Mercurial > repos > iuc > samtools_view

annotate samtools_view.xml @ 15:6be888be75f9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
author iuc
date Mon, 20 Nov 2023 22:17:43 +0000
parents 5826298f6a73
children 2dce91e11ca7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
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1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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">
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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
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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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
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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 = ''
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101 #set $reg_filters = ''
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102 #if $with_filtering:
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103 ## build string of all user-configured filter options
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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104 #if str($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):
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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
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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
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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)
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148 #end if
0
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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.
15
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157 sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` &&
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 {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` &&
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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 --subsample-seed $seed
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176 #if str($mode.subsample_config.subsampling_mode.select_subsample) == "target":
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177 ##this is calculated at execution time before the main samtools command
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178 --subsample \${sample_fragment}
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179 #else:
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180 #set $fraction = 1 / float($mode.subsample_config.subsampling_mode.factor)
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181 --subsample $fraction
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182 #end if
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183 #end if
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184
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185 ## output options
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186 #if str($mode.output_options.reads_report_type) == 'count':
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187 -o outfile
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188 #else:
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189 ## output options
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190 #if str($mode.output_options.output_format.oformat) == 'sam':
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191 ${mode.output_options.output_format.with_header}
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192 #end if
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193 ${mode.output_options.adv_output.collapsecigar}
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194 #for $s in $mode.output_options.adv_output.readtags:
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195 -x '${s.readtag}'
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196 #end for
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197 #if str($mode.output_options.reads_report_type) == 'retained'
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198 -o outfile
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199 #if $with_non_selected_reads_output:
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200 -U inv_outfile
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201 #end if
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202 #else:
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203 -U outfile
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204 #if $with_non_selected_reads_output:
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205 -o inv_outfile
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206 #else:
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207 -o /dev/null
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208 #end if
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209 #end if
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210
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211 ##currently reference based CRAM is disabled (see https://github.com/galaxyproject/tools-iuc/pull/1963)
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212 #if $mode.output_options.output_format.oformat == 'cram':
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213 --output-fmt-option no_ref
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214 #end if
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215 #end if
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216
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217 @REF_DATA@
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218
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219 infile
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220
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221 ## region filter needs to be at the end
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222 $reg_filters
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223
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224 #if str($mode.output_options.reads_report_type) != 'count':
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225 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
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226 ## then sort the output by coordinate,
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227 #if not $input.is_of_type('bam') and str($mode.output_options.output_format.oformat) == 'bam':
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228 && samtools sort
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229 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
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230 -O bam
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231 -o tmpsam
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232 outfile
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233 && mv tmpsam outfile
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234 #if $with_non_selected_reads_output:
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235 && samtools sort
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236 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
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237 -O bam
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238 -o tmpsam
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239 inv_outfile
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240 && mv tmpsam inv_outfile
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241 #end if
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242 #end if
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243 #end if
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244
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245 ##end of reads and count-specific section
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246 #end if
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247 ]]></command>
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248 <inputs>
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249 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
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250 <param name="input" format="sam,unsorted.bam,cram" type="data" label="SAM/BAM/CRAM data set" />
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251 <conditional name="mode">
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252 <param name="outtype" type="select" label="What would you like to look at?">
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253 <option value="all_reads">All reads in the input dataset</option>
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254 <option value="selected_reads">A filtered/subsampled selection of reads</option>
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255 <option value="header">Just the input header (-H)</option>
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256 </param>
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257 <when value="all_reads">
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258 <conditional name="output_options">
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259 <param name="reads_report_type" type="select" label="What would you like to have reported?">
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260 <option value="retained">The actual reads</option>
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261 <option value="count">The count of reads (-c)</option>
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262 </param>
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263 <when value="retained">
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264 <expand macro="read_output_formatting" />
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265 <expand macro="output_format_selector">
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266 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True"
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267 label="Include SAM header in the output?" />
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268 </expand>
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269 </when>
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270 <when value="count" />
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271 </conditional>
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272 </when>
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273 <when value="selected_reads">
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274 <section name="filter_config" title="Configure filters" expanded="false">
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275 <conditional name="cond_region">
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276 <param name="select_region" type="select" label="Filter by regions">
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277 <option value="no" selected="True">No</option>
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278 <option value="text">Manualy specify regions</option>
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279 <option value="bed">Regions from BED file</option>
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280 </param>
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281 <when value="no"/>
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282 <when value="text">
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283 <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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284 </when>
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285 <when value="bed">
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286 <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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287 </when>
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288 </conditional>
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289 <conditional name="cond_rg">
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290 <param name="select_rg" type="select" label="Filter by readgroup">
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291 <option value="no" selected="True">No</option>
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292 <option value="text">Single read group </option>
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293 <option value="file">Read groups from file</option>
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294 </param>
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295 <when value="no"/>
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296 <when value="text">
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297 <param name="readgr" type="text" argument="-r" label="Filter by read group" help="Only output alignments in read group." />
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298 </when>
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299 <when value="file">
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300 <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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301 </when>
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302 </conditional>
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303 <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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304 <param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" />
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305 <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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306 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
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307 <expand macro="flag_options" />
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308 </param>
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309 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
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310 <expand macro="flag_options" />
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311 </param>
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312 <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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313 <expand macro="flag_options" />
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314 </param>
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315 <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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316 <!-- TODO implement -D -->
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317 <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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318 </section>
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319 <section name="subsample_config" title="Configure subsampling" expanded="false">
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320 <conditional name="subsampling_mode">
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321 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment">
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322 <option value="fraction">Specify a downsampling factor</option>
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323 <option value="target">Specify a target # of reads</option>
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324 </param>
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325 <when value="fraction">
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326 <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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327 <expand macro="seed_input" />
