Mercurial > repos > iuc > samtools_view

annotate samtools_view.xml @ 17:32dc5f781059 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:27:39 +0000
parents 2dce91e11ca7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy3" 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"
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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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02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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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[
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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45 @ADDTHREADS@
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46 @ADDMEMORY@
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47 ## prepare reference data
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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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
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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53 ## -b to produce BAM-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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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 = ''
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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101 #set $reg_filters = ''
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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102 #if $with_filtering:
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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103 ## build string of all user-configured filter options
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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104 #if str($mode.filter_config.cond_region.select_region) == 'bed':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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105 #set std_filters = $std_filters + " -L '%s'" % str($mode.filter_config.cond_region.bedfile)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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106 #elif str($mode.filter_config.cond_region.select_region) == 'text':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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107 #set $reg_filters = "'%s'" % str($mode.filter_config.cond_region.regions).strip()
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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108 #end if
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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109
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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110 #if $mode.filter_config.cond_rg.select_rg == 'text':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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111 #set $std_filters = $std_filters + " -r '%s'" % str($mode.filter_config.cond_rg.readgr)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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112 #else if $mode.filter_config.cond_rg.select_rg == 'file':
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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113 #set $std_filters = $std_filters + " -R '%s'" % str($mode.filter_config.cond_rg.rgfile)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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114 #end if
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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115 #if str($mode.filter_config.quality) != '' and int($mode.filter_config.quality) > 0:
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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116 #set $std_filters = $std_filters + " -q %s" % str($mode.filter_config.quality)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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117 #end if
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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118 #if str($mode.filter_config.library):
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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119 #set $std_filters = $std_filters + " -l '%s'" % str($mode.filter_config.library)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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120 #end if
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121 #if str($mode.filter_config.cigarcons):
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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122 #set $std_filters = $std_filters + " -m %s" % str($mode.filter_config.cigarcons)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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123 #end if
10
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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124 #set $filter = $mode.filter_config.inclusive_filter
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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125 @FLAGS@
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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126 #set $std_filters = $std_filters + " -f %s" % str($flags)
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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127 #set $filter = $mode.filter_config.exclusive_filter
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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128 @FLAGS@
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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129 #set $std_filters = $std_filters + " -F %s" % str($flags)
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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130 #set $filter = $mode.filter_config.exclusive_filter_all
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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131 @FLAGS@
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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132 #set $std_filters = $std_filters + " -G %s" % str($flags)
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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133 #if $mode.filter_config.tag:
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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134 #set $std_filters = $std_filters + " --tag '%s'" % $mode.filter_config.tag
7
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135 #end if
10
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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'" % $mode.filter_config.qname_file
2
02afb5ea2fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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138 #end if
16
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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139 #if str($cond_expr.select_expr) == "yes":
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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140 #set std_filters = $std_filters + " -e '%s'" % $cond_expr.expression
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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141 #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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142 #end if
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143
7
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144 #if $with_subsampling:
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145 ## handle seed and fraction calculation for subsampling
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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146 #import random
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147 #if str($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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148 #set $seed = int($mode.subsample_config.subsampling_mode.seed)
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149 #else:
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150 #set $seed = random.randrange(32768)
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151 #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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152
7
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153 #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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154 ##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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155 #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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156 ## 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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157 ## not dealing with all of the reads in the indexed
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 ## 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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159 ## count the reads to subsample.
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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160 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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161 #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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162 ## We can get the count of reads to subsample using
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163 ## an inexpensive call to idxstats.
