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comparison 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
comparison
equal deleted inserted replaced
1:83b8e36e9cbe 2:a312a0fdaf31
1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy2"> 1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy3">
2 <description>marks duplicate alignments</description> 2 <description>marks duplicate alignments</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
29 $stats 29 $stats
30 $supp 30 $supp
31 coordsort.sam 31 coordsort.sam
32 '$output' 32 '$output'
33 #if $stats 33 #if $stats
34 2> '$stats_output' 34 2> >(tee -a '$stats_output' >&2)
35 #end if 35 #end if
36 ]]></command> 36 ]]></command>
37 <inputs> 37 <inputs>
38 <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Alignment" /> 38 <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Alignment" />
39 <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" /> 39 <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" />
42 <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" /> 42 <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" />
43 </inputs> 43 </inputs>
44 <outputs> 44 <outputs>
45 <!-- output bam, if input was name sorted then restore this sorting order --> 45 <!-- output bam, if input was name sorted then restore this sorting order -->
46 <data name="output" format="bam"/> 46 <data name="output" format="bam"/>
47 <data name="stats_output" format="txt"> 47 <data name="stats_output" format="txt" label="${tool.name} on ${on_string}: statistics">
48 <filter>stats</filter> 48 <filter>stats</filter>
49 </data> 49 </data>
50 </outputs> 50 </outputs>
51 <tests> 51 <tests>
52 <!-- tests and data extracted from 52 <!-- tests and data extracted from
79 <param name="bamfile" value="5_markdup.sam" /> 79 <param name="bamfile" value="5_markdup.sam" />
80 <param name="stats" value="-s" /> 80 <param name="stats" value="-s" />
81 <output name="output" file="5_markdup.expected.bam" /> 81 <output name="output" file="5_markdup.expected.bam" />
82 <output name="stats_output" file="stats.txt" /> 82 <output name="stats_output" file="stats.txt" />
83 </test> 83 </test>
84 <!-- check that stderr is not swallowed w test data from fixmate -->
85 <test expect_num_outputs="2" expect_exit_code="1" expect_failure="true">
86 <param name="bamfile" value="7_two_read_mapped.sam" />
87 <param name="stats" value="true"/>
88 <!-- for some reason this is not possible at the moment
89 <output name="stats_output">
90 <assert_contents>
91 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
92 </assert_contents>
93 </output> -->
94 <assert_stderr>
95 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
96 </assert_stderr>
97 </test>
84 </tests> 98 </tests>
85 <help> 99 <help>
86 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. 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.
87 101
88 Note: The Galaxy tool sorts the data automatically if the input is SAM or query name sorted. 102 Note: The Galaxy tool sorts the data automatically if the input is SAM or query name sorted.