Mercurial > repos > iuc > samtools_markdup

comparison samtools_markdup.xml @ 10:229ba92a3b55 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 c508c3af0f4121dcc38e0be63db00a604e997b8a
author iuc
date Thu, 19 Jun 2025 13:00:18 +0000
parents 40fa6c240105
children
comparison
equal deleted inserted replaced
9:40fa6c240105 10:229ba92a3b55
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" ftype="sam" /> 105 <param name="bamfile" value="2_remove_dups.sam" ftype="sam" />
106 <param name="remove" value="-r" /> 106 <param name="remove" value="true" />
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="true" />
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> 114 <assert_command>
115 <has_text text="samtools sort" negate="true"/> 115 <has_text text="samtools sort" negate="true"/>
116 </assert_command> 116 </assert_command>
117 </test> 117 </test>
118 <!-- 4) test stats output --> 118 <!-- 4) test stats output -->
119 <test expect_num_outputs="2"> 119 <test expect_num_outputs="2">
120 <param name="bamfile" value="1_markdup.sam" ftype="sam"/> 120 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
121 <param name="stats" value="yes" /> 121 <section name="output_options">
122 <param name="stats" value="yes" />
123 </section>
122 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" /> 124 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" />
123 <output name="stats_output" file="stats.txt" lines_diff="2" /> 125 <output name="stats_output" file="stats.txt" lines_diff="2" />
124 </test> 126 </test>
125 <!-- 5) check that stderr is not swallowed w test data from fixmate --> 127 <!-- 5) check that stderr is not swallowed w test data from fixmate -->
126 <test expect_exit_code="1" expect_failure="true"> 128 <test expect_exit_code="1" expect_failure="true">
127 <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" /> 129 <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" />
128 <param name="stats" value="yes"/> 130 <section name="output_options">
131 <param name="stats" value="yes"/>
132 </section>
129 <assert_stderr> 133 <assert_stderr>
130 <has_line line="samtools markdup: error, no MC tag. Please run samtools fixmate on file first."/> 134 <has_line line="samtools markdup: error, no MC tag. Please run samtools fixmate on file first."/>
131 <has_line line="samtools markdup: error, unable to assign pair hash key."/> 135 <has_line line="samtools markdup: error, unable to assign pair hash key."/>
132 </assert_stderr> 136 </assert_stderr>
133 </test> 137 </test>
134 <!-- 6) check optical distance and check -c option --> 138 <!-- 6) check optical distance and check -c option -->
135 <test expect_num_outputs="1"> 139 <test expect_num_outputs="1">
136 <param name="bamfile" value="1_markdup.sam" ftype="sam"/> 140 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
137 <param name="odist" value="10" /> 141 <param name="odist" value="10" />
138 <param name="existing_tags" value="-c" /> 142 <param name="existing_tags" value="true" />
139 <output name="output" file="6_markdup.expected.bam" ftype="bam" lines_diff="4" /> 143 <output name="output" file="6_markdup.expected.bam" ftype="bam" lines_diff="4" />
140 </test> 144 </test>
141 <!-- 7) check new mode s --> 145 <!-- 7) check new mode s -->
142 <test expect_num_outputs="1"> 146 <test expect_num_outputs="1">
143 <param name="bamfile" value="1_markdup.sam" ftype="sam"/> 147 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
151 <output name="output" file="8_markdup.expected.bam" ftype="bam" lines_diff="4" /> 155 <output name="output" file="8_markdup.expected.bam" ftype="bam" lines_diff="4" />
152 </test> 156 </test>
153 <!-- 9) test sam format --> 157 <!-- 9) test sam format -->
154 <test expect_num_outputs="1"> 158 <test expect_num_outputs="1">
155 <param name="bamfile" value="1_markdup.sam" ftype="sam"/> 159 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
156 <param name="select_oformat" value="SAM" /> 160 <section name="output_options">
161 <conditional name="output_format">
162 <param name="select_oformat" value="SAM" />
163 </conditional>
164 </section>
157 <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" /> 165 <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" />
158 </test> 166 </test>
159 <!-- 10) essentially the same as test 9 (just converted input to sorted bam .. but telling Galaxy its qname sorted) 167 <!-- 10) essentially the same as test 9 (just converted input to sorted bam .. but telling Galaxy its qname sorted)
160 to test qname sorted bam format and ensure that sorting happens in the tool 168 to test qname sorted bam format and ensure that sorting happens in the tool
161 ie. the qname_sorted bam is not converted implicitly --> 169 ie. the qname_sorted bam is not converted implicitly -->
162 <test expect_num_outputs="1"> 170 <test expect_num_outputs="1">
163 <param name="bamfile" value="1_markdup.qname_sorted.bam" ftype="qname_sorted.bam" /> 171 <param name="bamfile" value="1_markdup.qname_sorted.bam" ftype="qname_sorted.bam" />
164 <param name="select_oformat" value="SAM" /> 172 <section name="output_options">
173 <conditional name="output_format">
174 <param name="select_oformat" value="SAM" />
175 </conditional>
176 </section>
165 <output name="output" file="9_markdup.expected.sam" lines_diff="4" /> 177 <output name="output" file="9_markdup.expected.sam" lines_diff="4" />
166 <assert_command> 178 <assert_command>
167 <has_text text="samtools sort"/> 179 <has_text text="samtools sort"/>
168 </assert_command> 180 </assert_command>
169 </test> 181 </test>
170 182
171 <!-- 11) test cram format --> 183 <!-- 11) test cram format -->
172 <test expect_num_outputs="1"> 184 <test expect_num_outputs="1">
173 <param name="bamfile" value="10_markdup.sam" ftype="sam"/> 185 <param name="bamfile" value="10_markdup.sam" ftype="sam"/>
174 <param name="select_oformat" value="CRAM" /> 186 <section name="output_options">
175 <param name="ref_file" value="test.fa" /> 187 <conditional name="output_format">
188 <param name="select_oformat" value="CRAM" />
189 <param name="ref_file" value="test.fa" />
190 </conditional>
191 </section>
176 <output name="output" file="11_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/> 192 <output name="output" file="11_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/>
177 <assert_command> 193 <assert_command>
178 <has_text text="samtools sort"/> 194 <has_text text="samtools sort"/>
179 </assert_command> 195 </assert_command>
180 </test> 196 </test>