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164 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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165 #end if
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166 #end if
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167 #end if
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168
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169 ## call samtools view
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170 samtools view
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171 -@ \$addthreads
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172 $fmtopt
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173
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174 ## filter options (except regions filter, which is the last parameter)
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175 $std_filters
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176 #if $with_subsampling:
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177 --subsample-seed $seed
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178 #if str($mode.subsample_config.subsampling_mode.select_subsample) == "target":
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179 ##this is calculated at execution time before the main samtools command
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180 --subsample \${sample_fragment}
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181 #else:
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182 #set $fraction = 1 / float($mode.subsample_config.subsampling_mode.factor)
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183 --subsample $fraction
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184 #end if
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185 #end if
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186
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187 ## output options
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188 #if str($mode.output_options.reads_report_type) == 'count':
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189 -o outfile
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190 #else:
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191 ## output options
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192 #if str($mode.output_options.output_format.oformat) == 'sam':
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193 ${mode.output_options.output_format.with_header}
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194 #end if
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195 ${mode.output_options.adv_output.collapsecigar}
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196 #for $s in $mode.output_options.adv_output.readtags:
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197 -x '${s.readtag}'
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198 #end for
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199 #if str($mode.output_options.reads_report_type) == 'retained'
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200 -o outfile
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201 #if $with_non_selected_reads_output:
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202 -U inv_outfile
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203 #end if
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204 #else:
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205 -U outfile
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206 #if $with_non_selected_reads_output:
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207 -o inv_outfile
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208 #else:
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209 -o /dev/null
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210 #end if
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211 #end if
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212
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213 ##currently reference based CRAM is disabled (see https://github.com/galaxyproject/tools-iuc/pull/1963)
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214 #if $mode.output_options.output_format.oformat == 'cram':
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215 --output-fmt-option no_ref
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216 #end if
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217 #end if
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218
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219 @REF_DATA@
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220
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221 infile
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222
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223 ## region filter needs to be at the end
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224 $reg_filters
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225
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226 #if str($mode.output_options.reads_report_type) != 'count':
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227 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
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228 ## then sort the output by coordinate,
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229 #if not $input.is_of_type('bam') and str($mode.output_options.output_format.oformat) == 'bam':
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230 && samtools sort
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231 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
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232 -O bam
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233 -o tmpsam
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234 outfile
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235 && mv tmpsam outfile
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236 #if $with_non_selected_reads_output:
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237 && samtools sort
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238 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
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239 -O bam
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240 -o tmpsam
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241 inv_outfile
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242 && mv tmpsam inv_outfile
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243 #end if
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244 #end if
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245 #end if
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246
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247 ##end of reads and count-specific section
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248 #end if
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249 ]]></command>
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250 <inputs>
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251 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
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252 <param name="input" format="sam,unsorted.bam,cram" type="data" label="SAM/BAM/CRAM data set" />
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253 <conditional name="mode">
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254 <param name="outtype" type="select" label="What would you like to look at?">
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255 <option value="all_reads">All reads in the input dataset</option>
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256 <option value="selected_reads">A filtered/subsampled selection of reads</option>
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257 <option value="header">Just the input header (-H)</option>
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258 </param>
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259 <when value="all_reads">
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260 <conditional name="output_options">
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261 <param name="reads_report_type" type="select" label="What would you like to have reported?">
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262 <option value="retained">The actual reads</option>
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263 <option value="count">The count of reads (-c)</option>
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264 </param>
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265 <when value="retained">
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266 <expand macro="read_output_formatting" />
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267 <expand macro="output_format_selector">
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268 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True"
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269 label="Include SAM header in the output?" />
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270 </expand>
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271 </when>
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272 <when value="count" />
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273 </conditional>
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274 </when>
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275 <when value="selected_reads">
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276 <section name="filter_config" title="Configure filters" expanded="false">
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277 <conditional name="cond_region">
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278 <param name="select_region" type="select" label="Filter by regions">
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279 <option value="no" selected="True">No</option>
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280 <option value="text">Manualy specify regions</option>
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281 <option value="bed">Regions from BED file</option>
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282 </param>
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283 <when value="no"/>
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284 <when value="text">
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285 <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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286 </when>
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287 <when value="bed">
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288 <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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289 </when>
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290 </conditional>
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291 <conditional name="cond_rg">
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292 <param name="select_rg" type="select" label="Filter by readgroup">
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293 <option value="no" selected="True">No</option>
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294 <option value="text">Single read group </option>
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295 <option value="file">Read groups from file</option>
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296 </param>
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297 <when value="no"/>
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298 <when value="text">
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299 <param name="readgr" type="text" argument="-r" label="Filter by read group" help="Only output alignments in read group." />
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300 </when>
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301 <when value="file">
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302 <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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303 </when>
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304 </conditional>
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305 <conditional name="cond_expr">
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306 <param name="select_expr" type="select" label="Filter by expression">
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307 <option value="no" selected="True">No</option>
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308 <option value="yes">Filter using an expression (see manual)</option>
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309 </param>
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310 <when value="no"/>
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311 <when value="yes">
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312 <param name="expression" type="text" argument="-e" label="Filter by expression - for example sclen&gt;0 will filter all soft clipped reads" help="See Samtools manual for Filter expression syntax">
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313 <sanitizer invalid_char="">
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314 <valid initial="string.printable">
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315 <remove value="'"/>
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316 </valid>
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317 </sanitizer>
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318 </param>
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319 </when>
