640 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
641 <conditional name="addref_cond">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
642 <param name="addref_select" value="history" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
643 <param name="ref" value="test.fa" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
644 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
645 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
646 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
647 <!-- 19) -->
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
648 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
649 <param name="input" value="test_15.cram" ftype="cram" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
650 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
651 <param name="outtype" value="selected_reads" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
652 <section name="filter_config">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
653 <conditional name="cond_region">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
654 <param name="select_region" value="text"/>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
655 <param name="regions" value="CHROMOSOME_I" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
656 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
657 </section>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
658 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
659 <conditional name="output_format">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
660 <param name="oformat" value="bam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
661 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
662 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
663 </conditional>
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
664 <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
665 <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
666 <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
667 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
668 <output name="outputsam" file="test_19.bam" ftype="bam" lines_diff="4"/>
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
669 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
670 <!-- 20) -->
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
671 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
672 <param name="input" value="test_15.cram" ftype="cram" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
673 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
674 <param name="outtype" value="selected_reads" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
675 <section name="filter_config">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
676 <conditional name="cond_region">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
677 <param name="select_region" value="bed" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
678 <param name="bedfile" value="test.bed" ftype="bed" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
679 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
680 </section>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
681 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
682 <conditional name="output_format">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
683 <param name="oformat" value="bam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
684 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
685 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
686 </conditional>
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
687 <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
688 <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
689 <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
690 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
691 <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
692 </test>
14
5826298f6a73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents: 13
diff changeset
693 <!-- 21) sampling options target < total reads -->
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents: 1
diff changeset
694 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
695 <param name="input" value="in_test_15.sam" ftype="sam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
696 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
697 <param name="outtype" value="selected_reads" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
698 <section name="subsample_config">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
699 <conditional name="subsampling_mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
700 <param name="select_subsample" value="target" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
701 <param name="target" value="2" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
702 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
703 </section>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
704 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
705 <conditional name="output_format">
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
706 <param name="oformat" value="input" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
707 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
708 </conditional>
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents: 1
diff changeset
709 </conditional>
14
5826298f6a73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents: 13
diff changeset
710 <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" />
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents: 1
diff changeset
711 </test>
14
5826298f6a73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents: 13
diff changeset
712 <!-- 22) target > total reads -->
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents: 1
diff changeset
713 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
714 <param name="input" value="in_test_15.sam" ftype="sam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
715 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
716 <param name="outtype" value="selected_reads" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
717 <section name="subsample_config">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
718 <conditional name="subsampling_mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
719 <param name="select_subsample" value="target" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
720 <param name="target" value="20" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
721 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
722 </section>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
723 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
724 <conditional name="output_format">
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
725 <param name="oformat" value="input" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
726 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
727 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
728 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
729 <output name="outputsam" file="test_22.sam" ftype="sam" lines_diff="2"/>
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
730 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
731 <!-- 23) -->
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
732 <test>
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
733 <!-- subsampling SAM input without reads -->
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
734 <param name="input" value="in_test_23.sam" ftype="sam" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
735 <conditional name="mode">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
736 <param name="outtype" value="selected_reads" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
737 <section name="subsample_config">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
738 <conditional name="subsampling_mode">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
739 <param name="select_subsample" value="target" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
740 <param name="target" value="20" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
741 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
742 </section>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
743 <conditional name="output_options">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
744 <conditional name="output_format">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
745 <param name="oformat" value="input" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
746 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
747 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
748 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
749 <output name="outputsam" file="test_23.sam" ftype="sam" lines_diff="2"/>
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
750 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
751 <!-- 24) -->
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
752 <test>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
753 <!-- subsampling BAM input without reads -->
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
754 <param name="input" value="in_test_24.bam" ftype="bam" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
755 <conditional name="mode">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
756 <param name="outtype" value="selected_reads" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
757 <section name="subsample_config">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
758 <conditional name="subsampling_mode">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
759 <param name="select_subsample" value="target" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
760 <param name="target" value="20" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
761 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
762 </section>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
763 <conditional name="output_options">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
764 <conditional name="output_format">
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
765 <param name="oformat" value="input" />
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
766 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
767 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
768 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
769 <output name="outputsam" file="test_24.bam" ftype="bam" lines_diff="2" />
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
770 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
771 <!-- 25) -->
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
772 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
773 <param name="input" value="in_test_15.sam" ftype="sam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
774 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
775 <param name="outtype" value="selected_reads" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
776 <section name="subsample_config">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
777 <conditional name="subsampling_mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
778 <param name="select_subsample" value="target" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
779 <param name="seed" value="7" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
780 <param name="target" value="2" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
781 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
782 </section>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
783 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
784 <conditional name="output_format">
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
785 <param name="oformat" value="input" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
786 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
787 </conditional>
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents: 1
diff changeset
788 </conditional>
14
5826298f6a73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents: 13
