Mercurial > repos > iuc > bigwig_outlier_bed

comparison bigwig_outlier_bed.xml @ 4:2488bcddaf14 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
author iuc
date Mon, 30 Sep 2024 01:42:34 +0000
parents 00b3da7776a0
children
comparison
equal deleted inserted replaced
3:00b3da7776a0 4:2488bcddaf14
1 <tool name="Bigwig extremes to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> 1 <tool name="Bigwig outliers to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
2 <description>Writes high and low bigwig runs as features in a bed file</description> 2 <description>Writes high and low bigwig runs as features in a bed file</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.2.0</token> 4 <token name="@TOOL_VERSION@">0.2.0</token>
5 <token name="@PYTHON_VERSION@">3.12.3</token> 5 <token name="@PYTHON_VERSION@">3.12.3</token>
6 <token name="@VERSION_SUFFIX@">1</token> 6 <token name="@VERSION_SUFFIX@">2</token>
7 </macros> 7 </macros>
8 <edam_topics> 8 <edam_topics>
9 <edam_topic>topic_0157</edam_topic> 9 <edam_topic>topic_0157</edam_topic>
10 <edam_topic>topic_0092</edam_topic> 10 <edam_topic>topic_0092</edam_topic>
11 </edam_topics> 11 </edam_topics>
41 --bedouthi '$bedouthi' 41 --bedouthi '$bedouthi'
42 #end if 42 #end if
43 #if $outbeds in ['outlo', 'outall', 'outlohi']: 43 #if $outbeds in ['outlo', 'outall', 'outlohi']:
44 --bedoutlo '$bedoutlo' 44 --bedoutlo '$bedoutlo'
45 #end if 45 #end if
46 #if $outbeds in ['outzero']:
47 --bedoutzero '$bedoutzero'
48 #end if
46 --minwin '$minwin' 49 --minwin '$minwin'
47 #if $qhi: 50 #if $qhi:
48 --qhi '$qhi' 51 --qhi '$qhi'
49 #end if 52 #end if
50 #if $qlo: 53 #if $qlo:
65 <param name="outbeds" type="select" label="Select the required bed file outputs or none for a bigwig value distribution report" 68 <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"> 69 help="Any combination of the 3 different kinds of bed file output can be made">
67 <option value="outhilo" selected="true">Make 1 bed output with both low and high regions</option> 70 <option value="outhilo" selected="true">Make 1 bed output with both low and high regions</option>
68 <option value="outhi">Make 1 bed output with high regions only</option> 71 <option value="outhi">Make 1 bed output with high regions only</option>
69 <option value="outlo">Make 1 bed output with low regions only</option> 72 <option value="outlo">Make 1 bed output with low regions only</option>
73 <option value="outzero">Make 1 bed output for regions with contiguous zero values only</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> 74 <option value="outall">Make 3 bed outputs with low and high together in one, 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> 75 <option value="outlohi">Make 2 bed outputs with high in one and low in the other</option>
72 <option value="outtab">NO bed outputs. Report bigwig value distribution only</option> 76 <option value="outtab">NO bed outputs. Report bigwig value distribution table only</option>
73 </param> 77 </param>
74 <param name="tableout" type="select" label="Write a table showing contig statistics for each bigwig input" help=""> 78 <param name="tableout" type="select" label="Write a table showing contig statistics for each bigwig input" help="">
75 <option value="donotmake">Do not create this report</option> 79 <option value="donotmake">Do not create this report</option>
76 <option value="create" selected="true">Create this report</option> 80 <option value="create" selected="true">Create this report</option>
77 </param> 81 </param>
84 <filter>outbeds in ["outall", "outlohi", "outhi"]</filter> 88 <filter>outbeds in ["outall", "outlohi", "outhi"]</filter>
85 </data> 89 </data>
86 <data name="bedoutlo" format="bed" label="Low bed"> 90 <data name="bedoutlo" format="bed" label="Low bed">
87 <filter>outbeds in ["outall", "outlohi", "outlo"]</filter> 91 <filter>outbeds in ["outall", "outlohi", "outlo"]</filter>
88 </data> 92 </data>
93 <data name="bedoutzero" format="bed" label="Zeros only bed">
94 <filter>outbeds in ["outzero"]</filter>
95 </data>
89 <data name="tableoutfile" format="txt" label="Contig statistics"> 96 <data name="tableoutfile" format="txt" label="Contig statistics">
90 <filter>tableout == "create" or outbeds == "outtab"</filter> 97 <filter>tableout == "create" or outbeds == "outtab"</filter>
91 </data> 98 </data>
92 </outputs> 99 </outputs>
93 <tests> 100 <tests>
148 <param name="minwin" value="10"/> 155 <param name="minwin" value="10"/>
149 <param name="qhi" value="0.5"/> 156 <param name="qhi" value="0.5"/>
150 <param name="qlo" value="0.5"/> 157 <param name="qlo" value="0.5"/>
151 <param name="tableout" value="create"/> 158 <param name="tableout" value="create"/>
152 </test> 159 </test>
153 160 <test expect_num_outputs="1">
154 161 <output name="bedoutzero" value="bedoutzero_sample" compare="diff" lines_diff="0"/>
155 162 <param name="outbeds" value="outzero"/>
163 <param name="bigwig" value="fake.bigwig,bigwig_sample"/>
164 <param name="minwin" value="2"/>
165 <param name="qhi" value="0.5"/>
166 <param name="qlo" value="0.5"/>
167 <param name="tableout" value="donotmake"/>
168 </test>
156 </tests> 169 </tests>
157 <help><![CDATA[ 170 <help><![CDATA[
158 171
159 **Purpose** 172 **Purpose**
160 173