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328 </when>
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329 <when value="target">
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330 <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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331 <expand macro="seed_input" />
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332 </when>
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333 </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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334 </section>
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335 <conditional name="output_options">
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336 <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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337 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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338 help="Hint: To invert all of the filtering/subsampling logic configured above, choose 'Reads dropped during filtering and subsampling'.">
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339 <option value="retained">All reads retained after filtering and subsampling</option>
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340 <option value="dropped">Reads dropped during filtering and subsampling</option>
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341 <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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342 </param>
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343 <when value="retained">
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344 <expand macro="read_output_formatting">
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345 <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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346 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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347 </expand>
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348 <expand macro="output_format_selector">
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349 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True"
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350 label="Include SAM header in the output?" />
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351 </expand>
0
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352 </when>
7
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353 <when value="dropped">
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354 <expand macro="read_output_formatting">
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355 <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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356 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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357 </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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358 <expand macro="output_format_selector">
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359 <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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360 label="Include SAM header in the output?" />
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361 </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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362 </when>
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363 <when value="count" />
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364 </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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365 </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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366 <when value="header">
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367 <conditional name="output_options">
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368 <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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369 <option value="">The header in ...</option>
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370 </param>
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371 <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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372 <expand macro="output_format_selector" />
0
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373 </when>
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374 </conditional>
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375 </when>
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376 </conditional>
10
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377 <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
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378 </inputs>
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379 <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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380 <!-- TODO do I need an action for dbkey? -->
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381 <data name="outputsam" format_source="input" from_work_dir="outfile" label="${tool.name} on ${on_string}: filtered alignments">
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382 <filter>mode['outtype'] == 'header' or mode['output_options']['reads_report_type'] != 'count'</filter>
0
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383 <change_format>
7
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384 <when input="mode.output_options.output_format.oformat" value="sam" format="sam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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385 <when input="mode.output_options.output_format.oformat" value="bam" format="bam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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386 <when input="mode.output_options.output_format.oformat" value="cram" format="cram" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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387 </change_format>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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388 </data>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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389 <data name="invoutputsam" format_source="input" from_work_dir="inv_outfile" label="${tool.name} on ${on_string}: unfiltered alignments">
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390 <filter>mode['outtype'] == 'selected_reads' and mode['output_options']['reads_report_type'] != 'count' and mode['output_options']['complementary_output']</filter>
0
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391 <change_format>
7
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392 <when input="mode.output_options.output_format.oformat" value="sam" format="sam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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393 <when input="mode.output_options.output_format.oformat" value="bam" format="bam" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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394 <when input="mode.output_options.output_format.oformat" value="cram" format="cram" />
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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395 </change_format>
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396 </data>
8
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397 <data name="outputcnt" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts">
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398 <filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter>
0
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399 </data>
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400 </outputs>
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401 <tests>
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402 <!-- 1) sam to bam (copied from the sam_to_bam tool) -->
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403 <test expect_num_outputs="1">
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404 <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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405 <output name="outputsam" ftype="bam" file="test_1.bam" lines_diff="4" />
0
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406 </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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407 <!-- 2) -->
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408 <test expect_num_outputs="1">
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
409 <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
410 <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
411 <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
412 <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
413 </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
414 <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
415 </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
416 <!-- 3) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
417 <test expect_num_outputs="1">
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
418 <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
419 <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
420 <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
421 <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
422 </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
423 <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
424 </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
425 <!-- 4) cram to bam -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
426 <test expect_num_outputs="1">
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
427 <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
428 <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
429 <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
430 <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
431 </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
432 <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
433 </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
434 <!-- 5) within bam operations expected to result in sorting or not -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
435 <test expect_num_outputs="1">
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
436 <!-- 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
437 <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
438 <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
439 <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
440 </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
441 <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
442 </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
443 <!-- 6) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
444 <test expect_num_outputs="1">
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
445 <!-- 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
446 <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
447 <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
448 <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
449 <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
450 <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
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>
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
453 </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
454 <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
455 <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
456 </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
457 <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
458 </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
459 <!-- 7) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
460 <test expect_num_outputs="1">
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
461 <!-- 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
462 <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
463 <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
464 <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
465 </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
466 <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
467 </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
468 <!-- 8) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
469 <test expect_num_outputs="1">
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
470 <!-- ... 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
471 <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
472 <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
473 <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
474 <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
475 <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
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>
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
478 </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
479 <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
480 <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
481 </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
482 <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
483 </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
484 <!-- 9) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
485 <test expect_num_outputs="1">
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
486 <!-- 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
487 <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
488 <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
489 <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
490 </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
491 <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
492 </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
493 <!-- 10) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
494 <test expect_num_outputs="1">
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
495 <!-- ... ... 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
496 <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
497 <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
498 <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
499 <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
500 <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
501 </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
502 </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
503 </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
504 <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
505 <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
506 </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
507 <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
508 </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
509 <!-- 11) bam to sam + header options (adapted from bam_to_sam tool)-->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
510 <test expect_num_outputs="1">
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
511 <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
512 <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
513 <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
514 <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
515 <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
516 <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