diff changeset
789 <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" />
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents: 1
diff changeset
790 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
791 <!-- 26) -->
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents: 1
diff changeset
792 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
793 <param name="input" value="in_test_14.bam" ftype="bam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
794 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
795 <param name="outtype" value="selected_reads" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
796 <section name="subsample_config">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
797 <conditional name="subsampling_mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
798 <param name="select_subsample" value="target" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
799 <param name="seed" value="7" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
800 <param name="target" value="2" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
801 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
802 </section>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
803 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
804 <conditional name="output_format">
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
805 <param name="oformat" value="input" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
806 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
807 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
808 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
809 <output name="outputsam" file="test_26.bam" ftype="bam" lines_diff="2" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
810 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
811 <!-- 27) -->
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
812 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
813 <param name="input" value="in_test_14.bam" ftype="bam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
814 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
815 <param name="outtype" value="selected_reads" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
816 <section name="subsample_config">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
817 <conditional name="subsampling_mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
818 <param name="select_subsample" value="target" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
819 <param name="seed" value="7" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
820 <param name="target" value="20" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
821 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
822 </section>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
823 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
824 <conditional name="output_format">
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
825 <param name="oformat" value="input" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
826 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
827 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
828 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
829 <output name="outputsam" file="test_27.bam" ftype="bam" lines_diff="2"/>
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
830 </test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
831 <!-- 28) -->
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
832 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
833 <param name="input" value="in_test_14.bam" ftype="bam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
834 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
835 <param name="outtype" value="selected_reads" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
836 <section name="subsample_config">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
837 <conditional name="subsampling_mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
838 <param name="select_subsample" value="fraction" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
839 <param name="seed" value="7" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
840 <param name="factor" value="5" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
841 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
842 </section>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
843 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
844 <conditional name="output_format">
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
845 <param name="oformat" value="input" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
846 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
847 </conditional>
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents: 1
diff changeset
848 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
849 <output name="outputsam" file="test_28.bam" ftype="bam" lines_diff="2" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
850 </test>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
851 <!-- 29) -->
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents: 1
diff changeset
852 <test>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
853 <param name="input" value="in_test_14.bam" ftype="bam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
854 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
855 <param name="outtype" value="selected_reads" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
856 <section name="subsample_config">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
857 <conditional name="subsampling_mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
858 <param name="select_subsample" value="fraction" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
859 <param name="seed" value="7" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
860 <param name="factor" value="1.25" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
861 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
862 </section>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
863 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
864 <param name="reads_report_type" value="dropped" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
865 <conditional name="output_format">
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
866 <param name="oformat" value="input" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
867 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
868 </conditional>
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents: 1
diff changeset
869 </conditional>
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
870 <output name="outputsam" file="test_29.bam" ftype="bam" lines_diff="2"/>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
871 </test>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
872 <!-- 30) testing tag filtering -->
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
873 <test>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
874 <param name="input" value="in_test_30.bam" ftype="bam" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
875 <conditional name="mode">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
876 <param name="outtype" value="selected_reads" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
877 <section name="filter_config">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
878 <param name="tag" value="XS:-18" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
879 </section>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
880 <conditional name="output_options">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
881 <conditional name="output_format">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
882 <param name="oformat" value="bam" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
883 </conditional>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
884 </conditional>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
885 </conditional>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
886 <assert_command>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
887 <has_text text="--tag 'XS:-18'"/>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
888 </assert_command>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
889 <output name="outputsam" file="test_30.bam" ftype="bam" lines_diff="2" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
890 </test>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
891 <!-- 31) testing readname filtering -->
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
892 <test>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
893 <param name="input" value="in_test_30.bam" ftype="bam" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
894 <conditional name="mode">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
895 <param name="outtype" value="selected_reads" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
896 <section name="filter_config">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
897 <param name="qname_file" value="readnames.txt" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
898 </section>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
899 <conditional name="output_options">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
900 <conditional name="output_format">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
901 <param name="oformat" value="bam" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
902 </conditional>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
903 </conditional>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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parents: 9
diff changeset
904 </conditional>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
905 <assert_command>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
906 <has_text text="--qname-file"/>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
907 </assert_command>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
908 <output name="outputsam" file="test_31.bam" ftype="bam" lines_diff="2" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
909 </test>
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
910 </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
911 <help>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
912 **What it does**
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
913
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
914 Samtools view can:
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
915
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
916 1. convert between alignment formats (SAM, BAM, CRAM)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
917 2. filter and subsample alignments according to user-specified criteria
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
918 3. count the reads in the input dataset or those retained after filtering
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
919 and subsampling
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
920 4. obtain just the header of the input in any supported format
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
921
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
922 In addition, the tool has (limited) options to modify read records during conversion and/or filtering by:
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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parents:
diff changeset
923
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
924 - stripping them of user-specified tags
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
925 - collapsing backward CIGAR operations if they are specified in their CIGAR
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
926 fields
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
927
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
928 With default settings, the tool generates a BAM dataset with the header and
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
929 reads found in the input dataset (which can be in SAM, BAM, or CRAM format).
