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comparison eggnog_macros.xml @ 12:9d1fbff733cf draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
author galaxyp
date Tue, 19 Jul 2022 15:14:52 +0000
parents 5a30ae278db0
children 844fa988236b
comparison
equal deleted inserted replaced
11:5a30ae278db0 12:9d1fbff733cf
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">2.1.8</token> 3 <token name="@TOOL_VERSION@">2.1.8</token>
4 <token name="@VERSION_SUFFIX@">2.1.8</token> 4 <token name="@VERSION_SUFFIX@">3</token>
5 <token name="@EGGNOG_DB_VERSION@">5.0.2</token> 5 <token name="@EGGNOG_DB_VERSION@">5.0.2</token>
6 <!-- 6 <!--
7 # DB versionning was super confusing for eggnog-mapper 2.0.x: 7 # DB versionning was super confusing for eggnog-mapper 2.0.x:
8 # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5) 8 # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5)
9 # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0) 9 # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0)
62 <has_text text="@EGGNOG_DB_VERSION@" /> 62 <has_text text="@EGGNOG_DB_VERSION@" />
63 </assert_contents> 63 </assert_contents>
64 </output> 64 </output>
65 </test> 65 </test>
66 </xml> 66 </xml>
67
68 <xml name="fasta_input">
69 <param argument="-i" name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
70 <conditional name="input_trans">
71 <param argument="--itype" type="select" label="Type of sequences">
72 <option value="proteins" selected="true">proteins</option>
73 <option value="CDS">CDS</option>
74 <option value="genome">genome</option>
75 <option value="metagenome">metagenome</option>
76 </param>
77 <when value="proteins"/>
78 <when value="CDS">
79 <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
80 label="Translate CDS to proteins before search"/>
81 </when>
82 <when value="genome">
83 <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
84 label="Translate predicted CDS from blastx hits to proteins"/>
85 <param argument="--genepred" type="select" label="Type of sequences">
86 <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option>
87 <option value="prodigal" selected="true">Performed using Prodigal</option>
88 </param>
89 </when>
90 <when value="metagenome">
91 <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
92 label="Translate predicted CDS from blastx hits to proteins"/>
93 <param argument="--genepred" type="select" label="Type of sequences">
94 <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option>
95 <option value="prodigal" selected="true">Performed using Prodigal</option>
96 </param>
97 </when>
98 </conditional>
99 </xml>
100 <!-- Common options for search filtering (applies to diamond and mmseqs only) -->
101 <xml name="common_search_options">
102 <param argument="--query_cover" type="integer" optional="true" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of query cover" />
103 <param argument="--subject_cover" type="integer" optional="true" min="0" max="100" label="Minimum subject coverage" help="Report only alignments above the given percentage of subject cover" />
104 <param argument="--pident" type="integer" optional="true" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of identity" />
105 <param argument="--evalue" type="float" optional="true" min="0" label="Minimum query coverage" help="Report only alignments below or equal the e-value" />
106 <param argument="--score" type="float" value="0.001" optional="true" min="0" label="Minimum query coverage" help="Report only alignments above or equal the score" />
107 </xml>
108 <token name="@SEED_ORTHOLOG_COLUMNS@">query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,query_start,query_end,seed_start,seed_end,pident,query_cov,seed_cov</token>
109
67 <xml name="stdout_assertion"> 110 <xml name="stdout_assertion">
68 <assert_stdout> 111 <assert_stdout>
69 <has_line line="# emapper-@TOOL_VERSION@"/> 112 <has_line line="# emapper-@TOOL_VERSION@"/>
70 <has_line line="FINISHED"/> 113 <has_line line="FINISHED"/>
114 <yield/>
71 </assert_stdout> 115 </assert_stdout>
72 </xml> 116 </xml>
117 <xml name="seed_orthologs_assertion">
118 <output name="seed_orthologs" ftype="tabular">
119 <assert_contents>
120 <has_line line="#qseqid&#009;sseqid&#009;evalue&#009;bitscore&#009;qstart&#009;qend&#009;sstart&#009;send&#009;pident&#009;qcov&#009;scov"/>
121 <has_line_matching expression="(\S+\t){2}[-+.e\d]+\t[.\d]+(\t\d+){4}(\t[.\d]+){3}" n="1"/>
122 </assert_contents>
123 </output>
124 </xml>
125 <xml name="annotations_assertion" token_columns="21" token_add_metadata_columm_names="" token_add_column_names="" token_add_column_re="">
126 <output name="annotations" ftype="tabular">
127 <metadata name="columns" value="@COLUMNS@" />
128 <!-- <metadata name="column_names" value="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs@ADD_METADATA_COLUMN_NAMES@" /> -->
129 <assert_contents>
130 <has_line line="#query&#009;seed_ortholog&#009;evalue&#009;score&#009;eggNOG_OGs&#009;max_annot_lvl&#009;COG_category&#009;Description&#009;Preferred_name&#009;GOs&#009;EC&#009;KEGG_ko&#009;KEGG_Pathway&#009;KEGG_Module&#009;KEGG_Reaction&#009;KEGG_rclass&#009;BRITE&#009;KEGG_TC&#009;CAZy&#009;BiGG_Reaction&#009;PFAMs@ADD_COLUMN_NAMES@"/>
131 <has_line_matching expression="(\S+\t){2}[-+.e\d]+\t[.\d]+(\t\S+){7}\tko:\S+(\t\S+){9}@ADD_COLUMN_RE@" n="1"/>
132 </assert_contents>
133 </output>
134 </xml>
135 <xml name="annotations_orthologs_assertion">
136 <output name="annotations_orthologs" ftype="tabular">
137 <metadata name="columns" value="4" />
138 <metadata name="column_names" value="query,orth_type,species,orthologs" />
139 <assert_contents>
140 <has_line line="#query&#009;orth_type&#009;species&#009;orthologs"/>
141 <has_line_matching expression="\S+\t(one2one|many2one|one2many|many2many|seed)(\t[^\t]+){2}" n="2"/>
142 </assert_contents>
143 </output>
144 </xml>
73 </macros> 145 </macros>