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320 </conditional>
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321 <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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322 <param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" />
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323 <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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324 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
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325 <expand macro="flag_options" />
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326 </param>
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327 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
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328 <expand macro="flag_options" />
0
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329 </param>
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330 <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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331 <expand macro="flag_options" />
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332 </param>
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333 <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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334 <!-- TODO implement -D -->
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335 <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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336 </section>
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337 <section name="subsample_config" title="Configure subsampling" expanded="false">
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338 <conditional name="subsampling_mode">
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339 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment">
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340 <option value="fraction">Specify a downsampling factor</option>
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341 <option value="target">Specify a target # of reads</option>
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342 </param>
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343 <when value="fraction">
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344 <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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345 <expand macro="seed_input" />
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346 </when>
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347 <when value="target">
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348 <param name="target" type="integer" optional="False" min="1" value="" label="Target # of reads" help="Sets the approx. target number of reads to subsample." />
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349 <expand macro="seed_input" />
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350 </when>
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351 </conditional>
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352 </section>
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353 <conditional name="output_options">
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354 <param name="reads_report_type" type="select"
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355 label="What would you like to have reported?"
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356 help="Hint: To invert all of the filtering/subsampling logic configured above, choose 'Reads dropped during filtering and subsampling'.">
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357 <option value="retained">All reads retained after filtering and subsampling</option>
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358 <option value="dropped">Reads dropped during filtering and subsampling</option>
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359 <option value="count">The count of retained reads (-c)</option>
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360 </param>
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361 <when value="retained">
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362 <expand macro="read_output_formatting">
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363 <param name="complementary_output" type="boolean" truevalue="yes" falsevalue="no" checked="false"
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364 label="Produce extra dataset with dropped reads?" />
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365 </expand>
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366 <expand macro="output_format_selector">
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367 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True"
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368 label="Include SAM header in the output?" />
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369 </expand>
0
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370 </when>
7
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371 <when value="dropped">
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372 <expand macro="read_output_formatting">
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373 <param name="complementary_output" type="boolean" truevalue="yes" falsevalue="no" checked="false"
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374 label="Produce extra dataset with retained reads?" />
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375 </expand>
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376 <expand macro="output_format_selector">
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377 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True"
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378 label="Include SAM header in the output?" />
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379 </expand>
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380 </when>
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381 <when value="count" />
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382 </conditional>
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383 </when>
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384 <when value="header">
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385 <conditional name="output_options">
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386 <param name="reads_report_type" type="select" label="What would you like to have reported?">
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387 <option value="">The header in ...</option>
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388 </param>
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389 <when value="">
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390 <expand macro="output_format_selector" />
0
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391 </when>
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392 </conditional>
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393 </when>
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394 </conditional>
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395 <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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396 </inputs>
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397 <outputs>
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398 <!-- TODO do I need an action for dbkey? -->
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399 <data name="outputsam" format_source="input" from_work_dir="outfile" label="${tool.name} on ${on_string}: filtered alignments">
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400 <filter>mode['outtype'] == 'header' or mode['output_options']['reads_report_type'] != 'count'</filter>
0
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401 <change_format>
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402 <when input="mode.output_options.output_format.oformat" value="sam" format="sam" />
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403 <when input="mode.output_options.output_format.oformat" value="bam" format="bam" />
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404 <when input="mode.output_options.output_format.oformat" value="cram" format="cram" />
0
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405 </change_format>
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406 </data>
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407 <data name="invoutputsam" format_source="input" from_work_dir="inv_outfile" label="${tool.name} on ${on_string}: unfiltered alignments">
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408 <filter>mode['outtype'] == 'selected_reads' and mode['output_options']['reads_report_type'] != 'count' and mode['output_options']['complementary_output']</filter>
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
409 <change_format>
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
410 <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"
iuc
parents: 6
diff changeset
411 <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"
iuc
parents: 6
diff changeset
412 <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
iuc
parents:
diff changeset
413 </change_format>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
414 </data>
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
415 <data name="outputcnt" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts">
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
416 <filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter>
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
417 </data>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
418 </outputs>
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 <tests>
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
420 <!-- 1) sam to bam (copied from the sam_to_bam tool) -->
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
421 <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
422 <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"
iuc
parents: 9
diff changeset
423 <output name="outputsam" ftype="bam" file="test_1.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 <!-- 2) -->
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" 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
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="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
430 <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
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" 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
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 <!-- 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
435 <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
436 <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
437 <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
438 <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
439 <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
440 </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
441 <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
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 <!-- 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
444 <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
445 <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
446 <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
447 <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
448 <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
449 </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
450 <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
451 </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
452 <!-- 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
453 <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
454 <!-- 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
455 <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
456 <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
457 <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
458 </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
459 <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
460 </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
461 <!-- 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
462 <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
463 <!-- 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
464 <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
465 <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
466 <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
467 <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
468 <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
469 </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
470 </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
471 </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
472 <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
473 <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
474 </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
475 <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
476 </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
477 <!-- 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
478 <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
479 <!-- 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
480 <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
