Mercurial > repos > iuc > samtools_markdup
comparison samtools_markdup.xml @ 10:229ba92a3b55 draft default tip
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 |
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| 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> |