Mercurial > repos > iuc > gtdbtk_classify_wf

comparison gtdbtk_classify_wf.xml @ 4:65d52c693b8e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 94a1996b09d7597793f823307cbac6208e20f1d1
author iuc
date Fri, 01 Mar 2024 07:19:45 +0000
parents f8f56dd6449f
children a68b985913ab
comparison
equal deleted inserted replaced
3:f8f56dd6449f 4:65d52c693b8e
69 <tests> 69 <tests>
70 <!-- The commented test here is valid if we could store the GTDB-Tk database --> 70 <!-- The commented test here is valid if we could store the GTDB-Tk database -->
71 <!-- 71 <!--
72 <test expect_num_outputs="4"> 72 <test expect_num_outputs="4">
73 <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/> 73 <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
74 <param name="gtdbtk_db" value="gtdbtk202"/> 74 <param name="gtdbtk_db" value="gtdbtk214"/>
75 <output_collection name="output_summary" type="list" count="1"> 75 <output_collection name="output_summary" type="list" count="1">
76 <element name="gtdbtk.ar122.summary" ftype="tsv"> 76 <element name="gtdbtk.ar53.summary" ftype="tsv">
77 <assert_contents> 77 <assert_contents>
78 <has_text text="user_genome"/> 78 <has_text text="user_genome"/>
79 </assert_contents> 79 </assert_contents>
80 </element> 80 </element>
81 </output_collection> 81 </output_collection>
82 <output_collection name="output_identfy" type="list" count="4"> 82 <output_collection name="output_identfy" type="list" count="4">
83 <element name="gtdbtk.ar122.markers_summary" ftype="tsv"> 83 <element name="gtdbtk.ar53.markers_summary" ftype="tsv">
84 <assert_contents> 84 <assert_contents>
85 <has_text text="number_unique_genes"/> 85 <has_text text="number_unique_genes"/>
86 </assert_contents> 86 </assert_contents>
87 </element> 87 </element>
88 <element name="gtdbtk.bac120.markers_summary" ftype="tsv"> 88 <element name="gtdbtk.bac120.markers_summary" ftype="tsv">
99 <assert_contents> 99 <assert_contents>
100 <has_text text="genome_1_fna_gz"/> 100 <has_text text="genome_1_fna_gz"/>
101 </assert_contents> 101 </assert_contents>
102 </element> 102 </element>
103 </output_collection> 103 </output_collection>
104 <output_collection name="output_classify" type="list" count="3"> 104 <output_collection name="output_classify" type="list" count="1">
105 <element name="gtdbtk.ar122.classify.tree.6" ftype="newick"> 105 <element name="gtdbtk.ar53.classify" ftype="newick">
106 <assert_contents>
107 <has_text text="GB_GCA_"/>
108 </assert_contents>
109 </element>
110 <element name="gtdbtk.ar122" ftype="newick">
111 <assert_contents>
112 <has_text text="user_genome"/>
113 </assert_contents>
114 </element>
115 <element name="gtdbtk.backbone.ar122.classify" ftype="newick">
116 <assert_contents> 106 <assert_contents>
117 <has_text text="GB_GCA_"/> 107 <has_text text="GB_GCA_"/>
118 </assert_contents> 108 </assert_contents>
119 </element> 109 </element>
120 </output_collection> 110 </output_collection>
121 <output_collection name="output_align" type="list" count="2"> 111 <output_collection name="output_align" type="list" count="2">
122 <element name="gtdbtk.ar122.msa" ftype="fasta.gz"> 112 <element name="gtdbtk.ar53.msa" ftype="fasta.gz" decompress="true">
123 <assert_contents> 113 <assert_contents>
124 <has_text text="GB_GCA_000008085"/> 114 <has_text text="GB_GCA_000008085"/>
125 </assert_contents> 115 </assert_contents>
126 </element> 116 </element>
127 <element name="gtdbtk.ar122.user_msa" ftype="fasta"> 117 <element name="gtdbtk.ar53.user_msa" ftype="fasta.gz" decompress="true">
128 <assert_contents> 118 <assert_contents>
129 <has_text text="genome_1_fna_gz"/> 119 <has_text text="genome_1_fna_gz"/>
130 </assert_contents> 120 </assert_contents>
131 </element> 121 </element>
132 </output_collection> 122 </output_collection>