481 <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
482 <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
483 </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
484 <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
485 </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
486 <!-- 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
487 <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
488 <!-- ... 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
489 <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
490 <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
491 <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
492 <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
493 <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
494 </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
495 </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
496 </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
497 <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
498 <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
499 </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
500 <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
501 </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
502 <!-- 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
503 <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
504 <!-- 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
505 <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
506 <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
507 <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
508 </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
509 <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
510 </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
511 <!-- 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
512 <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
513 <!-- ... ... 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
514 <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
515 <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
516 <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
517 <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
518 <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
519 </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
520 </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
521 </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
522 <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
523 <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
524 </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
525 <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
526 </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
527 <!-- 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
528 <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
529 <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
530 <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
531 <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
532 <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
533 <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
534 <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
535 </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
536 </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
537 </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
538 <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
539 </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
540 <!-- 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
541 <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
542 <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
543 <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
544 <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
545 <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
546 <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
547 <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
548 </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
549 </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
550 </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
551 <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
552 </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
553 <!-- 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
554 <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
555 <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
556 <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
557 <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
558 <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
559 <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
560 <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
561 </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
562 </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
563 </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
564 <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
565 </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
566 <!-- 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
567 <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
568 <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
569 <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
570 <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
571 <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
572 <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
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>
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
575 <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
576 </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
577 <!-- 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
578 <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
579 <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
580 <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
581 <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
582 <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
583 <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
584 <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
585 </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
586 </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
587 <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
588 <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
589 <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
590 </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
591 </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
592 </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
593 <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
594 <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
595 <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
596 </conditional>
16
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
597 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="500" />
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
598 </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
599 <!-- 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
600 <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
601 <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
602 <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
603 <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
604 <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
605 <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
606 <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
607 </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
608 </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
609 <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
610 <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
611 <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
612 </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
613 </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
614 </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
615 <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
616 <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
617 <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
618 </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
619 <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
620 </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
621 <!-- 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
622 <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
623 <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
624 <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
625 <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
626 <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
627 <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
628 <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
629 </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
630 </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
631 <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
632 <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
633 <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
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 </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
636 </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
637 <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
638 <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
639 <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
640 </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
641 <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
642 </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
643 <!-- 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
644 <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
645 <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
646 <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
647 <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
648 <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
649 <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
650 <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
651 <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
652 </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
653 </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
654 <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
655 <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
656 <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
657 </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
658 </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
659 </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
660 <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
661 <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
662 <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
663 </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
664 <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
665 </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
666 <!-- 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
667 <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
668 <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
669 <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
670 <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
671 <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
672 <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
673 <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
674 <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
675 </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
676 </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
677 <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
678 <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
679 <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
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 </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
682 </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
683 <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
684 <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
685 <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
686 </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
687 <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
688 </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
689 <!-- 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
690 <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
691 <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
692 <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
693 <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
694 <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
695 <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
696 <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
697 <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
698 </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
699 </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
700 <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
701 <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
702 <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
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 </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
705 </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
706 <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
707 <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
708 <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
