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comparison eggnog_mapper.xml @ 5:a5a3bdd0954b draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
author galaxyp
date Mon, 11 Nov 2019 11:50:36 -0500
parents 2667d24b58a0
children 3cb37af59360
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4:2667d24b58a0 5:a5a3bdd0954b
1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@"> 1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@.1">
2 <description>functional sequence annotation by orthology</description> 2 <description>functional sequence annotation by orthology</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">1.0.3</token> 4 <import>eggnog_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro="requirements"/>
7 <requirement type="package" version="@VERSION@">eggnog-mapper</requirement> 7 <expand macro="version_command"/>
8 </requirements>
9 <version_command>emapper.py --version</version_command>
10 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
11 emapper.py 9 emapper.py
12 --data_dir '$eggnog_data.fields.db' 10 --data_dir '$eggnog_data.fields.path'
13 -m $db.mode 11 -m $db.mode
14 $translate 12 $translate
15 #if ($db.mode == 'hmmer'): 13 #if ($db.mode == 'hmmer'):
16 --database=$db.database.fields.db 14 #if $db.database.fields.path:
15 --database=$db.database.fields.path
16 #else
17 --database=$db.database
18 #end if
17 #if $db.hmm_options.hmm_settings == 'specified': 19 #if $db.hmm_options.hmm_settings == 'specified':
18 --hmm_maxhits=$db.hmm_options.hmm_maxhits 20 --hmm_maxhits=$db.hmm_options.hmm_maxhits
19 --hmm_evalue=$db.hmm_options.hmm_evalue 21 --hmm_evalue=$db.hmm_options.hmm_evalue
20 --hmm_score=$db.hmm_options.hmm_score 22 --hmm_score=$db.hmm_options.hmm_score
21 --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen 23 --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen
51 --cpu "\${GALAXY_SLOTS:-4}" 53 --cpu "\${GALAXY_SLOTS:-4}"
52 ]]></command> 54 ]]></command>
53 <inputs> 55 <inputs>
54 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/> 56 <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
55 <param name="eggnog_data" type="select" label="Version of eggNOG Database"> 57 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
56 <options from_data_table="eggnog_mapper"> 58 <options from_data_table="eggnog_mapper_db"/>
57 <filter type="static_value" name="type" value="data" column="2"/>
58 </options>
59 </param> 59 </param>
60 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false" 60 <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
61 label="Are these coding DNA sequences that need to be translated?"/> 61 label="Are these coding DNA sequences that need to be translated?"/>
62 <conditional name="db"> 62 <conditional name="db">
63 <param name="mode" type="select" label="Annotation Type"> 63 <param name="mode" type="select" label="Annotation Type">
64 <option value="hmmer">HMM</option> 64 <option value="hmmer">HMM</option>
65 <option value="diamond">DIAMOND</option> 65 <option value="diamond">DIAMOND</option>
66 </param> 66 </param>
67 <when value="hmmer"> 67 <when value="hmmer">
68 <param name="database" type="select" label="HMM target database" help="Choose either the full eggNOG database or a subset of it. Contact your Galaxy admin to have additional HMM databases installed."> 68 <param name="database" type="select" label="HMM target database" help="Choose either the full eggNOG database or a subset of it. Contact your Galaxy admin to have additional HMM databases installed.">
69 <options from_data_table="eggnog_mapper"> 69 <options from_data_table="eggnog_mapper_hmm_dbs">
70 <filter type="static_value" value="hmmer" column="2"/> 70 <!--
71 <filter type="param_value" ref="eggnog_data" column="1" />
72 <filter type="unique_value" column="3" />
71 <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." /> 73 <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." />
74 -->
72 </options> 75 </options>
73 </param> 76 </param>
74 <conditional name="hmm_options"> 77 <conditional name="hmm_options">
75 <param name="hmm_settings" type="select" label="HMM Search Options"> 78 <param name="hmm_settings" type="select" label="HMM Search Options">
76 <option value="default">Use defaults</option> 79 <option value="default">Use defaults</option>
393 <tests> 396 <tests>
394 <test> 397 <test>
395 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/> 398 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
396 <param name="database" value="ENOG411CB2I"/> 399 <param name="database" value="ENOG411CB2I"/>
397 <param name="mode" value="hmmer"/> 400 <param name="mode" value="hmmer"/>
401 <!--
398 <param name="test" value="true"/> 402 <param name="test" value="true"/>
399 <param name="eggnog_data" value="eggNOG_4.5"/> 403 -->
404 <param name="eggnog_data" value="4.5"/>
400 <param name="no_annot" value="true"/> 405 <param name="no_annot" value="true"/>
401 <param name="no_file_comments" value="true"/> 406 <param name="no_file_comments" value="true"/>
402 <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/> 407 <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/>
403 </test> 408 </test>
404 <test> 409 <test>
405 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/> 410 <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
406 <param name="eggnog_data" value="eggNOG_4.5"/> <!-- not passed in test, but required for test to work --> 411 <param name="eggnog_data" value="4.5"/> <!-- not passed in test, but required for test to work -->
407 <param name="no_annot" value="true"/> 412 <param name="no_annot" value="true"/>
408 <param name="mode" value="diamond"/> 413 <param name="mode" value="diamond"/>
409 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/> 414 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
410 </test> 415 </test>
411 </tests> 416 </tests>
466 - ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode) 471 - ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode)
467 - ``COG functional categories``: COG functional category inferred from best matching OG 472 - ``COG functional categories``: COG functional category inferred from best matching OG
468 - ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG 473 - ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG
469 474
470 ]]></help> 475 ]]></help>
471 <citations> 476 <expand macro="citations"/>
472 <citation type="doi">10.1093/nar/gkv1248</citation>
473 </citations>
474 </tool> 477 </tool>