Mercurial > repos > iuc > bigwig_outlier_bed

comparison bigwig_outlier_bed.xml @ 3:00b3da7776a0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 06c54e8066ecbc6292167e7c5bdfb8af945a41ba
author iuc
date Sun, 15 Sep 2024 17:08:45 +0000
parents 61946b8bd43b
children 2488bcddaf14
comparison
equal deleted inserted replaced
2:61946b8bd43b 3:00b3da7776a0
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 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="@PYTHON_VERSION@">3.12.3</token> 5 <token name="@PYTHON_VERSION@">3.12.3</token>
6 <token name="@VERSION_SUFFIX@">0</token> 6 <token name="@VERSION_SUFFIX@">1</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>
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>
26 <version_command><![CDATA[python -c "import pybigtools; from importlib.metadata import version; print(version('pybigtools'))"]]></version_command> 26 <version_command><![CDATA[python -c "import pybigtools; from importlib.metadata import version; print(version('pybigtools'))"]]></version_command>
27 <command><![CDATA[python '${__tool_directory__}/bigwig_outlier_bed.py' 27 <command><![CDATA[python '${__tool_directory__}/bigwig_outlier_bed.py'
28 --bigwig 28 #set bwns = [x.name for x in $bigwig]
29 #for bw in $bigwig: 29 #set bwfs = [x for x in $bigwig]
30 '$bw' 30 #for $bwf in $bwfs:
31 --bigwig '$bwf'
31 #end for 32 #end for
32 --bigwiglabels 33 #for $bwn in $bwns:
33 #for bw in $bigwig: 34 --bigwiglabels '$bwn'
34 '$bw.name'
35 #end for 35 #end for
36 --outbeds '$outbeds' 36 --outbeds '$outbeds'
37 #if $outbeds in ['outhilo', 'outall']: 37 #if $outbeds in ['outhilo', 'outall']:
38 --bedouthilo '$bedouthilo' 38 --bedouthilo '$bedouthilo'
39 #end if 39 #end if
92 </outputs> 92 </outputs>
93 <tests> 93 <tests>
94 <test expect_num_outputs="1"> 94 <test expect_num_outputs="1">
95 <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/> 95 <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/>
96 <param name="outbeds" value="outhilo"/> 96 <param name="outbeds" value="outhilo"/>
97 <param name="bigwig" value="bigwig_sample"/> 97 <param name="bigwig" value="fake.bigwig"/>
98 <param name="minwin" value="10"/> 98 <param name="minwin" value="10"/>
99 <param name="qhi" value="0.99"/> 99 <param name="qhi" value="0.6"/>
100 <param name="qlo" value="0.01"/> 100 <param name="qlo" value="0.01"/>
101 <param name="tableout" value="donotmake"/> 101 <param name="tableout" value="donotmake"/>
102 </test> 102 </test>
103 <test expect_num_outputs="1"> 103 <test expect_num_outputs="1">
104 <output name="tableoutfile" value="table_only_sample" compare="diff" lines_diff="0"/> 104 <output name="tableoutfile" value="table_only_sample" compare="diff" lines_diff="0"/>
105 <param name="outbeds" value="outtab"/> 105 <param name="outbeds" value="outtab"/>
106 <param name="bigwig" value="bigwig_sample,1.bigwig"/> 106 <param name="bigwig" value="fake.bigwig"/>
107 <param name="minwin" value="10"/> 107 <param name="minwin" value="10"/>
108 <param name="qhi" value="0.99"/> 108 <param name="qhi" value="0.7"/>
109 <param name="qlo" value="0.01"/> 109 <param name="qlo" value="0.3"/>
110 <param name="tableout" value="create"/> 110 <param name="tableout" value="create"/>
111 </test> 111 </test>
112 <test expect_num_outputs="2"> 112 <test expect_num_outputs="2">
113 <output name="bedouthilo" value="bedouthilo_sample" compare="diff" lines_diff="0"/> 113 <output name="bedouthilo" value="bedouthilo_sample_2" compare="diff" lines_diff="0"/>
114 <output name="tableoutfile" value="table_sample" compare="diff" lines_diff="0"/> 114 <output name="tableoutfile" value="table_sample" compare="diff" lines_diff="0"/>
115 <param name="outbeds" value="outhilo"/> 115 <param name="outbeds" value="outhilo"/>