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>
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
519 </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
520 <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
521 </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
522 <!-- 12) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
523 <test expect_num_outputs="1">
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
524 <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
525 <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
526 <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
527 <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
528 <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
529 <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
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>
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
532 </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
533 <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
534 </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
535 <!-- 13) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
536 <test expect_num_outputs="1">
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
537 <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
538 <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
539 <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
540 <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
541 <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
542 <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
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>
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
545 </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
546 <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
547 </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
548 <!-- 14) count alignments -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
549 <test expect_num_outputs="1">
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
550 <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
551 <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
552 <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
553 <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
554 <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
555 </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
556 </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
557 <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
558 </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
559 <!-- 15) region filters -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
560 <test expect_num_outputs="1">
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
561 <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
562 <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
563 <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
564 <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
565 <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
566 <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
567 </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
568 </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
569 <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
570 <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
571 <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
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>
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
574 </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
575 <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
576 <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
577 <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
578 </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
579 <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
580 </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
581 <!-- 16) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
582 <test expect_num_outputs="1">
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
583 <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
584 <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
585 <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
586 <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
587 <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
588 <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
589 </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
590 </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
591 <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
592 <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
593 <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
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>
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 <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
598 <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
599 <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
600 </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
601 <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
602 </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
603 <!-- 17) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
604 <test expect_num_outputs="1">
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
605 <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
606 <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
607 <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
608 <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
609 <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
610 <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
611 </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
612 </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
613 <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
614 <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
615 <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
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>
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 <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
620 <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
621 <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
622 </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
623 <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
624 </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
625 <!-- 18) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
626 <test expect_num_outputs="1">
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
627 <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
628 <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
629 <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
630 <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
631 <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
632 <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
633 <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
634 </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
635 </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
636 <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
637 <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
638 <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
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>
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 <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
643 <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
644 <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
645 </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
646 <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
647 </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
648 <!-- 19) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
649 <test expect_num_outputs="1">
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
650 <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
651 <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
652 <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
653 <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
654 <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
655 <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
656 <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
657 </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
658 </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
659 <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
660 <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
661 <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
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>
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
664 </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
665 <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
666 <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
667 <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
668 </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
669 <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
670 </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
671 <!-- 20) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
672 <test expect_num_outputs="1">
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
673 <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
674 <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
675 <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
676 <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
677 <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
678 <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
679 <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
680 </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
681 </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
682 <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
683 <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
684 <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
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>
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
687 </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
688 <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
689 <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
690 <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
691 </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
692 <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
693 </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
694 <!-- 21) sampling options target < total reads -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
695 <test expect_num_outputs="1">
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
696 <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
697 <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
698 <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
699 <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
700 <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
701 <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
702 <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
703 </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
704 </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
705 <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
706 <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
707 <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
708 </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
709 </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
710 </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
711 <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
712 </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
713 <!-- 22) target > total reads -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
714 <test expect_num_outputs="1">
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
715 <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
716 <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
717 <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
718 <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
719 <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
720 <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
721 <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
722 </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
723 </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
724 <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
725 <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
726 <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
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>
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
729 </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
730 <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
731 </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
732 <!-- 23) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
733 <test expect_num_outputs="1">
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
734 <!-- 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
735 <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
736 <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
737 <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
738 <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
739 <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
740 <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
741 <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
742 </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
743 </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
744 <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
745 <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
746 <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
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>
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
749 </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
750 <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
751 </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
752 <!-- 24) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
753 <test expect_num_outputs="1">
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
754 <!-- 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
755 <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
756 <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
757 <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
758 <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
759 <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
760 <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
761 <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
762 </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
763 </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
764 <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
765 <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
766 <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
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>
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
769 </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
770 <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
771 </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
772 <!-- 25) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
773 <test expect_num_outputs="1">
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
774 <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
775 <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
776 <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
