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comparison samtools_markdup.xml @ 7:ce32171c6d44 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit deb37086489259607f5edcba25750434bbf4823e
author iuc
date Fri, 07 Apr 2023 21:47:07 +0000
parents b5527cc104ab
children a389f74c3630
comparison
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6:b5527cc104ab 7:ce32171c6d44
1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" > 1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy1" 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"/>
83 </inputs> 83 </inputs>
84 <outputs> 84 <outputs>
85 <!-- output bam, if input was name sorted then restore this sorting order --> 85 <!-- output bam, if input was name sorted then restore this sorting order -->
86 <data name="output" format="bam" from_work_dir="outfile" label="${tool.name} on ${on_string}"> 86 <data name="output" format="bam" from_work_dir="outfile" label="${tool.name} on ${on_string}">
87 <change_format> 87 <change_format>
88 <when input="output_format.select_oformat" value="SAM" format="sam" /> 88 <when input="output_options.output_format.select_oformat" value="SAM" format="sam" />
89 <when input="output_format.select_oformat" value="BAM" format="bam" /> 89 <when input="output_options.output_format.select_oformat" value="BAM" format="bam" />
90 <when input="output_format.select_oformat" value="CRAM" format="cram" /> 90 <when input="output_options.output_format.select_oformat" value="CRAM" format="cram" />
91 </change_format> 91 </change_format>
92 </data> 92 </data>
93 <data name="stats_output" format="txt" label="${tool.name} on ${on_string}: statistics"> 93 <data name="stats_output" format="txt" label="${tool.name} on ${on_string}: statistics">
94 <filter>(output_options['stats'] == 'yes')</filter> 94 <filter>(output_options['stats'] == 'yes')</filter>
95 </data> 95 </data>
96 </outputs> 96 </outputs>
97 <tests> 97 <tests>
98 <!-- 1) --> 98 <!-- 1) -->
99 <test expect_num_outputs="1"> 99 <test expect_num_outputs="1">
100 <param name="bamfile" value="1_markdup.sam" /> 100 <param name="bamfile" value="1_markdup.sam" ftype="sam" />
101 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" /> 101 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" />
102 </test> 102 </test>
103 <!-- 2) --> 103 <!-- 2) -->
104 <test expect_num_outputs="1"> 104 <test expect_num_outputs="1">
105 <param name="bamfile" value="2_remove_dups.sam" /> 105 <param name="bamfile" value="2_remove_dups.sam" ftype="sam" />
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" /> 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 </test> 114 </test>
115 <!-- 4) test stats output --> 115 <!-- 4) test stats output -->
116 <test expect_num_outputs="2"> 116 <test expect_num_outputs="2">
117 <param name="bamfile" value="1_markdup.sam" /> 117 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
118 <param name="stats" value="yes" /> 118 <param name="stats" value="yes" />
119 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" /> 119 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" />
120 <output name="stats_output" file="stats.txt" lines_diff="2" /> 120 <output name="stats_output" file="stats.txt" lines_diff="2" />
121 </test> 121 </test>
122 <!-- 5) check that stderr is not swallowed w test data from fixmate --> 122 <!-- 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"> 123 <test expect_num_outputs="2" expect_exit_code="1" expect_failure="true">
124 <param name="bamfile" value="3_two_read_mapped.sam" /> 124 <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" />
125 <param name="stats" value="yes"/> 125 <param name="stats" value="yes"/>
126 <!-- for some reason this is not possible at the moment 126 <!-- for some reason this is not possible at the moment
127 <output name="stats_output"> 127 <output name="stats_output">
128 <assert_contents> 128 <assert_contents>
129 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/> 129 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
133 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/> 133 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
134 </assert_stderr> 134 </assert_stderr>
135 </test> 135 </test>
136 <!-- 6) check optical distance and check -c option --> 136 <!-- 6) check optical distance and check -c option -->
137 <test expect_num_outputs="1"> 137 <test expect_num_outputs="1">
138 <param name="bamfile" value="1_markdup.sam" /> 138 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
139 <param name="odist" value="10" /> 139 <param name="odist" value="10" />
140 <param name="existing_tags" value="-c" /> 140 <param name="existing_tags" value="-c" />
141 <output name="output" file="6_markdup.expected.bam" ftype="bam" lines_diff="4" /> 141 <output name="output" file="6_markdup.expected.bam" ftype="bam" lines_diff="4" />
142 </test> 142 </test>
143 <!-- 7) check new mode s --> 143 <!-- 7) check new mode s -->
144 <test expect_num_outputs="1"> 144 <test expect_num_outputs="1">
145 <param name="bamfile" value="1_markdup.sam" /> 145 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
146 <param name="mode" value="s" /> 146 <param name="mode" value="s" />
147 <output name="output" file="7_markdup.expected.bam" ftype="bam" lines_diff="4" /> 147 <output name="output" file="7_markdup.expected.bam" ftype="bam" lines_diff="4" />
148 </test> 148 </test>
149 <!-- 8) check include-fails --> 149 <!-- 8) check include-fails -->
150 <test expect_num_outputs="1"> 150 <test expect_num_outputs="1">
151 <param name="bamfile" value="1_markdup.sam" /> 151 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
152 <param name="include_fails" value="true" /> 152 <param name="include_fails" value="true" />
153 <output name="output" file="8_markdup.expected.bam" ftype="bam" lines_diff="4" /> 153 <output name="output" file="8_markdup.expected.bam" ftype="bam" lines_diff="4" />
154 </test> 154 </test>
155 <!-- 9) test sam format --> 155 <!-- 9) test sam format -->
156 <test expect_num_outputs="1"> 156 <test expect_num_outputs="1">
157 <param name="bamfile" value="1_markdup.sam" /> 157 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
158 <param name="select_oformat" value="SAM" /> 158 <param name="select_oformat" value="SAM" />
159 <output name="output" file="9_markdup.expected.sam" lines_diff="4" /> 159 <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" />
160 </test> 160 </test>
161 <!-- 10) test cram format --> 161 <!-- 10) test cram format -->
162 <test expect_num_outputs="1"> 162 <test expect_num_outputs="1">
163 <param name="bamfile" value="10_markdup.sam" /> 163 <param name="bamfile" value="10_markdup.sam" ftype="sam"/>
164 <param name="select_oformat" value="CRAM" /> 164 <param name="select_oformat" value="CRAM" />
165 <param name="ref_file" value="test.fa" /> 165 <param name="ref_file" value="test.fa" />
166 <output name="output" file="10_markdup.expected.cram" compare="sim_size" delta="250"/> 166 <output name="output" file="10_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/>
167 </test> 167 </test>
168 </tests> 168 </tests>
169 <help> 169 <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. 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.
171 171