709 </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
710 <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
711 </test>
14
5826298f6a73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents: 13
diff changeset
712 <!-- 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
713 <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
714 <param name="input" value="in_test_15.sam" ftype="sam" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
715 <conditional name="mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
716 <param name="outtype" value="selected_reads" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
717 <section name="subsample_config">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
718 <conditional name="subsampling_mode">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
719 <param name="select_subsample" value="target" />
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
720 <param name="target" value="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
721 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
722 </section>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
723 <conditional name="output_options">
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
724 <conditional name="output_format">
8
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
725 <param name="oformat" value="input" />
7
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
726 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
727 </conditional>
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
728 </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
729 <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
730 </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
731 <!-- 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
732 <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
733 <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
734 <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
735 <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
736 <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
737 <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
738 <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
739 <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
740 </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
741 </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
742 <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
743 <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
744 <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
745 </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
746 </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
747 </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
748 <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
749 </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
750 <!-- 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
751 <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
752 <!-- 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
753 <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
754 <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
755 <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
756 <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
757 <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
758 <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
759 <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
760 </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
761 </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
762 <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
763 <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
764 <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
765 </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
766 </conditional>
bf328cec6a42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents: 7
diff changeset
767 </conditional>
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
768 <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
769 </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
770 <!-- 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
771 <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
772 <!-- 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
773 <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
774 <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
775 <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
776 <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
777 <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
778 <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
779 <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
780 </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
781 </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
782 <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
783 <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
784 <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
785 </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
786 </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
787 </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
788 <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
789 </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
790 <!-- 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
791 <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
792 <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
793 <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
794 <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
795 <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
796 <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
797 <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
798 <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
799 <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
800 </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
801 </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
802 <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
803 <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
804 <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
805 </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
806 </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
807 </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
808 <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
809 </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
810 <!-- 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
811 <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
812 <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
813 <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
814 <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
815 <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
816 <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
817 <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
818 <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
819 <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
820 </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
821 </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
822 <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
823 <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
824 <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
825 </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
826 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
827 </conditional>
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
828 <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
829 </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
830 <!-- 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
831 <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
832 <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
833 <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
834 <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
835 <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
836 <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
837 <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
838 <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
839 <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
840 </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
841 </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
842 <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
843 <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
844 <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
845 </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
846 </conditional>
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
847 </conditional>
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
848 <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
849 </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
850 <!-- 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
851 <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
852 <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
853 <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
854 <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
855 <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
856 <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
857 <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
858 <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
859 <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
860 </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
861 </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
862 <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
863 <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
864 <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
865 </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
866 </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
867 </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
868 <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
869 </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
870 <!-- 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
871 <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
872 <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
873 <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
874 <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
875 <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
876 <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
877 <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
878 <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
879 <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
880 </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
881 </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
882 <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
883 <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
884 <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
885 <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
886 </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
887 </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
888 </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
889 <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
890 </test>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
891 <!-- 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
892 <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
893 <param name="input" value="in_test_30.bam" ftype="bam" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
894 <conditional name="mode">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
895 <param name="outtype" value="selected_reads" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
896 <section name="filter_config">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
897 <param name="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
898 </section>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
899 <conditional name="output_options">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
900 <conditional name="output_format">
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
901 <param name="oformat" value="bam" />
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
902 </conditional>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
903 </conditional>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
904 </conditional>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
905 <assert_command>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
906 <has_text text="--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
907 </assert_command>
350bbc5c2ffd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 9
diff changeset
908 <output name="outputsam" file="test_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
909 </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
910 <!-- 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
911 <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
912 <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
913 <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
914 <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
915 <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
916 <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
917 </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
918 <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
919 <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
920 <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
