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annotate samtools_markdup.xml @ 8:a389f74c3630 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit cd62639660bef041ba14ecff337fb98e84e75d8a
author iuc
date Mon, 20 Nov 2023 22:15:54 +0000
parents ce32171c6d44
children 40fa6c240105
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a389f74c3630 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit cd62639660bef041ba14ecff337fb98e84e75d8a
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1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" >
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2 <description>marks duplicate alignments</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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9 <command><![CDATA[
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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10 @ADDTHREADS@
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d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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11 ## coordinate sort input
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12 #if not $bamfile.is_of_type('bam'):
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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13 samtools sort
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14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
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15 -O sam
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16 -o coordsort.sam
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17 '$bamfile' &&
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18 #else:
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19 ln -s '$bamfile' coordsort.sam &&
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20 #end if
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21
5
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22 ## copy fasta reference if needed
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23 ## because samtools will try to write a .fai file next to it
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24 #if $output_options.output_format.select_oformat == "CRAM"
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25 ln -s '$output_options.output_format.ref_file' ref_file.fa &&
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26 #end if
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27
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28 samtools markdup
0
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046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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30 -@ \$addthreads
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31 #if str($maxlen) != '':
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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32 -l $maxlen
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33 #end if
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34 $remove
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35 $supp
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36 #if $odist:
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37 -d $odist
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38 #end if
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39 $existing_tags
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40 -m $mode
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41 $include_fails
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42 #if $output_options.stats == 'yes'
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43 -s
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44 -f '$stats_output'
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45 #end if
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46 -O $output_options.output_format.select_oformat
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47 #if $output_options.output_format.select_oformat == "CRAM"
5
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48 --reference ref_file.fa
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49 #end if
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50 coordsort.sam
0
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51 '$output'
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52 ]]></command>
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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53 <inputs>
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54 <param name="bamfile" type="data" format="sam,unsorted.bam,cram" optional="false" label="Alignment" />
0
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55 <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" />
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56 <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" />
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57 <param name="existing_tags" type="boolean" argument="-c" truevalue="-c" falsevalue="" label="Clear previous duplicate settings and tags." />
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58 <param name="maxlen" type="integer" optional="true" argument="-l" min="0" label="Expected maximum read length of INT bases. (default 300, min=0)"/>
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59 <param name="odist" type="integer" optional="true" argument="-d" min="1" label="Optical distance (if set, marks with dt tag, min=1)"/>
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60 <param argument="--mode" type="select" label="Duplicate decision method for paired reads.">
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61 <option selected="true" value="t">(t) measure positions based on template start/end.</option>
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62 <option value="s">(s) measure positions based on sequence start. </option>
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63 </param>
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64 <param argument="--include-fails" type="boolean" truevalue="--include-fails" falsevalue="" label="Include quality check failed reads." />
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65 <section name="output_options" title="Output Options" expanded="true">
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66 <param name="stats" type="select" argument="-s" label="Print basic statistics">
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67 <option value="yes">Yes</option>
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68 <option value="no" selected="True">No</option>
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69 </param>
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70 <conditional name="output_format">
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71 <param name="select_oformat" type="select" label="Output format" help="Specify output format">
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72 <option value="SAM">SAM</option>
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73 <option value="BAM" selected="True">BAM</option>
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74 <option value="CRAM">CRAM</option>
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75 </param>
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76 <when value="SAM" />
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77 <when value="BAM" />
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78 <when value="CRAM">
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79 <param name="ref_file" type="data" format="fasta" label="Reference FASTA file" />
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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80 </when>
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81 </conditional>
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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82 </section>
0
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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83 </inputs>
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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84 <outputs>
1
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85 <!-- output bam, if input was name sorted then restore this sorting order -->
3
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86 <data name="output" format="bam" from_work_dir="outfile" label="${tool.name} on ${on_string}">
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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87 <change_format>
7
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88 <when input="output_options.output_format.select_oformat" value="SAM" format="sam" />
ce32171c6d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit deb37086489259607f5edcba25750434bbf4823e
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89 <when input="output_options.output_format.select_oformat" value="BAM" format="bam" />
ce32171c6d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit deb37086489259607f5edcba25750434bbf4823e
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90 <when input="output_options.output_format.select_oformat" value="CRAM" format="cram" />
3
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91 </change_format>
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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92 </data>
2
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93 <data name="stats_output" format="txt" label="${tool.name} on ${on_string}: statistics">
3
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94 <filter>(output_options['stats'] == 'yes')</filter>
1
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95 </data>
0
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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96 </outputs>
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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97 <tests>
3
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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98 <!-- 1) -->
1
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99 <test expect_num_outputs="1">
7
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100 <param name="bamfile" value="1_markdup.sam" ftype="sam" />
3
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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101 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" />
0
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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102 </test>
3
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103 <!-- 2) -->
1
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104 <test expect_num_outputs="1">
7