777 <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
778 <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
779 <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
780 <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
781 <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
782 </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
783 </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
784 <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
785 <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
786 <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
787 </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
788 </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
789 </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
790 <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
791 </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
792 <!-- 26) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
793 <test expect_num_outputs="1">
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
794 <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
795 <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
796 <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
797 <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
798 <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
799 <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
800 <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
801 <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
802 </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
803 </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
804 <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
805 <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
806 <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
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>
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
809 </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
810 <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
811 </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
812 <!-- 27) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
813 <test expect_num_outputs="1">
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
814 <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
815 <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
816 <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
817 <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
818 <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
819 <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
820 <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
821 <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
822 </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
823 </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
824 <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
825 <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
826 <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
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>
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
829 </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
830 <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
831 </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
832 <!-- 28) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
833 <test expect_num_outputs="1">
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
834 <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
835 <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
836 <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
837 <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
838 <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
839 <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
840 <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
841 <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
842 </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
843 </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
844 <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
845 <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
846 <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
847 </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
848 </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
849 </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
850 <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
851 </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
852 <!-- 29) -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
853 <test expect_num_outputs="1">
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
854 <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
855 <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
856 <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
857 <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
858 <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
859 <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
860 <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
861 <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
862 </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
863 </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
864 <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
865 <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
866 <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
867 <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
868 </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
869 </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
870 </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
871 <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
872 </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
873 <!-- 30) testing tag filtering -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
874 <test expect_num_outputs="1">
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
875 <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
876 <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
877 <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
878 <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
879 <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
880 </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
881 <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
882 <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
883 <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
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 </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
887 <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
888 <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
889 </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
890 <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
891 </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
892 <!-- 31) testing readname filtering -->
15
6be888be75f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 14
diff changeset
893 <test expect_num_outputs="1">
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
894 <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
895 <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
896 <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
897 <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
898 <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
899 </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
900 <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
901 <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
902 <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"
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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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diff changeset
904 </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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diff changeset
905 </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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diff changeset
906 <assert_command>
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
907 <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
908 </assert_command>
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
909 <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
910 </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
911 </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
912 <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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parents:
diff changeset
913 **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
914
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
915 Samtools view can:
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
916
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
917 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"
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parents: 6
diff changeset
918 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
919 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
920 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
921 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"
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diff changeset
922
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
923 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
924
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
925 - 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"
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parents: 6
diff changeset
926 - 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
927 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
928
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 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
930 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
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parents:
diff changeset
931
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
932 **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
933
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
934 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
935 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
936 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
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parents:
diff changeset
937
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
938 .. 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
939
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
940 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
941 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
942 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
943
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
944 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
945
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
946 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
947
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 **Filtering alignments**
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
949
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
950 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
951 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
952 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
953 *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
954
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
955 - 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"
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parents: 6
diff changeset
956 - 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"
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parents: 6
diff changeset
957
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 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
959 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
960 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
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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
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 **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
964
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 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
966
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
967 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
968
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
969 .. 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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diff changeset
970
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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diff changeset
971 When multiple regions are given, some alignments may be output multiple times if they overlap more than one of the specified regions.
0
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parents:
diff changeset
972
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 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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diff changeset
974
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
975 ``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 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"
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parents: 6
diff changeset
977
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 ``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
979 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
980
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 ``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
982 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
983
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
984 ``*``
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 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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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 ``.``
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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988 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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989
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 **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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991
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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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992 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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993
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 ## 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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995
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 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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997 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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998 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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999
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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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1000 </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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1001 <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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1002 </tool>