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comparison idr.xml @ 1:de7795890bc5 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ commit 29f0ab9141fd270da200f3daa4c43b80ba9cf3c4"
author iuc
date Mon, 23 Nov 2020 22:51:17 +0000
parents d3ebbf39b1c5
children
comparison
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0:d3ebbf39b1c5 1:de7795890bc5
93 <param name="primus" value="idr_input1.1.bed" ftype="bed" /> 93 <param name="primus" value="idr_input1.1.bed" ftype="bed" />
94 <param name="secundus" value="idr_input1.2.bed" ftype="bed" /> 94 <param name="secundus" value="idr_input1.2.bed" ftype="bed" />
95 <param name="rank" value="default" /> 95 <param name="rank" value="default" />
96 <param name="plot" value="True" /> 96 <param name="plot" value="True" />
97 <output name="idr_values" file="idr_out1.bed" ftype="bed" /> 97 <output name="idr_values" file="idr_out1.bed" ftype="bed" />
98 <output name="idr_plot" file="idr_out1.png" ftype="png" /> 98 <output name="idr_plot" file="idr_out1.png" ftype="png" compare="sim_size" delta="1000"/>
99 </test> 99 </test>
100 <test> 100 <test>
101 <param name="primus" value="idr_input2.1.bed" ftype="bed" /> 101 <param name="primus" value="idr_input2.1.bed" ftype="bed" />
102 <param name="secundus" value="idr_input2.2.bed" ftype="bed" /> 102 <param name="secundus" value="idr_input2.2.bed" ftype="bed" />
103 <param name="rank" value="default" /> 103 <param name="rank" value="default" />
104 <param name="plot" value="True" /> 104 <param name="plot" value="True" />
105 <output name="idr_values" file="idr_out2.bed" ftype="bed" /> 105 <output name="idr_values" file="idr_out2.bed" ftype="bed" />
106 <output name="idr_plot" file="idr_out2.png" ftype="png" /> 106 <output name="idr_plot" file="idr_out2.png" ftype="png" compare="sim_size" delta="1000"/>
107 </test> 107 </test>
108 <test> 108 <test>
109 <param name="primus" value="idr_input3.1.bed" ftype="bed" /> 109 <param name="primus" value="idr_input3.1.bed" ftype="bed" />
110 <param name="secundus" value="idr_input3.2.bed" ftype="bed" /> 110 <param name="secundus" value="idr_input3.2.bed" ftype="bed" />
111 <param name="peak_list" value="idr_input3.3.bed" ftype="bed" /> 111 <param name="peak_list" value="idr_input3.3.bed" ftype="bed" />
112 <param name="rank" value="default" /> 112 <param name="rank" value="default" />
113 <param name="plot" value="True" /> 113 <param name="plot" value="True" />
114 <output name="idr_values" file="idr_out3.bed" ftype="bed" /> 114 <output name="idr_values" file="idr_out3.bed" ftype="bed" />
115 <output name="idr_plot" file="idr_out3.png" ftype="png" /> 115 <output name="idr_plot" file="idr_out3.png" ftype="png" compare="sim_size" delta="1000"/>
116 </test> 116 </test>
117 <test> 117 <test>
118 <param name="primus" value="idr_input4.1.gff" ftype="gff" /> 118 <param name="primus" value="idr_input4.1.gff" ftype="gff" />
119 <param name="secundus" value="idr_input4.2.gff" ftype="gff" /> 119 <param name="secundus" value="idr_input4.2.gff" ftype="gff" />
120 <param name="input_file_type" value="gff" /> 120 <param name="input_file_type" value="gff" />
121 <param name="rank" value="default" /> 121 <param name="rank" value="default" />
122 <param name="plot" value="True" /> 122 <param name="plot" value="True" />
123 <output name="idr_values" file="idr_out4.gff" ftype="gff" /> 123 <output name="idr_values" file="idr_out4.gff" ftype="gff" />
124 <output name="idr_plot" file="idr_out4.png" ftype="png" /> 124 <output name="idr_plot" file="idr_out4.png" ftype="png" compare="sim_size" delta="1000"/>
125 </test> 125 </test>
126 </tests> 126 </tests>
127 <help> 127 <help>
128 <![CDATA[ 128 <![CDATA[
129 The `IDR <https://github.com/nboley/idr/blob/master/README.md>`__ (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. Unlike the usual scalar measures of reproducibility, the IDR approach creates a curve, which quantitatively assesses when the findings are no longer consistent across replicates. 129 The `IDR <https://github.com/nboley/idr/blob/master/README.md>`__ (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. Unlike the usual scalar measures of reproducibility, the IDR approach creates a curve, which quantitatively assesses when the findings are no longer consistent across replicates.
130 ]]> 130 ]]>
131 </help> 131 </help>
132 <citations> 132 <citations>
133 <citation type="doi">10.1214/11-AOAS466</citation> 133 <citation type="doi">10.1214/11-AOAS466</citation>
134 </citations> 134 </citations>