Mercurial > repos > iuc > bigwig_outlier_bed

comparison bigwig_outlier_bed.xml @ 2:61946b8bd43b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
author iuc
date Thu, 25 Jul 2024 14:38:34 +0000
parents 8377a6abb4da
children 00b3da7776a0
comparison
equal deleted inserted replaced
1:8377a6abb4da 2:61946b8bd43b
1 <tool name="Bigwig extremes to bed features" id="bigwig_outlier_bed" version="@TOOL_VERSION@" profile="22.05"> 1 <tool name="Bigwig extremes 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="@NUMPY_VERSION@">2.0.0</token>
6 <token name="@PYTHON_VERSION@">3.12.3</token> 5 <token name="@PYTHON_VERSION@">3.12.3</token>
6 <token name="@VERSION_SUFFIX@">0</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>
15 <xrefs> 15 <xrefs>
16 <xref type="bio.tools">bigtools</xref> 16 <xref type="bio.tools">bigtools</xref>
17 </xrefs> 17 </xrefs>
18 <requirements> 18 <requirements>
19 <requirement type="package" version="@PYTHON_VERSION@">python</requirement> 19 <requirement type="package" version="@PYTHON_VERSION@">python</requirement>
20 <requirement type="package" version="@NUMPY_VERSION@">numpy</requirement> 20 <requirement type="package" version="2.0.0">numpy</requirement>
21 <requirement type="package" version="@TOOL_VERSION@">pybigtools</requirement> 21 <requirement type="package" version="@TOOL_VERSION@">pybigtools</requirement>
22 </requirements> 22 </requirements>
23 <required_files> 23 <required_files>
24 <include path="bigwig_outlier_bed.py"/> 24 <include path="bigwig_outlier_bed.py"/>
25 </required_files> 25 </required_files>
48 --qhi '$qhi' 48 --qhi '$qhi'
49 #end if 49 #end if
50 #if $qlo: 50 #if $qlo:
51 --qlo '$qlo' 51 --qlo '$qlo'
52 #end if 52 #end if
53 #if $tableout == "create": 53 #if $tableout == "create" or $outbeds == "outtab":
54 --tableoutfile '$tableoutfile' 54 --tableoutfile '$tableoutfile'
55 #end if 55 #end if
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>
72 <option value="outtab">NO bed outputs. Report bigwig value distribution only</option>
70 </param> 73 </param>
71 <param name="tableout" type="select" label="Write a table showing contig statistics for each bigwig input" help=""> 74 <param name="tableout" type="select" label="Write a table showing contig statistics for each bigwig input" help="">
72 <option value="donotmake">Do not create this report</option> 75 <option value="donotmake">Do not create this report</option>
73 <option value="create" selected="true">Create this report</option> 76 <option value="create" selected="true">Create this report</option>
74 </param> 77 </param>
75 </inputs> 78 </inputs>
76 <outputs> 79 <outputs>
77 <data name="bedouthilo" format="bed" label="High_and_low_bed" hidden="false"> 80 <data name="bedouthilo" format="bed" label="High_and_low_bed">
78 <filter>outbeds in ["outall", "outhilo"]</filter> 81 <filter>outbeds in ["outall", "outhilo"]</filter>
79 </data> 82 </data>
80 <data name="bedouthi" format="bed" label="High bed" hidden="false"> 83 <data name="bedouthi" format="bed" label="High bed">
81 <filter>outbeds in ["outall", "outlohi", "outhi"]</filter> 84 <filter>outbeds in ["outall", "outlohi", "outhi"]</filter>
82 </data> 85 </data>
83 <data name="bedoutlo" format="bed" label="Low bed" hidden="false"> 86 <data name="bedoutlo" format="bed" label="Low bed">
84 <filter>outbeds in ["outall", "outlohi", "outlo"]</filter> 87 <filter>outbeds in ["outall", "outlohi", "outlo"]</filter>
85 </data> 88 </data>
86 <data name="tableoutfile" format="tabular" label="Contig statistics" hidden="false"> 89 <data name="tableoutfile" format="txt" label="Contig statistics">
87 <filter>tableout == "create"</filter> 90 <filter>tableout == "create" or outbeds == "outtab"</filter>
88 </data> 91 </data>
89 </outputs> 92 </outputs>
90 <tests> 93 <tests>
91 <test expect_num_outputs="1"> 94 <test expect_num_outputs="1">
92 <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/> 95 <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/>
94 <param name="bigwig" value="bigwig_sample"/> 97 <param name="bigwig" value="bigwig_sample"/>
95 <param name="minwin" value="10"/> 98 <param name="minwin" value="10"/>
96 <param name="qhi" value="0.99"/> 99 <param name="qhi" value="0.99"/>
97 <param name="qlo" value="0.01"/> 100 <param name="qlo" value="0.01"/>
98 <param name="tableout" value="donotmake"/> 101 <param name="tableout" value="donotmake"/>
102 </test>
103 <test expect_num_outputs="1">
104 <output name="tableoutfile" value="table_only_sample" compare="diff" lines_diff="0"/>
105 <param name="outbeds" value="outtab"/>
106 <param name="bigwig" value="bigwig_sample,1.bigwig"/>
107 <param name="minwin" value="10"/>
108 <param name="qhi" value="0.99"/>
109 <param name="qlo" value="0.01"/>
110 <param name="tableout" value="create"/>
99 </test> 111 </test>
100 <test expect_num_outputs="2"> 112 <test expect_num_outputs="2">
101 <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/> 113 <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/>
102 <output name="tableoutfile" value="table_sample" compare="diff" lines_diff="0"/> 114 <output name="tableoutfile" value="table_sample" compare="diff" lines_diff="0"/>
103 <param name="outbeds" value="outhilo"/> 115 <param name="outbeds" value="outhilo"/>