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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla commit ce081671d5ad816158825b089a0e62682f5f7963
author iuc
date Tue, 27 Feb 2024 10:34:27 +0000
parents ca3ec50bfd94
children
comparison
equal deleted inserted replaced
0:ca3ec50bfd94 1:8badcbe5792c
1 <tool id="peakzilla" name="Peakzilla" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="peakzilla" name="Peakzilla" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Identify transcription factor binding sites from ChIP-seq and ChIP-exo experiments</description> 2 <description>Identify transcription factor binding sites from ChIP-seq and ChIP-exo experiments</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.0</token> 4 <token name="@TOOL_VERSION@">1.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="2.7">python</requirement> 8 <requirement type="package" version="2.7">python</requirement>
9 <requirement type="package" version="@TOOL_VERSION@">peakzilla</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">peakzilla</requirement>
10 </requirements> 10 </requirements>
61 </section> 61 </section>
62 </inputs> 62 </inputs>
63 <outputs> 63 <outputs>
64 <data name="results" format="tabular" label="${tool.name} on ${on_string}"/> 64 <data name="results" format="tabular" label="${tool.name} on ${on_string}"/>
65 <data name="log" format="txt" from_work_dir="log.txt" label="Log file for ${tool.name} on ${on_string}"> 65 <data name="log" format="txt" from_work_dir="log.txt" label="Log file for ${tool.name} on ${on_string}">
66 <filter>log</filter> 66 <filter>outputs["log"]</filter>
67 </data> 67 </data>
68 <data name="negative_peaks" format="tabular" from_work_dir="negative_peaks.tsv" label="Negative peaks for ${tool.name} on ${on_string}"> 68 <data name="negative_peaks" format="tabular" from_work_dir="negative_peaks.tsv" label="Negative peaks for ${tool.name} on ${on_string}">
69 <filter>negative</filter> 69 <filter>outputs["negative"]</filter>
70 </data> 70 </data>
71 </outputs> 71 </outputs>
72 <tests> 72 <tests>
73 <test expect_num_outputs="1">
74 <param name="chip_bed" value="chip.bed" />
75 <param name="input_bed" value="input.bed" />
76 <output name="results" file="results_1.tsv">
77 <assert_contents>
78 <has_text text="Peak_1" />
79 </assert_contents>
80 </output>
81 </test>
73 <test expect_num_outputs="3"> 82 <test expect_num_outputs="3">
74 <param name="chip_bed" value="chip.bed" /> 83 <param name="chip_bed" value="chip.bed" />
75 <param name="input_bed" value="input.bed" /> 84 <param name="input_bed" value="input.bed" />
76 <param name="model_peaks" value="200" /> 85 <param name="model_peaks" value="200" />
77 <param name="fragment_size" value="50" /> 86 <param name="fragment_size" value="50" />
78 <param name="enrichment_cutoff" value="2" /> 87 <param name="enrichment_cutoff" value="2" />
79 <param name="score_cutoff" value="1" /> 88 <param name="score_cutoff" value="1" />
80 <param name="log" value="true" /> 89 <param name="log" value="true" />
81 <param name="negative" value="true" /> 90 <param name="negative" value="true" />
82 <output name="results" file="results.tsv"> 91 <output name="results" file="results_2.tsv">
83 <assert_contents> 92 <assert_contents>
84 <has_text text="Peak_1" /> 93 <has_text text="Peak_1" />
85 </assert_contents> 94 </assert_contents>
86 </output> 95 </output>
87 <output name="log" file="log.txt" lines_diff="30"> 96 <output name="log" file="log.txt" lines_diff="30">