Mercurial > repos > iuc > samtools_markdup

annotate samtools_markdup.xml @ 2:a312a0fdaf31 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
author iuc
date Thu, 22 Apr 2021 12:58:55 +0000
parents 83b8e36e9cbe
children d0a568e1904b
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a312a0fdaf31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
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1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy3">
0
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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>
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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"/>
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9 <command><![CDATA[
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10 @ADDTHREADS@
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11 ## coordinate sort input
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12 #if not $bamfile.is_of_type('bam'):
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13 samtools sort
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14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
0
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15 -O sam
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16 -o coordsort.sam
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17 '$bamfile' &&
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18 #else:
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19 ln -s '$bamfile' coordsort.sam &&
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20 #end if
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21
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22 samtools markdup
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23
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24 -@ \$addthreads
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25 #if str($maxlen) != '':
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26 -l $maxlen
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27 #end if
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28 $remove
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29 $stats
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30 $supp
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31 coordsort.sam
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32 '$output'
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33 #if $stats
2
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34 2> >(tee -a '$stats_output' >&2)
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35 #end if
0
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36 ]]></command>
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37 <inputs>
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38 <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Alignment" />
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39 <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" />
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40 <param name="maxlen" type="integer" optional="true" argument="-l" min="0" label="Expected maximum read length of INT bases. (default 300)"/>
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41 <param name="stats" type="boolean" argument="-s" truevalue="-s" falsevalue="" label="Print basic statistics" />
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42 <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" />
0
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43 </inputs>
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44 <outputs>
1
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45 <!-- output bam, if input was name sorted then restore this sorting order -->
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46 <data name="output" format="bam"/>
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47 <data name="stats_output" format="txt" label="${tool.name} on ${on_string}: statistics">
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48 <filter>stats</filter>
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49 </data>
0
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50 </outputs>
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51 <tests>
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52 <!-- tests and data extracted from
1
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53 https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2616
0
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54 TODO the 1st 4 tests are negative, I do not know how to test for the error code
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55 -->
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56 <!-- test_cmd($opts, out=>'markdup/1_name_sort.expected.sam', err=>'1_name_sort.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/1_name_sort.sam -", expect_fail=>1);
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57 test_cmd($opts, out=>'markdup/2_bad_order.expected.sam', err=>'2_bad_order.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/2_bad_order.sam -", expect_fail=>1);
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58 test_cmd($opts, out=>'markdup/3_missing_mc.expected.sam', err=>'3_missing_mc.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/3_missing_mc.sam -", expect_fail=>1);
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59 test_cmd($opts, out=>'markdup/4_missing_ms.expected.sam', err=>'4_missing_ms.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/4_missing_ms.sam -", expect_fail=>1);-->
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60 <!-- test_cmd($opts, out=>'markdup/5_markdup.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/5_markdup.sam -");-->
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61 <test expect_num_outputs="1">
0
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62 <param name="bamfile" value="5_markdup.sam" />
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63 <output name="output" file="5_markdup.expected.bam" />
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64 </test>
1
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65 <!-- test_cmd($opts, out=>'markdup/6_remove_dups.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam -r $$opts{path}/markdup/6_remove_dups.sam -");-->
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66 <test expect_num_outputs="1">
0
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67 <param name="bamfile" value="6_remove_dups.sam" />
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68 <param name="remove" value="-r" />
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69 <output name="output" file="6_remove_dups.expected.bam" />
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70 </test>
1
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71 <!-- test_cmd($opts, out=>'markdup/7_mark_supp_dup.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -S -O sam $$opts{path}/markdup/7_mark_supp_dup.sam -");-->
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72 <test expect_num_outputs="1">
0
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73 <param name="bamfile" value="7_mark_supp_dup.bam" />
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74 <param name="supp" value="-S" />
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75 <output name="output" file="7_mark_supp_dup.expected.bam" />
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76 </test>
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77 <!-- test stats output -->
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78 <test expect_num_outputs="2">
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79 <param name="bamfile" value="5_markdup.sam" />
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80 <param name="stats" value="-s" />
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81 <output name="output" file="5_markdup.expected.bam" />
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82 <output name="stats_output" file="stats.txt" />
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83 </test>
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84 <!-- check that stderr is not swallowed w test data from fixmate -->
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85 <test expect_num_outputs="2" expect_exit_code="1" expect_failure="true">
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86 <param name="bamfile" value="7_two_read_mapped.sam" />
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87 <param name="stats" value="true"/>
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88 <!-- for some reason this is not possible at the moment
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89 <output name="stats_output">
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90 <assert_contents>
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91 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
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92 </assert_contents>
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93 </output> -->
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94 <assert_stderr>
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95 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
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96 </assert_stderr>
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97 </test>
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98 </tests>
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99 <help>
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100 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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101
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102 Note: The Galaxy tool sorts the data automatically if the input is SAM or query name sorted.
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103 The output is BAM (which is query name sorted again if the input is).
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104
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105 The optional basic statistics output of samtools markdup can be visualized with MultiQC.
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106
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107 </help>
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108 <expand macro="citations"/>
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109 </tool>