Mercurial > repos > iuc > hyphy_annotate

comparison hyphy_annotate.xml @ 15:2dbd8f857b5f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy commit 00107ff4b116892cd55d7aa5bfd1ee1855d511af
author iuc
date Wed, 25 Feb 2026 20:59:24 +0000
parents dd0deea7ac09
children
comparison
equal deleted inserted replaced
14:dd0deea7ac09 15:2dbd8f857b5f
14 #else: 14 #else:
15 --list '$selection_method.list_file' 15 --list '$selection_method.list_file'
16 #end if 16 #end if
17 --label '$label' 17 --label '$label'
18 --reroot '$reroot' 18 --reroot '$reroot'
19 '$invert' 19 $invert
20 --internal-nodes '$internal_nodes' 20 --internal-nodes '$internal_nodes'
21 --leaf-nodes '$leaf_nodes' 21 --leaf-nodes '$leaf_nodes'
22 > annotate_stdout.md 2>/dev/null 22 > annotate_stdout.md 2>/dev/null
23 @ERRORS@ 23 @ERRORS@
24 ]]></command> 24 ]]></command>
64 <param name="method" value="regexp"/> 64 <param name="method" value="regexp"/>
65 <param name="regexp" value="_USA_"/> 65 <param name="regexp" value="_USA_"/>
66 </conditional> 66 </conditional>
67 <param name="label" value="Annotated"/> 67 <param name="label" value="Annotated"/>
68 <param name="reroot" value="None"/> 68 <param name="reroot" value="None"/>
69 <param name="invert" value="No"/> 69 <param name="invert" value="false"/>
70 <param name="internal_nodes" value="All descendants"/> 70 <param name="internal_nodes" value="All descendants"/>
71 <param name="leaf_nodes" value="Label"/> 71 <param name="leaf_nodes" value="Label"/>
72 <output name="labeled_tree"> 72 <output name="labeled_tree">
73 <assert_contents> 73 <assert_contents>
74 <has_text text="{Annotated}"/> 74 <has_text text="{Annotated}"/>
89 <param name="method" value="list"/> 89 <param name="method" value="list"/>
90 <param name="list_file" ftype="txt" value="annotate-list1.txt"/> 90 <param name="list_file" ftype="txt" value="annotate-list1.txt"/>
91 </conditional> 91 </conditional>
92 <param name="label" value="Annotated"/> 92 <param name="label" value="Annotated"/>
93 <param name="reroot" value="None"/> 93 <param name="reroot" value="None"/>
94 <param name="invert" value="No"/> 94 <param name="invert" value="false"/>
95 <param name="internal_nodes" value="All descendants"/> 95 <param name="internal_nodes" value="All descendants"/>
96 <param name="leaf_nodes" value="Label"/> 96 <param name="leaf_nodes" value="Label"/>
97 <output name="labeled_tree"> 97 <output name="labeled_tree">
98 <assert_contents> 98 <assert_contents>
99 <has_text text="{Annotated}"/> 99 <has_text text="{Annotated}"/>
100 <has_text text="gb_MW540268"/> 100 <has_text text="gb_MW540268"/>
101 <not_has_text text="REFERENCE{Annotated}"/> 101 <not_has_text text="REFERENCE{Annotated}"/>
102 </assert_contents>
103 </output>
104 <output name="annotate_md_report">
105 <assert_contents>
106 <has_text text="Analysis Description"/>
107 </assert_contents>
108 </output>
109 </test>
110 <test expect_num_outputs="2">
111 <param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/>
112 <conditional name="selection_method">
113 <param name="method" value="regexp"/>
114 <param name="regexp" value="_USA_"/>
115 </conditional>
116 <param name="label" value="Annotated"/>
117 <param name="reroot" value="None"/>
118 <param name="invert" value="true"/>
119 <param name="internal_nodes" value="All descendants"/>
120 <param name="leaf_nodes" value="Label"/>
121 <output name="labeled_tree">
122 <assert_contents>
123 <has_text text="{Annotated}"/>
124 <not_has_text text="gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA{Annotated}"/>
125 <has_text text="REFERENCE{Annotated}"/>
126 <has_text text="gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND"/>
102 </assert_contents> 127 </assert_contents>
103 </output> 128 </output>
104 <output name="annotate_md_report"> 129 <output name="annotate_md_report">
105 <assert_contents> 130 <assert_contents>
106 <has_text text="Analysis Description"/> 131 <has_text text="Analysis Description"/>