Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_mapper.xml @ 11:1f2be4ae431f draft default tip

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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 15:14:11 +0000
parents 3d30526975d7
children
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3d30526975d7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
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1 <tool id="eggnog_mapper" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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2 <description>functional sequence annotation by orthology</description>
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44f3e55293d8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99
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3 <macros>
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59501122d153 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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4 <import>eggnog_macros.xml</import>
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44f3e55293d8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 16eed6250e9a238dacfa4c775d9db4e232817b99
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5 </macros>
5
59501122d153 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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6 <expand macro="requirements"/>
59501122d153 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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9 #if $ortho_method.m == "no_search"
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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10 cat
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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11 #for aht in $ortho_method.annotate_hits_table
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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12 $aht
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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13 #end for
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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14 > annotate_hits_table.tsv
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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15 &&
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9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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16 #end if
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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17
11
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18 emapper.py
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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19 --data_dir '$eggnog_data.fields.path'
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20 -m '$ortho_method.m'
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1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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22 #if $ortho_method.m in ['diamond', 'mmseqs', 'cache']:
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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23 -i '$ortho_method.input'
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24 --itype '$ortho_method.input_trans.itype'
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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25 #if $ortho_method.input_trans.itype in ['CDS', 'genome', 'metagenome']:
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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26 $ortho_method.input_trans.translate
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27 #end if
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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28 #if $ortho_method.input_trans.itype in ['genome', 'metagenome']:
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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29 --genepred $ortho_method.input_trans.genepred
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30 #end if
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31 #elif $ortho_method.m == "no_search"
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32 --annotate_hits_table annotate_hits_table.tsv
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33 #end if
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1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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35 #if $ortho_method.m == 'cache'
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36 --cache '$ortho_method.cache'
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37 #end if
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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38
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39 #if $ortho_method.m in ['diamond', 'mmseqs']:
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40 ## Diamond option
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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41 #if $ortho_method.m == "diamond":
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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42 --matrix '$ortho_method.matrix_gapcosts.matrix'
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43 $ortho_method.matrix_gapcosts.gap_costs
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44 --sensmode $ortho_method.sensmode
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45 $ortho_method.dmnd_iterate
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46 $ortho_method.dmnd_ignore_warnings
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47 #elif $ortho_method.m == "mmseqs":
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48 --start_sens $ortho_method.start_sens
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49 --sens_steps $ortho_method.sens_steps
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50 --final_sens $ortho_method.final_sens
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51 #end if
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52
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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53 ## Common options for search filtering (applies to diamond and mmseqs only)
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54 #if str($ortho_method.query_cover):
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55 --query_cover $ortho_method.query_cover
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56 #end if
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57 #if str($ortho_method.subject_cover):
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58 --subject_cover $ortho_method.subject_cover
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59 #end if
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60 #if str($ortho_method.pident):
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61 --pident $ortho_method.pident
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62 #end if
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63 #if str($ortho_method.evalue):
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64 --evalue $ortho_method.evalue
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65 #end if
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66 #if str($ortho_method.score):
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67 --score $ortho_method.score
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68 #end if
0
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69 #end if
11
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70
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71 #if $annotation_options.no_annot == "--no_annot"
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72 --no_annot
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73 #else
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74 #if str($annotation_options.seed_ortholog_evalue):
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75 --seed_ortholog_evalue $annotation_options.seed_ortholog_evalue
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76 #end if
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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77 #if str($annotation_options.seed_ortholog_score):
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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78 --seed_ortholog_score $annotation_options.seed_ortholog_score
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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79 #end if
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
80 #if $annotation_options.tax_scope:
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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81 --tax_scope=$annotation_options.tax_scope
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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82 #end if
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
83 #if $annotation_options.target_orthologs:
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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84 --target_orthologs=$annotation_options.target_orthologs
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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85 #end if
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
86 #if $annotation_options.go_evidence:
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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87 --go_evidence=$annotation_options.go_evidence
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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88 #end if
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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89 #end if
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galaxyp
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diff changeset
90 $output_options.no_file_comments
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91 $output_options.report_orthologs
11
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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92 $output_options.md5
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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93 --output='results'
1
ca04bdc749da planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9505f2a447df1bcd46ceca7b5ddb532a2f8a1cd1
galaxyp
parents: 0
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94 --cpu "\${GALAXY_SLOTS:-4}"