116 <param name="bigwig" value="bigwig_sample"/> 116 <param name="bigwig" value="bigwig_sample"/>
117 <param name="minwin" value="10"/> 117 <param name="minwin" value="10"/>
118 <param name="qhi" value="0.99"/> 118 <param name="qhi" value="0.7"/>
119 <param name="qlo" value="0.01"/> 119 <param name="qlo" value="0.3"/>
120 <param name="tableout" value="create"/> 120 <param name="tableout" value="create"/>
121 </test> 121 </test>
122 <test expect_num_outputs="2"> 122 <test expect_num_outputs="2">
123 <output name="bedouthi" value="bedouthi_qlo_notset_sample" compare="diff" lines_diff="0"/> 123 <output name="bedouthi" value="bedouthi_qlo_notset_sample" compare="diff" lines_diff="0"/>
124 <output name="tableoutfile" value="table_qlo_notset_sample" compare="diff" lines_diff="0"/> 124 <output name="tableoutfile" value="table_qlo_notset_sample" compare="diff" lines_diff="0"/>
125 <param name="outbeds" value="outhi"/> 125 <param name="outbeds" value="outhi"/>
126 <param name="bigwig" value="bigwig_sample"/> 126 <param name="bigwig" value="bigwig_sample"/>
127 <param name="minwin" value="10"/> 127 <param name="minwin" value="10"/>
128 <param name="qhi" value="0.99"/> 128 <param name="qhi" value="0.69"/>
129 <param name="qlo" value=""/> 129 <param name="qlo" value=""/>
130 <param name="tableout" value="create"/> 130 <param name="tableout" value="create"/>
131 </test> 131 </test>
132 <test expect_num_outputs="3"> 132 <test expect_num_outputs="3">
133 <output name="bedouthi" value="bedouthi_sample" compare="diff" lines_diff="0"/> 133 <output name="bedouthi" value="bedouthi_sample" compare="diff" lines_diff="0"/>
134 <output name="bedoutlo" value="bedoutlo_sample" compare="diff" lines_diff="0"/> 134 <output name="bedoutlo" value="bedoutlo_sample" compare="diff" lines_diff="0"/>
135 <output name="tableoutfile" value="table3_sample" compare="diff" lines_diff="0"/> 135 <output name="tableoutfile" value="table3_sample" compare="diff" lines_diff="0"/>
136 <param name="outbeds" value="outlohi"/> 136 <param name="outbeds" value="outlohi"/>
137 <param name="bigwig" value="bigwig_sample"/> 137 <param name="bigwig" value="fake.bigwig"/>
138 <param name="minwin" value="1"/> 138 <param name="minwin" value="10"/>
139 <param name="qhi" value="0.9"/> 139 <param name="qhi" value="0.5"/>
140 <param name="qlo" value="0.1"/> 140 <param name="qlo" value="0.5"/>
141 <param name="tableout" value="create"/> 141 <param name="tableout" value="create"/>
142 </test> 142 </test>
143 <test expect_num_outputs="4"> 143 <test expect_num_outputs="2">
144 <output name="bedouthilo" value="bedouthilo2_sample" compare="diff" lines_diff="0"/>
145 <output name="bedoutlo" value="bedoutlo2_sample" compare="diff" lines_diff="0"/>
146 <output name="bedouthi" value="bedouthi2_sample" compare="diff" lines_diff="0"/> 144 <output name="bedouthi" value="bedouthi2_sample" compare="diff" lines_diff="0"/>
147 <output name="tableoutfile" value="table2_sample" compare="diff" lines_diff="0"/> 145 <output name="tableoutfile" value="table2_sample" compare="diff" lines_diff="0"/>
148 <param name="outbeds" value="outall"/> 146 <param name="outbeds" value="outhi"/>
149 <param name="bigwig" value="bigwig_sample,1.bigwig"/> 147 <param name="bigwig" value="fake.bigwig,bigwig_sample"/>
150 <param name="minwin" value="1"/> 148 <param name="minwin" value="10"/>
151 <param name="qhi" value="0.9"/> 149 <param name="qhi" value="0.5"/>
152 <param name="qlo" value="0.1"/> 150 <param name="qlo" value="0.5"/>
153 <param name="tableout" value="create"/> 151 <param name="tableout" value="create"/>
154 </test> 152 </test>
153
154
155
155 </tests> 156 </tests>
156 <help><![CDATA[ 157 <help><![CDATA[
157 158
158 **Purpose** 159 **Purpose**
159 160