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comparison hyphy_summary.xml @ 3:5f69ffa0186d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ec5db8349483b2cd46f9da23abe6cefcf65bc714"
author iuc
date Sat, 03 Jul 2021 08:35:10 +0000
parents 541766b1795c
children e30b084e3de5
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2:541766b1795c 3:5f69ffa0186d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_summary" version="1.1.0" name="HyPhy-Summary" profile="21.01"> 2 <tool id="hyphy_summary" version="1.2.0" name="HyPhy-Summary" profile="21.01">
3 <description>generate summary report of HyPhy analyses</description> 3 <description>generate summary report of HyPhy analyses</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.19.7">python-bioext</requirement> 5 <requirement type="package" version="0.20.1">python-bioext</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/scripts/hyphy_summary.py' 8 python '$__tool_directory__/scripts/hyphy_summary.py'
9 --mode $mode_conditional.mode 9 --mode $mode_conditional.mode
10 #if $mode_conditional.mode == 'summary': 10 #if $mode_conditional.mode == 'summary':
95 <param argument="--fel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-FEL output dataset" /> 95 <param argument="--fel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-FEL output dataset" />
96 <param argument="--cfel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-CFEL output dataset" /> 96 <param argument="--cfel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-CFEL output dataset" />
97 <param argument="--bgm" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-BGM output dataset" /> 97 <param argument="--bgm" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-BGM output dataset" />
98 </when> 98 </when>
99 <when value="merge"> 99 <when value="merge">
100 <param argument="--summary-inputs" type="data" format="hyphy_results.json" multiple="true" label="Segment annotations to merge" /> 100 <param argument="--summary-inputs" type="data" format="hyphy_results.json" multiple="true" label="Summaries to merge" />
101 <param argument="--annotation-inputs" type="data" format="hyphy_results.json" multiple="true" label="Site annotations to merge" /> 101 <param argument="--annotation-inputs" type="data" format="hyphy_results.json" multiple="true" label="Annotations to merge" />
102 </when> 102 </when>
103 </conditional> 103 </conditional>
104 </inputs> 104 </inputs>
105 <outputs> 105 <outputs>
106 <data name="summary" format="hyphy_results.json" label="${tool.name} on ${on_string} - Segment annotations" /> 106 <data name="summary" format="hyphy_results.json" label="${tool.name} on ${on_string} - Summary" />
107 <data name="annotation" format="hyphy_results.json" label="${tool.name} on ${on_string} - Site annotations" /> 107 <data name="annotation" format="hyphy_results.json" label="${tool.name} on ${on_string} - Annotation" />
108 </outputs> 108 </outputs>
109 <tests> 109 <tests>
110 <test> 110 <test>
111 <param name="mode" value="summary" /> 111 <param name="mode" value="summary" />
112 <param name="name" value="epi_isl_1009769" /> 112 <param name="name" value="REFERENCE" />
113 <param name="gene" value="nsp8" /> 113 <param name="gene" value="nsp8" />
114 <param name="combined" value="summary/nsp8.combined.fas" /> 114 <param name="combined" value="summary/nsp8.combined.fas" />
115 <param name="fade" value="summary/nsp8.FADE.json" /> 115 <param name="fade" value="summary/nsp8.FADE.json" />
116 <param name="prime" value="summary/nsp8.PRIME.json" /> 116 <param name="prime" value="summary/nsp8.PRIME.json" />
117 <param name="relax" value="summary/nsp8.RELAX.json" /> 117 <param name="relax" value="summary/nsp8.RELAX.json" />
126 <output name="summary" file="summary/nsp8-segment.json" /> 126 <output name="summary" file="summary/nsp8-segment.json" />
127 <output name="annotation" file="summary/nsp8-site.json" /> 127 <output name="annotation" file="summary/nsp8-site.json" />
128 </test> 128 </test>
129 <test> 129 <test>
130 <param name="mode" value="summary" /> 130 <param name="mode" value="summary" />
131 <param name="name" value="epi_isl_1009769" /> 131 <param name="name" value="REFERENCE" />
132 <param name="gene" value="ORF6" /> 132 <param name="gene" value="ORF6" />
133 <param name="combined" value="summary/ORF6.combined.fas" /> 133 <param name="combined" value="summary/ORF6.combined.fas" />
134 <param name="fade" value="summary/ORF6.FADE.json" /> 134 <param name="fade" value="summary/ORF6.FADE.json" />
135 <param name="meme_full" value="summary/ORF6.MEME-full.json" /> 135 <param name="meme_full" value="summary/ORF6.MEME-full.json" />
136 <param name="labels" value="summary/ORF6.labels.json" /> 136 <param name="labels" value="summary/ORF6.labels.json" />
138 <output name="summary" file="summary/ORF6-segment.json" /> 138 <output name="summary" file="summary/ORF6-segment.json" />
139 <output name="annotation" file="summary/ORF6-site.json" /> 139 <output name="annotation" file="summary/ORF6-site.json" />
140 </test> 140 </test>
141 <test> 141 <test>
142 <param name="mode" value="summary" /> 142 <param name="mode" value="summary" />
143 <param name="name" value="epi_isl_1009769" /> 143 <param name="name" value="REFERENCE" />
144 <param name="gene" value="nsp7" /> 144 <param name="gene" value="nsp7" />
145 <param name="combined" value="summary/nsp7.combined.fas" /> 145 <param name="combined" value="summary/nsp7.combined.fas" />
146 <param name="fade" value="summary/nsp7.FADE.json" /> 146 <param name="fade" value="summary/nsp7.FADE.json" />
147 <param name="meme_full" value="summary/nsp7.MEME-full.json" /> 147 <param name="meme_full" value="summary/nsp7.MEME-full.json" />
148 <param name="labels" value="summary/nsp7.labels.json" /> 148 <param name="labels" value="summary/nsp7.labels.json" />