11
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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95 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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96 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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97 ]]></command>
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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98 <inputs>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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99 <param name="eggnog_data" type="select" label="Version of eggNOG Database">
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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100 <options from_data_table="eggnog_mapper_db_versioned">
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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101 <filter type="static_value" column="3" value="@IDX_VERSION@" />
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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102 </options>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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103 </param>
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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104
11
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
105 <conditional name="ortho_method">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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106 <param argument="-m" type="select" label="Method to search seed orthologs">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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107 <option value="diamond" selected="true">Diamond</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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108 <option value="mmseqs">MMseqs2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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109 <option value="no_search">Skip search stage: annotate an existing seed orthologs data set</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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110 <option value="cache">Skip search stage: annotate based on cached annotations (see also --md5)</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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111 </param>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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112 <when value="diamond">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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113 <expand macro="fasta_input"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
114 <conditional name="matrix_gapcosts">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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115 <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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116 <option value="BLOSUM90">BLOSUM90</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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117 <option value="BLOSUM80">BLOSUM80</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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118 <option value="BLOSUM62" selected="true">BLOSUM62</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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119 <option value="BLOSUM50">BLOSUM50</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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120 <option value="BLOSUM45">BLOSUM45</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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121 <option value="PAM250">PAM250</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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122 <option value="PAM70">PAM70</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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123 <option value="PAM30">PAM30</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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124 </param>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
125 <when value="BLOSUM90">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
126 <param name="gap_costs" type="select" label="Gap Costs">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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127 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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128 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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129 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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130 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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131 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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132 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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133 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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134 </param>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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135 </when>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
136 <when value="BLOSUM80">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
137 <param name="gap_costs" type="select" label="Gap Costs">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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138 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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139 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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140 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
141 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
142 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
143 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
144 </param>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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145 </when>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
146 <when value="BLOSUM62">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
147 <param name="gap_costs" type="select" label="Gap Costs">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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148 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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149 <option value="--gapopen 10 --gapextend 2">Existence: 10 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
150 <option value="--gapopen 9 --gapextend 2">Existence: 9 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
151 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
152 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
153 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
154 <option value="--gapopen 13 --gapextend 1">Existence: 13 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
155 <option value="--gapopen 12 --gapextend 1">Existence: 12 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
156 <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
157 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
158 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
159 </param>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
160 </when>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
161 <when value="BLOSUM50">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
162 <param name="gap_costs" type="select" label="Gap Costs">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
163 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
164 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
165 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
166 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
167 <option value="--gapopen 9 --gapextend 3">Existence: 9 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
168 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
169 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
170 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
171 <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
172 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
173 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
174 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
175 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
176 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
177 <option value="--gapopen 15 --gapextend 1">Existence: 15 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
178 </param>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
179 </when>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
180 <when value="BLOSUM45">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
181 <param name="gap_costs" type="select" label="Gap Costs">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
182 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
183 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
184 <option value="--gapopen 11 --gapextend 3">Existence: 11 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
185 <option value="--gapopen 10 --gapextend 3">Existence: 10 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
186 <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
187 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
188 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
189 <option value="--gapopen 12 --gapextend 2">Existence: 12 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
190 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
191 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
192 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
193 <option value="--gapopen 16 --gapextend 1">Existence: 16 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
194 </param>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
195 </when>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
196 <when value="PAM250">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
197 <param name="gap_costs" type="select" label="Gap Costs">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
198 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
199 <option value="--gapopen 14 --gapextend 3">Existence: 14 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
