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comparison coverageBed.xml @ 47:2892111d91f8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:40:09 +0000
parents 64e2edfe7a2c
children
comparison
equal deleted inserted replaced
46:64e2edfe7a2c 47:2892111d91f8
70 <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/> 70 <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
71 </outputs> 71 </outputs>
72 <tests> 72 <tests>
73 <test> 73 <test>
74 <param name="inputA" value="coverageBedA.bed" ftype="bed"/> 74 <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
75 <param name="inputB" value="coverageBedB.bed" ftype="bed"/> 75 <param name="reduce_or_iterate|inputB" value="coverageBedB.bed" ftype="bed"/>
76 <output name="output" file="coverageBed_result1.bed" ftype="bed"/> 76 <output name="output" file="coverageBed_result1.bed" ftype="bed"/>
77 </test> 77 </test>
78 <test> 78 <test>
79 <param name="inputA" value="multiCov1.bed" ftype="bed"/> 79 <param name="inputA" value="multiCov1.bed" ftype="bed"/>
80 <param name="inputB" value="srma_in3.bam" ftype="bam"/> 80 <param name="reduce_or_iterate|inputB" value="srma_in3.bam" ftype="bam"/>
81 <param name="sorted" value="true"/> 81 <param name="sorted" value="true"/>
82 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/> 82 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>
83 </test> 83 </test>
84 <test> 84 <test>
85 <param name="inputA" value="multiCov1.bed" ftype="bed"/> 85 <param name="inputA" value="multiCov1.bed" ftype="bed"/>
86 <param name="reduce_or_iterate_selector" value="reduce"/> 86 <param name="reduce_or_iterate|reduce_or_iterate_selector" value="reduce"/>
87 <param name="inputB" value="srma_in3.bam" ftype="bam"/> 87 <param name="reduce_or_iterate|inputB" value="srma_in3.bam" ftype="bam"/>
88 <param name="sorted" value="true"/> 88 <param name="sorted" value="true"/>
89 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/> 89 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>
90 </test> 90 </test>
91 <test> 91 <test>
92 <param name="inputA" value="coverageBedA.bed" ftype="bed"/> 92 <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
93 <param name="inputB" value="coverageBedB.bed" ftype="bed"/> 93 <param name="reduce_or_iterate|inputB" value="coverageBedB.bed" ftype="bed"/>
94 <param name="overlap_b" value="1"/> 94 <param name="overlap_b" value="1"/>
95 <output name="output" file="coverageBed_result2_F1.bed" ftype="bed"/> 95 <output name="output" file="coverageBed_result2_F1.bed" ftype="bed"/>
96 </test> 96 </test>
97 <test> 97 <test>
98 <param name="inputA" value="coverageBedA.bed" ftype="bed"/> 98 <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
99 <param name="inputB" value="coverageBedB.bed" ftype="bed"/> 99 <param name="reduce_or_iterate|inputB" value="coverageBedB.bed" ftype="bed"/>
100 <param name="overlap_a" value="1E-5"/> 100 <param name="overlap_a" value="1E-5"/>
101 <param name="reciprocal_overlap" value="true"/> 101 <param name="reciprocal_overlap" value="true"/>
102 <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed"/> 102 <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed"/>
103 </test> 103 </test>
104 <test> 104 <test>
105 <param name="inputA" value="multiCov1.bed" ftype="bed"/> 105 <param name="inputA" value="multiCov1.bed" ftype="bed"/>
106 <param name="reduce_or_iterate_selector" value="reduce"/> 106 <param name="reduce_or_iterate|reduce_or_iterate_selector" value="reduce"/>
107 <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam"/> 107 <param name="reduce_or_iterate|inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam"/>
108 <param name="sorted" value="true"/> 108 <param name="sorted" value="true"/>
109 <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed"/> 109 <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed"/>
110 </test> 110 </test>
111 <test> 111 <test>
112 <param name="inputA" value="coverageBedA2.bed" ftype="bed"/> 112 <param name="inputA" value="coverageBedA2.bed" ftype="bed"/>
113 <param name="inputB" value="coverageBed.bam" ftype="bam"/> 113 <param name="reduce_or_iterate|inputB" value="coverageBed.bam" ftype="bam"/>
114 <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed"/> 114 <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed"/>
115 </test> 115 </test>
116 <test> 116 <test>
117 <param name="inputA" value="coverageBedA2.bed" ftype="bed"/> 117 <param name="inputA" value="coverageBedA2.bed" ftype="bed"/>
118 <param name="inputB" value="coverageBed.bam" ftype="bam"/> 118 <param name="reduce_or_iterate|inputB" value="coverageBed.bam" ftype="bam"/>
119 <param name="mean" value="true"/> 119 <param name="mean" value="true"/>
120 <output name="output" file="mean_coverage.bed" ftype="bed"/> 120 <output name="output" file="mean_coverage.bed" ftype="bed"/>
121 </test> 121 </test>
122 </tests> 122 </tests>
123 <help><![CDATA[ 123 <help><![CDATA[