921 </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
922 </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
923 </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
924 <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
925 <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
926 </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
927 <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
928 </test>
16
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
929 <!-- 32) testing expression filters -->
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
930 <test expect_num_outputs="1">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
931 <param name="input" value="in_test_30.bam" ftype="bam"/>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
932 <conditional name="mode">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
933 <param name="outtype" value="selected_reads" />
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
934 <section name="filter_config">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
935 <conditional name="cond_expr">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
936 <param name="select_expr" value="yes"/>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
937 <param name="expression" value="sclen>0"/>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
938 </conditional>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
939 </section>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
940 <conditional name="output_options">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
941 <conditional name="output_format">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
942 <param name="oformat" value="bam" />
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
943 </conditional>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
944 </conditional>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
945 </conditional>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
946 <assert_command>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
947 <has_text text="-e 'sclen>0'"/>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
948 </assert_command>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
949 <output name="outputsam" file="test_32.bam" ftype="bam" lines_diff="2" />
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
950 </test>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
951 <!-- 33) testing expression filters -->
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
952 <test expect_num_outputs="1">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
953 <param name="input" value="in_test_30.bam" ftype="bam"/>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
954 <conditional name="mode">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
955 <param name="outtype" value="selected_reads" />
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
956 <section name="filter_config">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
957 <conditional name="cond_expr">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
958 <param name="select_expr" value="yes"/>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
959 <param name="expression" value='rname!="chr13"'/>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
960 </conditional>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
961 </section>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
962 <conditional name="output_options">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
963 <conditional name="output_format">
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
964 <param name="oformat" value="bam" />
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
965 </conditional>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
966 </conditional>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
967 </conditional>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
968 <assert_command>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
969 <has_text text="-e 'rname!="/>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
970 </assert_command>
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
971 <output name="outputsam" file="test_33.bam" ftype="bam" lines_diff="2" />
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents: 15
diff changeset
972 </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
973 </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
974 <help>
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
975 **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
976
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
977 Samtools view can:
0
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff changeset
978
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
979 1. convert between alignment formats (SAM, BAM, CRAM)
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents: 6
diff changeset
980 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
981 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
982 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
983 4. obtain just the header of the input in any supported format
10
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984
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diff changeset
985 In addition, the tool has (limited) options to modify read records during conversion and/or filtering by:
0
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986
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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987 - 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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988 - 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"
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diff changeset
989 fields
b01db2684fa5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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990
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
991 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"
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diff changeset
992 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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993
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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994 **Alignment format conversion**
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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995
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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diff changeset
996 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"
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diff changeset
997 another 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
998 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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999
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
1000 .. 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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1001
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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diff changeset
1002 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"
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diff changeset
1003 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"
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diff changeset
1004 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
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1005
1
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diff changeset
1006 The Galaxy tool **currently generates only CRAM without reference sequence**.
0
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1007
1
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1008 For reference based CRAM input the correct refernce sequence needs to be specified.
0
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diff changeset
1009
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
1010 **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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1011
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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diff changeset
1012 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"
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diff changeset
1013 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"
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diff changeset
1014 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"
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diff changeset
1015 *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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diff changeset
1016
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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diff changeset
1017 - 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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diff changeset
1018 - 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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diff changeset
1019
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
1020 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"
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parents: 6
diff changeset
1021 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"
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diff changeset
1022 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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diff changeset
1023
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
1024
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
1025 **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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diff changeset
1026
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
1027 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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diff changeset
1028
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
1029 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
1030
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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diff changeset
1031 .. 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
1032
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
1033 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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diff changeset
1034
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
1035 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
1036
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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diff changeset
1037 ``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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diff changeset
1038 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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diff changeset
1039
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
1040 ``chr2:1000000``
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
1041 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"
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diff changeset
1042
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
1043 ``chr3:1000-2000``
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
1044 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"
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diff changeset
1045
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
1046 ``*``
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
1047 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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diff changeset
1048
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
1049 ``.``
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
1050 Output all alignments. (Mostly unnecessary as not specifying a region at all has the same effect.)
0
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diff changeset
1051
00d1f08bdcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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1052 **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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diff changeset
1053
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
1054 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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diff changeset
1055
16
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diff changeset
1056 **Filtering by Tag**
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
1057
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
1058 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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diff changeset
1059 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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diff changeset
1060 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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diff changeset
1061
16
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diff changeset
1062 **Filtering by Expression**
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diff changeset
1063
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diff changeset
1064
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1065 Filter expressions are used as an on-the-fly checking of incoming SAM, BAM or CRAM records, discarding records that do not match the specified expression.
