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comparison samtools_markdup.xml @ 8:a389f74c3630 draft default tip

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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
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7:ce32171c6d44 8:a389f74c3630
1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" > 1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" >
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"/>
49 #end if 49 #end if
50 coordsort.sam 50 coordsort.sam
51 '$output' 51 '$output'
52 ]]></command> 52 ]]></command>
53 <inputs> 53 <inputs>
54 <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Alignment" /> 54 <param name="bamfile" type="data" format="sam,unsorted.bam,cram" optional="false" label="Alignment" />
55 <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" /> 55 <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" />
56 <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" /> 56 <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" />
57 <param name="existing_tags" type="boolean" argument="-c" truevalue="-c" falsevalue="" label="Clear previous duplicate settings and tags." /> 57 <param name="existing_tags" type="boolean" argument="-c" truevalue="-c" falsevalue="" label="Clear previous duplicate settings and tags." />
58 <param name="maxlen" type="integer" optional="true" argument="-l" min="0" label="Expected maximum read length of INT bases. (default 300, min=0)"/> 58 <param name="maxlen" type="integer" optional="true" argument="-l" min="0" label="Expected maximum read length of INT bases. (default 300, min=0)"/>
59 <param name="odist" type="integer" optional="true" argument="-d" min="1" label="Optical distance (if set, marks with dt tag, min=1)"/> 59 <param name="odist" type="integer" optional="true" argument="-d" min="1" label="Optical distance (if set, marks with dt tag, min=1)"/>
106 <param name="remove" value="-r" /> 106 <param name="remove" value="-r" />
107 <output name="output" file="2_remove_dups.expected.bam" ftype="bam" lines_diff="4" /> 107 <output name="output" file="2_remove_dups.expected.bam" ftype="bam" lines_diff="4" />
108 </test> 108 </test>
109 <!-- 3) --> 109 <!-- 3) -->
110 <test expect_num_outputs="1"> 110 <test expect_num_outputs="1">
111 <param name="bamfile" value="3_mark_supp_dup.bam" ftype="bam" /> 111 <param name="bamfile" value="3_mark_supp_dup.bam" ftype="bam" />
112 <param name="supp" value="-S" /> 112 <param name="supp" value="-S" />
113 <output name="output" file="3_mark_supp_dup.expected.bam" ftype="bam" lines_diff="4" /> 113 <output name="output" file="3_mark_supp_dup.expected.bam" ftype="bam" lines_diff="4" />
114 <assert_command>
115 <has_text text="samtools sort" negate="true"/>
116 </assert_command>
114 </test> 117 </test>
115 <!-- 4) test stats output --> 118 <!-- 4) test stats output -->
116 <test expect_num_outputs="2"> 119 <test expect_num_outputs="2">
117 <param name="bamfile" value="1_markdup.sam" ftype="sam"/> 120 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
118 <param name="stats" value="yes" /> 121 <param name="stats" value="yes" />
119 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" /> 122 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" />
120 <output name="stats_output" file="stats.txt" lines_diff="2" /> 123 <output name="stats_output" file="stats.txt" lines_diff="2" />
121 </test> 124 </test>
122 <!-- 5) check that stderr is not swallowed w test data from fixmate --> 125 <!-- 5) check that stderr is not swallowed w test data from fixmate -->
123 <test expect_num_outputs="2" expect_exit_code="1" expect_failure="true"> 126 <test expect_exit_code="1" expect_failure="true">
124 <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" /> 127 <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" />
125 <param name="stats" value="yes"/> 128 <param name="stats" value="yes"/>
126 <!-- for some reason this is not possible at the moment
127 <output name="stats_output">
128 <assert_contents>
129 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
130 </assert_contents>
131 </output> -->
132 <assert_stderr> 129 <assert_stderr>
133 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/> 130 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
134 </assert_stderr> 131 </assert_stderr>
135 </test> 132 </test>
136 <!-- 6) check optical distance and check -c option --> 133 <!-- 6) check optical distance and check -c option -->
156 <test expect_num_outputs="1"> 153 <test expect_num_outputs="1">
157 <param name="bamfile" value="1_markdup.sam" ftype="sam"/> 154 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
158 <param name="select_oformat" value="SAM" /> 155 <param name="select_oformat" value="SAM" />
159 <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" /> 156 <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" />
160 </test> 157 </test>
161 <!-- 10) test cram format --> 158 <!-- 10) essentially the same as test 9 (just converted input to sorted bam .. but telling Galaxy its qname sorted)
159 to test qname sorted bam format and ensure that sorting happens in the tool
160 ie. the qname_sorted bam is not converted implicitly -->
161 <test expect_num_outputs="1">
162 <param name="bamfile" value="1_markdup.qname_sorted.bam" ftype="qname_sorted.bam" />
163 <param name="select_oformat" value="SAM" />
164 <output name="output" file="9_markdup.expected.sam" lines_diff="4" />
165 <assert_command>
166 <has_text text="samtools sort"/>
167 </assert_command>
168 </test>
169
170 <!-- 11) test cram format -->
162 <test expect_num_outputs="1"> 171 <test expect_num_outputs="1">
163 <param name="bamfile" value="10_markdup.sam" ftype="sam"/> 172 <param name="bamfile" value="10_markdup.sam" ftype="sam"/>
164 <param name="select_oformat" value="CRAM" /> 173 <param name="select_oformat" value="CRAM" />
165 <param name="ref_file" value="test.fa" /> 174 <param name="ref_file" value="test.fa" />
166 <output name="output" file="10_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/> 175 <output name="output" file="11_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/>
176 <assert_command>
177 <has_text text="samtools sort"/>
178 </assert_command>
167 </test> 179 </test>
168 </tests> 180 </tests>
169 <help> 181 <help>
170 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. 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.
171 183