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
930
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
931 **Alignment format conversion**
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
932
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
933 By changing the *Output format* it is possible to convert an input dataset to
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
934 another format.
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
935 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".
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
936
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
937 .. class:: infomark
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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parents:
diff changeset
938
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
939 The tool allows you 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 the reference sequence in the CRAM format is detailed.
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
940 CRAM is (primarily) a reference-based compressed format, i.e. only sequence differences between aligned reads and the reference are stored. As a consequence, the reference that was used during read mapping is needed in order to interpret the alignment records (a checksum stored in the CRAM file is used to verify that only the correct reference sequence can be used). This allows for more space-efficient storage than with BAM format, but such a CRAM file is not usable without its reference.
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
941 It is also possible, however, to use CRAM without a reference with the disadvantage that the reference sequence gets stored then explicitely (as in SAM and BAM).
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
942
1
6ade12d94f9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
iuc
parents: 0
diff changeset
943 The Galaxy tool **currently generates only CRAM without reference sequence**.
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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parents:
diff changeset
944
1
6ade12d94f9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
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parents: 0
diff changeset
945 For reference based CRAM input the correct refernce sequence needs to be specified.
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
946
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
947 **Filtering 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
948
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
949 If you ask for *A filtered/subsampled selection of reads*, the tool will allow
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
950 you to specify filter conditions and/or to choose a subsampling strategy, and
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
951 the output will contain one of the following depending on your choice under
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
952 *What would you like to have reported?*:
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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parents:
diff changeset
953
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
954 - All reads retained after filtering and subsampling
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
955 - Reads dropped during filtering and subsampling
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
956
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
957 If instead you want to *split* the input reads based on your criteria and
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
958 obtain *two* datasets, one with the retained and one with the dropped reads, check
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
959 the *Produce extra dataset with dropped/retained reads?* option.
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
960
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
961
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
diff changeset
962 **Filtering by regions**
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
diff changeset
963
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
diff changeset
964 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).
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
diff changeset
965
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
diff changeset
966 Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based.
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
967
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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parents: 6
diff changeset
968 .. class:: Warning mark
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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parents: 6
diff changeset
969
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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parents: 6
diff changeset
970 When multiple regions are given, some alignments may be output multiple times if they overlap more than one of the specified regions.
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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parents:
diff changeset
971
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
diff changeset
972 Examples of region specifications:
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
diff changeset
973
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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parents: 6
diff changeset
974 ``chr1``
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
975 Output all alignments mapped to the reference sequence named 'chr1' (i.e. @SQ SN:chr1).
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
976
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
977 ``chr2:1000000``
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
978 The region on chr2 beginning at base position 1,000,000 and ending at the end of the chromosome.
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
979
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
980 ``chr3:1000-2000``
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
981 The 1001bp region on chr3 beginning at base position 1,000 and ending at base position 2,000 (including both end positions).
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
982
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
983 ``*``
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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diff changeset
984 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.)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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985
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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986 ``.``
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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987 Output all alignments. (Mostly unnecessary as not specifying a region at all has the same effect.)
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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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988
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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989 **Filtering by quality**
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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990
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350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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991 This filters based on the MAPQ column of the SAM format which gives an estimate about the correct placement of the alignment. Note that aligners do not follow a consistent definition.
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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992
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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993 ## Filtering by Tag **
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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994
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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995 This filter allows to select reads based on tool or user specific tags, e.g., XS:i:-18 the alignment score tag of bowtie.
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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996 Thus to filter for a specific value of the tag you need the format STR1:STR2, e.g., XS:-18 to filter reads with an aligment score of -18.
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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997 You can also just write STR1 without the value STR2 hence the filter selects all reads with the tag STR1, e.g., XS.
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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998
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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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999 </help>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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1000 <expand macro="citations"/>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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1001 </tool>