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1066
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1067 The language used is primarily C style, but with a few differences in the precedence rules for bit operators and the inclusion of regular expression
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1068 matching.
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1069
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1070 The operator precedence, from strongest binding to weakest, is
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diff changeset
1071
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1072 ::
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diff changeset
1073
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1074 Grouping (, ) E.g. &quot;(1+2)&#42;3&quot;
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1075 Values: literals, vars Numbers, strings and variables
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1076 Unary ops: +, -, !, ~ E.g. -10 +10, !10 (not), ~5 (bit not)
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1077 Math ops: \*, /, % Multiply, division and (integer) modulo
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1078 Math ops: +, - Addition / subtraction
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1079 Bit-wise: &amp; Integer AND
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1080 Bit-wise ^ Integer XOR
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1081 Bit-wise | Integer OR
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1082 Conditionals: &gt;, &gt;=, &lt;, &lt;=
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1083 Equality: \=\=, !=, =~, !~ =~ and !~ match regular expressions
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1084 Boolean: &amp;&amp;, || Logical AND / OR
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1085
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diff changeset
1086
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1087 Expressions are computed using floating point mathematics, so &quot;10 / 4&quot; evaluates to 2.5 rather than 2. They may be written as integers in decimal or
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1088 &quot;0x&quot; plus hexadecimal, and floating point with or without exponents.However operations that require integers first do an implicit type conversion, so
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diff changeset
1089 &quot;7.9 % 5&quot; is 2 and &quot;7.9 &amp; 4.1&quot; is equivalent to &quot;7 &amp; 4&quot;, which is 4. Strings are always specified using double quotes. To get a double quote in a
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1090 string, use backslash. Similarly a double backslash is used to get a literal backslash. For example ab\&quot;c\\d is the string ab&quot;c\d.
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1091
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1092 Comparison operators are evaluated as a match being 1 and a mismatch being 0, thus &quot;(2 &gt; 1) + (3 &lt; 5)&quot; evaluates as 2. All comparisons involving undefined (null) values are deemed to be false.
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1093
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1094 The variables are where the file format specifics are accessed from the expression. The variables correspond to SAM fields, for example to find paired
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diff changeset
1095 alignments with high mapping quality and a very large insert size, we may use the expression &quot;mapq &gt;= 30 &amp;&amp; (tlen &gt;= 100000 || tlen &lt;= -100000)&quot;. Valid
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1096 variable names and their data types are:
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1097
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1098 ::
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diff changeset
1099
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1100 endpos int Alignment end position (1-based)
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1101 flag int Combined FLAG field
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1102 flag.paired int Single bit, 0 or 1
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1103 flag.proper_pair int Single bit, 0 or 2
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1104 flag.unmap int Single bit, 0 or 4
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1105 flag.munmap int Single bit, 0 or 8
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1106 flag.reverse int Single bit, 0 or 16
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1107 flag.mreverse int Single bit, 0 or 32
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1108 flag.read1 int Single bit, 0 or 64
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1109 flag.read2 int Single bit, 0 or 128
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1110 flag.secondary int Single bit, 0 or 256
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1111 flag.qcfail int Single bit, 0 or 512
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1112 flag.dup int Single bit, 0 or 1024
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1113 flag.supplementary int Single bit, 0 or 2048
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1114 hclen int Number of hard-clipped bases
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1115 library string Library (LB header via RG)
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1116 mapq int Mapping quality
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1117 mpos int Synonym for pnext
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1118 mrefid int Mate reference number (0 based)
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1119 mrname string Synonym for rnext
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1120 ncigar int Number of cigar operations
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1121 pnext int Mate's alignment position (1-based)
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1122 pos int Alignment position (1-based)
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1123 qlen int Alignment length: no. query bases
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1124 qname string Query name
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1125 qual string Quality values (raw, 0 based)
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1126 refid int Integer reference number (0 based)
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1127 rlen int Alignment length: no. reference bases
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1128 rname string Reference name
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1129 rnext string Mate's reference name
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1130 sclen int Number of soft-clipped bases
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1131 seq string Sequence
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1132 tlen int Template length (insert size)
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1133 [XX] int / string XX tag value
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1134
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1135
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1136 Flags are returned either as the whole flag value or by checking for a single bit. Hence the filter expression flag.dup is equivalent to flag &amp; 1024.
