Mercurial > repos > fubar > bigwig_outlier_bed
comparison bigwig_outlier_bed.xml @ 8:032e930ef6a1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 7eac2f224d3126002edd2c02d1133b23ac1a4881
| author | fubar |
|---|---|
| date | Wed, 24 Jul 2024 09:19:08 +0000 |
| parents | c8e22efcaeda |
| children |
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| 7:c8e22efcaeda | 8:032e930ef6a1 |
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| 56 ]]></command> | 56 ]]></command> |
| 57 <inputs> | 57 <inputs> |
| 58 <param name="bigwig" type="data" optional="false" label="Choose one or more bigwig file(s) to return outlier regions as a bed file" | 58 <param name="bigwig" type="data" optional="false" label="Choose one or more bigwig file(s) to return outlier regions as a bed file" |
| 59 help="If more than one, MUST all use the same reference sequence to be displayable. Feature names will include the bigwig label." format="bigwig" multiple="true"/> | 59 help="If more than one, MUST all use the same reference sequence to be displayable. Feature names will include the bigwig label." format="bigwig" multiple="true"/> |
| 60 <param name="minwin" type="integer" value="10" label="Minimum continuous bases to count as a high or low bed feature" | 60 <param name="minwin" type="integer" value="10" label="Minimum continuous bases to count as a high or low bed feature" |
| 61 help="Continuous features as long or longer than this window size will appear as bed features"/> | 61 help="Minimum continuous length to count as a bed feature. If windowed bigwig, must be bigger than window size to have any effect"/> |
| 62 <param name="qhi" type="float" value="0.99" label="Quantile cutoff for a high region - 0.99 will cut off at or above the 99th percentile" help="Required" optional="false"/> | 62 <param name="qhi" type="float" value="0.99999" label="Quantile cutoff for a high region - 0.99999 will cut off at about 1 in 100,000" |
| 63 <param name="qlo" type="float" value="0.01" label="Quantile cutoff for a low region - 0.01 will cut off at or below the 1st percentile." help="Optional" optional="true"/> | 63 help="1 per 100k might be a few thousand features in a 200M chromosome - depends on the distribution - see the table output" optional="false"/> |
| 64 <param name="outbeds" type="select" label="Select the required bed file outputs" help="Any combination of the 3 different kinds of bed file output can be made"> | 64 <param name="qlo" type="float" value="0.00001" label="Quantile cutoff for a low region - 0.01 will cut off at or below the 1st percentile." help="Optional" optional="true"/> |
| 65 <param name="outbeds" type="select" label="Select the required bed file outputs or none for a bigwig value distribution report" | |
| 66 help="Any combination of the 3 different kinds of bed file output can be made"> | |
| 65 <option value="outhilo" selected="true">Make 1 bed output with both low and high regions</option> | 67 <option value="outhilo" selected="true">Make 1 bed output with both low and high regions</option> |
| 66 <option value="outhi">Make 1 bed output with high regions only</option> | 68 <option value="outhi">Make 1 bed output with high regions only</option> |
| 67 <option value="outlo">Make 1 bed output with low regions only</option> | 69 <option value="outlo">Make 1 bed output with low regions only</option> |
| 68 <option value="outall">Make 3 bed outputs with low and high together in one, high in one and low in the other</option> | 70 <option value="outall">Make 3 bed outputs with low and high together in one, high in one and low in the other</option> |
| 69 <option value="outlohi">Make 2 bed outputs with high in one and low in the other</option> | 71 <option value="outlohi">Make 2 bed outputs with high in one and low in the other</option> |
| 73 <option value="donotmake">Do not create this report</option> | 75 <option value="donotmake">Do not create this report</option> |
| 74 <option value="create" selected="true">Create this report</option> | 76 <option value="create" selected="true">Create this report</option> |
| 75 </param> | 77 </param> |
| 76 </inputs> | 78 </inputs> |
| 77 <outputs> | 79 <outputs> |
| 78 <data name="bedouthilo" format="bed" label="High_and_low_bed" hidden="false"> | 80 <data name="bedouthilo" format="bed" label="High_and_low_bed"> |
| 79 <filter>outbeds in ["outall", "outhilo"]</filter> | 81 <filter>outbeds in ["outall", "outhilo"]</filter> |
| 80 </data> | 82 </data> |
| 81 <data name="bedouthi" format="bed" label="High bed" hidden="false"> | 83 <data name="bedouthi" format="bed" label="High bed"> |
| 82 <filter>outbeds in ["outall", "outlohi", "outhi"]</filter> | 84 <filter>outbeds in ["outall", "outlohi", "outhi"]</filter> |
| 83 </data> | 85 </data> |
| 84 <data name="bedoutlo" format="bed" label="Low bed" hidden="false"> | 86 <data name="bedoutlo" format="bed" label="Low bed"> |
| 85 <filter>outbeds in ["outall", "outlohi", "outlo"]</filter> | 87 <filter>outbeds in ["outall", "outlohi", "outlo"]</filter> |
| 86 </data> | 88 </data> |
| 87 <data name="tableoutfile" format="txt" label="Contig statistics" hidden="false"> | 89 <data name="tableoutfile" format="txt" label="Contig statistics"> |
| 88 <filter>tableout == "create"</filter> | 90 <filter>tableout == "create" or outbeds == "outtab"</filter> |
| 89 </data> | 91 </data> |
| 90 </outputs> | 92 </outputs> |
| 91 <tests> | 93 <tests> |
| 92 <test expect_num_outputs="1"> | 94 <test expect_num_outputs="1"> |
| 93 <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/> | 95 <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/> |