Mercurial > repos > ufz > vibrant

comparison vibrant.xml @ 1:353fc14d89aa draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b
author ufz
date Mon, 12 May 2025 13:57:42 +0000
parents b238f5afa054
children
comparison
equal deleted inserted replaced
0:b238f5afa054 1:353fc14d89aa
1 <tool id="vibrant" name="VIBRANT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> 1 <tool id="vibrant" name="VIBRANT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.2.1</token> 4 <token name="@TOOL_VERSION@">1.2.1</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">VIBRANT</xref> 8 <xref type="bio.tools">VIBRANT</xref>
9 </xrefs> 9 </xrefs>
10 <requirements> 10 <requirements>
105 <filter>"phages_lytic_ffn" in outputs and not protein</filter> 105 <filter>"phages_lytic_ffn" in outputs and not protein</filter>
106 </data> 106 </data>
107 <data name="phages_lytic_fna" format="txt" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_lytic.fna" label="${tool.name} on ${on_string}: Lytic virus genomes"> 107 <data name="phages_lytic_fna" format="txt" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_lytic.fna" label="${tool.name} on ${on_string}: Lytic virus genomes">
108 <filter>"phages_lytic_fna" in outputs and not protein</filter> 108 <filter>"phages_lytic_fna" in outputs and not protein</filter>
109 </data> 109 </data>
110 <data name="AMG_counts" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_AMG_counts_input.tsv" label="${tool.name} on ${on_string}: Predicted virus AMGs"> 110 <data name="AMG_counts" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_AMG_counts_input.tsv" label="${tool.name} on ${on_string}: Predicted virus AMGs">
111 <filter>"AMG_counts" in outputs</filter> 111 <filter>"AMG_counts" in outputs</filter>
112 </data> 112 </data>
113 <data name="AMG_individuals" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_AMG_individuals_input.tsv" label="${tool.name} on ${on_string}: Individual predicted virus AMGs"> 113 <data name="AMG_individuals" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_AMG_individuals_input.tsv" label="${tool.name} on ${on_string}: Individual predicted virus AMGs">
114 <filter>"AMG_individuals" in outputs</filter> 114 <filter>"AMG_individuals" in outputs</filter>
115 </data> 115 </data>
116 <data name="AMG_pathways" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_AMG_pathways_input.tsv" label="${tool.name} on ${on_string}: KEGG metabolic pathways corresponding to virus AMGs"> 116 <data name="AMG_pathways" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_AMG_pathways_input.tsv" label="${tool.name} on ${on_string}: KEGG metabolic pathways corresponding to virus AMGs">
117 <filter>"AMG_pathways" in outputs</filter> 117 <filter>"AMG_pathways" in outputs</filter>
118 </data> 118 </data>
119 <data name="annotations" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_annotations_input.tsv" label="${tool.name} on ${on_string}: Annotations for KEGG, Pfam and VOG"> 119 <data name="annotations" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_annotations_input.tsv" label="${tool.name} on ${on_string}: Annotations for KEGG, Pfam and VOG">
120 <filter>"annotations" in outputs</filter> 120 <filter>"annotations" in outputs</filter>
121 </data> 121 </data>
122 <data name="complete_circular" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_complete_circular_input.tsv" label="${tool.name} on ${on_string}: Complete circular genomes "> 122 <data name="complete_circular" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_complete_circular_input.tsv" label="${tool.name} on ${on_string}: Complete circular genomes ">
123 <filter>"complete_circular" in outputs and not protein</filter> 123 <filter>"complete_circular" in outputs and not protein</filter>
124 </data> 124 </data>
125 <data name="figure_PCA" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_figure_PCA_input.tsv" label="${tool.name} on ${on_string}: Scaffold coordinates on the PCA plot"> 125 <data name="figure_PCA" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_figure_PCA_input.tsv" label="${tool.name} on ${on_string}: Scaffold coordinates on the PCA plot">
126 <filter>"figure_PCA" in outputs</filter> 126 <filter>"figure_PCA" in outputs</filter>
127 </data> 127 </data>
128 <data name="genbank_table" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_genbank_table_input.tsv" label="${tool.name} on ${on_string}: Single annotation used for all predicted virus proteins"> 128 <data name="genbank_table" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_genbank_table_input.tsv" label="${tool.name} on ${on_string}: Single annotation used for all predicted virus proteins">
129 <filter>"genbank_table" in outputs</filter> 129 <filter>"genbank_table" in outputs</filter>
130 </data> 130 </data>
131 <data name="genome_quality" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_genome_quality_input.tsv" label="${tool.name} on ${on_string}: Predicted genome quality and type"> 131 <data name="genome_quality" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_genome_quality_input.tsv" label="${tool.name} on ${on_string}: Predicted genome quality and type">
132 <filter>"genome_quality" in outputs</filter> 132 <filter>"genome_quality" in outputs</filter>
133 </data> 133 </data>
134 <data name="integrated_prophage_coordinates" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_integrated_prophage_coordinates_input.tsv" label="${tool.name} on ${on_string}: Coordinates of integrated provirus"> 134 <data name="integrated_prophage_coordinates" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_integrated_prophage_coordinates_input.tsv" label="${tool.name} on ${on_string}: Coordinates of integrated provirus">
135 <filter>"integrated_prophage_coordinates" in outputs</filter> 135 <filter>"integrated_prophage_coordinates" in outputs</filter>
136 </data> 136 </data>
137 <data name="machine" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_machine_input.tsv" label="${tool.name} on ${on_string}: Predictions of the neural network classifier"> 137 <data name="machine" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_machine_input.tsv" label="${tool.name} on ${on_string}: Predictions of the neural network classifier">
138 <filter>"machine" in outputs</filter> 138 <filter>"machine" in outputs</filter>
139 </data> 139 </data>
140 <data name="summary_normalized" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_summary_normalized_input.tsv" label="${tool.name} on ${on_string}: Normalized summary metrics"> 140 <data name="summary_normalized" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_summary_normalized_input.tsv" label="${tool.name} on ${on_string}: Normalized summary metrics">
141 <filter>"summary_normalized" in outputs</filter> 141 <filter>"summary_normalized" in outputs</filter>
142 </data> 142 </data>
143 <data name="summary_results" format="txt" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_summary_results_input.tsv" label="${tool.name} on ${on_string}: Summary metrics"> 143 <data name="summary_results" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_summary_results_input.tsv" label="${tool.name} on ${on_string}: Summary metrics">
144 <filter>"summary_results" in outputs</filter> 144 <filter>"summary_results" in outputs</filter>
145 </data> 145 </data>
146 <!-- files from VIBRANT_results_input. Folder containing useful tab-delimited files --> 146 <!-- files from VIBRANT_results_input. Folder containing useful tab-delimited files -->
147 <!-- 147 <!--
148 ├── input.prodigal.faa Prodigal predicted proteins for all input scaffolds. 148 ├── input.prodigal.faa Prodigal predicted proteins for all input scaffolds.