200 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
201 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
202 <option value="--gapopen 17 --gapextend 2">Existence: 17 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
203 <option value="--gapopen 16 --gapextend 2">Existence: 16 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
204 <option value="--gapopen 15 --gapextend 2">Existence: 15 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
205 <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
206 <option value="--gapopen 13 --gapextend 2">Existence: 13 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
207 <option value="--gapopen 21 --gapextend 1">Existence: 21 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
208 <option value="--gapopen 20 --gapextend 1">Existence: 20 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
209 <option value="--gapopen 19 --gapextend 1">Existence: 19 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
210 <option value="--gapopen 18 --gapextend 1">Existence: 18 Extension: 1</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
211 <option value="--gapopen 17 --gapextend 1">Existence: 17 Extension: 1</option>
7
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents: 6
diff changeset
212 </param>
11
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
213 </when>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
214 <when value="PAM70">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
215 <param name="gap_costs" type="select" label="Gap Costs">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
216 <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
217 <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
218 <option value="--gapopen 8 --gapextend 2">Existence: 8 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
219 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
220 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
221 <option value="--gapopen 11 --gapextend 1">Existence: 11 Extension: 1</option>
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222 <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10 Extension: 1</option>
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223 <option value="--gapopen 9 --gapextend 1">Existence: 9 Extension: 1</option>
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224 </param>
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225 </when>
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226 <when value="PAM30">
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227 <param name="gap_costs" type="select" label="Gap Costs">
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228 <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
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229 <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
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230 <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
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231 <option value="--gapopen 7 --gapextend 2">Existence: 7 Extension: 2</option>
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232 <option value="--gapopen 6 --gapextend 2">Existence: 6 Extension: 2</option>
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233 <option value="--gapopen 5 --gapextend 2">Existence: 5 Extension: 2</option>
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234 <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
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235 <option value="--gapopen 10 --gapextend 1">Existence: 10 Extension: 1</option>
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236 <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9 Extension: 1</option>
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237 <option value="--gapopen 8 --gapextend 1">Existence: 8 Extension: 1</option>
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238 </param>
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239 </when>
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240 </conditional>
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241 <param argument="--sensmode" type="select" label="Diamond's sensitivity mode">
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242 <option value="default">default</option>
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243 <option value="fast">fast</option>
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244 <option value="mid-sensitive">mid-sensitive</option>
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245 <option value="sensitive" selected="true">sensitive</option>
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246 <option value="more-sensitive">more-sensitive</option>
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247 <option value="very-sensitive">very-sensitive</option>
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248 <option value="ultra-sensitive">ultra-sensitive</option>
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249 </param>
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250 <param argument="--dmnd_iterate" type="boolean" truevalue="--dmnd_iterate yes" falsevalue="--dmnd_iterate no" checked="false"
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251 label="Run diamond in iterative mode, up to the sensitivity level"/>
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252 <param argument="--dmnd_ignore_warnings" type="boolean" truevalue="--dmnd_ignore_warnings" falsevalue="" checked="false"
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253 label="Ignore Diamond warnings on sequence content (e.g. when a protein contains only ATGC symbols)"/>
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254 <expand macro="common_search_options"/>
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255 </when>
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256 <when value="mmseqs">
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257 <expand macro="fasta_input"/>
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258 <param argument="--start_sens" type="integer" value="3" min="0" max="100" label="Starting sensitivity" />
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259 <param argument="--sens_steps" type="integer" value="3" min="0" max="100" label="Number of sensitivity steps" />
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260 <param argument="--final_sens" type="integer" value="7" min="0" max="100" label="Final sensititivy step" />
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261 <expand macro="common_search_options"/>
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262 </when>
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263 <when value="no_search">
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264 <param argument="--annotate_hits_table" type="data" multiple="true" format="tabular" label="Seed orthologs">
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265 <validator type="expression" message="No seed orthologs">value.metadata.columns == 11</validator>
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266 <!-- would be cool to replace with this validator:
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267 <validator type="expression" message="No seed orthologs">value.metadata.column_names == '@SEED_ORTHOLOG_COLUMNS@'.split()</validator>
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268 but this does not work (yet) in tool tests since column_names can not be set in uploads -->
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269 </param>
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270 </when>
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271 <when value="cache">
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272 <expand macro="fasta_input"/>
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273 <param argument="--cache" type="data" multiple="true" format="tabular" label="EggNOG Annotations with md5 hashes" help="Annotations computed with EggNOG mapper with enabled --md5 option">
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274 <validator type="expression" message="No seed orthologs">value.metadata.columns == 22</validator>
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275 </param>
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276 <param name="output_no_annotations" type="boolean" checked="true" label="Output sequences without annotation" help="Produce an additional FASTA file with the sequences of queries for which an existing annotation was not found using cache mode. This file can be used as input of another eggNOG-mapper run without using the cache, trying to annotate the sequences."/>
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277 </when>
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278 </conditional>
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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279
11
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280 <conditional name="annotation_options">
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281 <param argument="--no_annot" type="select" label="Annotate seed orthologs">
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282 <option value="">Yes</option>
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283 <option value="--no_annot">No</option>
0
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284 </param>
11
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285 <when value="">
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286 <param argument="--seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
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287 <help>
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288 Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
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289 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
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290 </help>
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291 </param>
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292 <param argument="--seed_ortholog_score" type="float" optional="true" min="0" label="Minimum bit score threshold">
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293 <help>
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294 Min bit score expected when searching for seed eggNOG ortholog.
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295 Queries not having a significant seed orthologs will not be annotated.