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1137
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1138 &quot;qlen&quot; and &quot;rlen&quot; are measured using the CIGAR string to count the number of query (sequence) and reference bases consumed. Note &quot;qlen&quot; may not exactly
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1139 match the length of the &quot;seq&quot; field if the sequence is &quot;&#42;&quot;.
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1140
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1141 &quot;sclen&quot; and &quot;hclen&quot; are the number of soft and hard-clipped bases respectively. The formula &quot;qlen-sclen&quot; gives the number of sequence bases used in the
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1142 alignment, distinguishing between global alignment and local alignment length.
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1143
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1144 &quot;endpos&quot; is the (1-based inclusive) position of the rightmost mapped base of the read, as measured using the CIGAR string, and for mapped reads is
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1145 equivalent to &quot;pos+rlen-1&quot;. For unmapped reads, it is the same as &quot;pos&quot;.
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1146
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1147 Reference names may be matched either by their string forms (&quot;rname&quot; and &quot;mrname&quot;) or as the Nth @SQ line (counting from zero) as stored in BAM using
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1148 &quot;tid&quot; and &quot;mtid&quot; respectively.
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1149
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1150 Auxiliary tags are described in square brackets and these expand to either integer or string as defined by the tag itself (XX:Z:string or XX:i:int).
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1151 For example [NM]&gt;=10 can be used to look for alignments with many mismatches and [RG]=~&quot;grp[ABC]-&quot; will match the read-group string.
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1152
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1153 If no comparison is used with an auxiliary tag it is taken simply to be a test for the existence of that tag. So [NM] will return any record containing
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1154 an NM tag, even if that tag is zero (NM:i:0). In htslib &lt;= 1.15 negating this with ![NM] gave misleading results as it was true if the tag did not exist
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1155 or did exist but was zero. Now this is strictly does-not-exist. An explicit exists([NM]) and !exists([NM]) function has also been added to make
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1156 this intention clear.
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1157
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1158 Similarly in htslib &lt;= 1.15 using [NM]!=0 was true both when the tag existed and was not zero as well as when the tag did not exist. From 1.16 onwards
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1159 all comparison operators are only true for tags that exist, so [NM]!=0 works as expected.
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1160
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1161 Some simple functions are available to operate on strings. These treat the strings as arrays of bytes, permitting their length, minimum, maximum and
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1162 average values to be computed. These are useful for processing Quality Scores.
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1163
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1164 ::
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1165
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1166 length(x) Length of the string (excluding nul char)
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1167 min(x) Minimum byte value in the string
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1168 max(x) Maximum byte value in the string
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1169 avg(x) Average byte value in the string
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1170
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1171
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1172 Note that &quot;avg&quot; is a floating point value and it may be NAN for empty strings. This means that &quot;avg(qual)&quot; does not produce an error for records that
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1173 have both seq and qual of &quot;&#42;&quot;. NAN values will fail any conditional checks, so e.g. &quot;avg(qual) &gt; 20&quot; works and will not report these records. NAN also
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1174 fails all equality, &lt; and &gt; comparisons, and returns zero when given as an argument to the exists function. It can be negated with !x in which case it
2dce91e11ca7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1175 becomes true.
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1176
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1177 Functions that operate on both strings and numerics:
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1178
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1179 ::
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1180
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1181 exists(x) True if the value exists (or is explicitly true).
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1182 default(x,d) Value x if it exists or d if not.
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1183
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1184 Functions that apply only to numeric values:
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1185
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1186 ::
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1187
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1188 qrt(x) Square root of x
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1189 og(x) Natural logarithm of x
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1190 ow(x, y) Power function, x to the power of y
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1191 xp(x) Base-e exponential, equivalent to pow(e,x)
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1192
0
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1193 </help>
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1194 <expand macro="citations"/>
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1195 </tool>