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105 <param name="bamfile" value="2_remove_dups.sam" ftype="sam" />
0
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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106 <param name="remove" value="-r" />
3
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parents: 2
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107 <output name="output" file="2_remove_dups.expected.bam" ftype="bam" lines_diff="4" />
0
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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108 </test>
3
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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109 <!-- 3) -->
1
83b8e36e9cbe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
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110 <test expect_num_outputs="1">
8
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111 <param name="bamfile" value="3_mark_supp_dup.bam" ftype="bam" />
0
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112 <param name="supp" value="-S" />
3
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113 <output name="output" file="3_mark_supp_dup.expected.bam" ftype="bam" lines_diff="4" />
8
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114 <assert_command>
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115 <has_text text="samtools sort" negate="true"/>
a389f74c3630 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit cd62639660bef041ba14ecff337fb98e84e75d8a
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116 </assert_command>
0
046cbf29795a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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117 </test>
3
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118 <!-- 4) test stats output -->
1
83b8e36e9cbe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
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parents: 0
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119 <test expect_num_outputs="2">
7
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120 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
3
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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diff changeset
121 <param name="stats" value="yes" />
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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122 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" />
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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diff changeset
123 <output name="stats_output" file="stats.txt" lines_diff="2" />
1
83b8e36e9cbe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
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124 </test>
3
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diff changeset
125 <!-- 5) check that stderr is not swallowed w test data from fixmate -->
8
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126 <test expect_exit_code="1" expect_failure="true">
7
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diff changeset
127 <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" />
3
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diff changeset
128 <param name="stats" value="yes"/>
2
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parents: 1
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129 <assert_stderr>
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130 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
a312a0fdaf31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
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131 </assert_stderr>
a312a0fdaf31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
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132 </test>
3
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133 <!-- 6) check optical distance and check -c option -->
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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134 <test expect_num_outputs="1">
7
ce32171c6d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit deb37086489259607f5edcba25750434bbf4823e
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diff changeset
135 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
3
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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diff changeset
136 <param name="odist" value="10" />
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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diff changeset
137 <param name="existing_tags" value="-c" />
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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138 <output name="output" file="6_markdup.expected.bam" ftype="bam" lines_diff="4" />
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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diff changeset
139 </test>
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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140 <!-- 7) check new mode s -->
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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141 <test expect_num_outputs="1">
7
ce32171c6d44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit deb37086489259607f5edcba25750434bbf4823e
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142 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
4
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diff changeset
143 <param name="mode" value="s" />
3
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144 <output name="output" file="7_markdup.expected.bam" ftype="bam" lines_diff="4" />
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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diff changeset
145 </test>
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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diff changeset
146 <!-- 8) check include-fails -->
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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147 <test expect_num_outputs="1">
7
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diff changeset
148 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
4
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diff changeset
149 <param name="include_fails" value="true" />
3
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diff changeset
150 <output name="output" file="8_markdup.expected.bam" ftype="bam" lines_diff="4" />
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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diff changeset
151 </test>
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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diff changeset
152 <!-- 9) test sam format -->
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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diff changeset
153 <test expect_num_outputs="1">
7
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diff changeset
154 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
3
d0a568e1904b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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diff changeset
155 <param name="select_oformat" value="SAM" />
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156 <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" />
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157 </test>
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158 <!-- 10) essentially the same as test 9 (just converted input to sorted bam .. but telling Galaxy its qname sorted)
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159 to test qname sorted bam format and ensure that sorting happens in the tool
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160 ie. the qname_sorted bam is not converted implicitly -->
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161 <test expect_num_outputs="1">
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162 <param name="bamfile" value="1_markdup.qname_sorted.bam" ftype="qname_sorted.bam" />
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163 <param name="select_oformat" value="SAM" />
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164 <output name="output" file="9_markdup.expected.sam" lines_diff="4" />
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165 <assert_command>
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166 <has_text text="samtools sort"/>
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167 </assert_command>
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168 </test>
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169
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170 <!-- 11) test cram format -->
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171 <test expect_num_outputs="1">
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172 <param name="bamfile" value="10_markdup.sam" ftype="sam"/>
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173 <param name="select_oformat" value="CRAM" />
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174 <param name="ref_file" value="test.fa" />
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175 <output name="output" file="11_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/>
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176 <assert_command>
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177 <has_text text="samtools sort"/>
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178 </assert_command>
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179 </test>
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180 </tests>
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181 <help>
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182 Mark duplicate alignments from a coordinate sorted file that has been run through fixmate with the -m option. This program relies on the MC and ms tags that fixmate provides.
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183
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184 Note: The Galaxy tool sorts the data automatically if the input is SAM or query name sorted.
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185 The output is BAM (which is query name sorted again if the input is).
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186
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187 The optional basic statistics output of samtools markdup can be visualized with MultiQC.
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188
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189 </help>
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190 <expand macro="citations"/>
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191 </tool>