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296 </help>
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297 </param>
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298 <param argument="--tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" />
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299 <param argument="--target_orthologs" type="select" label="target orthologs for functional transfer">
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300 <option value="one2one">one2one</option>
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301 <option value="many2one">many2one</option>
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302 <option value="one2many">one2many</option>
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303 <option value="many2many">many2many</option>
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304 <option value="all" selected="true">all</option>
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305 </param>
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306 <param argument="--go_evidence" type="select"
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307 label="Select the set of GO terms that should be used for annotation">
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308 <option value="experimental">experimental = Use only terms inferred from experimental evidence</option>
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309 <option value="non-electronic" selected="true">non-electronic = Use only non-electronically curated terms</option>
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310 <option value="all" selected="true">All (experimental + non-electronic)</option>
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311 </param>
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312 </when>
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313 <when value="--no_annot"/>
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314 </conditional>
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315
0
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316 <section name="output_options" expanded="false" title="Output Options">
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317 <param argument="--no_file_comments" type="boolean" truevalue="--no_file_comments" falsevalue="" checked="true"
0
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318 label="Exclude header lines and stats from output files"/>
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319 <param argument="--report_orthologs" type="boolean" truevalue="--report_orthologs" falsevalue="" checked="false"
0
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320 label="Output a file with the list of orthologs for each hits"/>
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321 <param argument="--md5" type="boolean" truevalue="--md5" falsevalue="" checked="false"
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322 label="Add md5 hash of each query to annotations"/>
0
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323 </section>
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324 </inputs>
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325 <outputs>
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326 <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
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327 <filter>ortho_method['m'] not in ['no_search', 'cache']</filter>
0
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328 <actions>
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329 <action name="column_names" type="metadata" default="@SEED_ORTHOLOG_COLUMNS@"/>
0
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330 </actions>
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331 </data>
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332 <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations">
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333 <filter>annotation_options['no_annot'] == ''</filter>
0
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334 <actions>
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335 <conditional name="output_options.md5">
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336 <when value="True">
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337 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs,md5"/>
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338 </when>
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339 <when value="False">
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340 <action name="column_names" type="metadata" default="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs"/>
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341 </when>
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342 </conditional>
0
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343 </actions>
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344 </data>
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345 <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: orthologs" from_work_dir="results.emapper.orthologs">
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346 <filter>ortho_method['m'] != 'cache' and output_options['report_orthologs']</filter>
0
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347 <actions>
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348 <action name="column_names" type="metadata" default="query,orth_type,species,orthologs"/>
0
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349 </actions>
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350 </data>
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351 <data name="no_annotations" format="fasta" label="${tool.name} on ${on_string}: Sequences wo annotation" from_work_dir="results.emapper.no_annotations.fasta">
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352 <filter>ortho_method['m'] == 'cache' and output_options['output_no_annotations']</filter>
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353 </data>
0
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354 </outputs>
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355 <tests>
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356 <!-- test producing only seed orthologs-->
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357 <test expect_num_outputs="1">
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358 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
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359 <conditional name="ortho_method">
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360 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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361 </conditional>
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362 <conditional name="annotation_options">
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363 <param name="no_annot" value="--no_annot"/>
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364 </conditional>
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365 <section name="output_options">
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366 <param name="no_file_comments" value="true"/>
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367 </section>
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368 <expand macro="seed_orthologs_assertion"/>
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369 <expand macro="stdout_assertion"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
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370 </test>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
371
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
372 <!-- test producing annotations form seed orthologs -->
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
373 <test expect_num_outputs="2">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
374 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
375 <conditional name="ortho_method">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
376 <param name="m" value="no_search"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
377 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
378 <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
379 </param>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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380 </conditional>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
381 <conditional name="annotation_options">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
382 </conditional>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
383 <section name="output_options">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
384 <param name="report_orthologs" value="true"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
385 <param name="no_file_comments" value="true"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
386 </section>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
387 <expand macro="annotations_assertion"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
388 <expand macro="annotations_orthologs_assertion"/>
10
3d30526975d7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
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diff changeset
389 <expand macro="stdout_assertion"/>
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
390 </test>
11
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
391
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
392 <!-- test producing seed orthologs and annotations at once (ie the same as the previous two tests but in a single tool run) -->
10
3d30526975d7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
galaxyp
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diff changeset
393 <test expect_num_outputs="3">
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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parents: 5
diff changeset
394 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
11
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
395 <conditional name="ortho_method">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
396 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
397 </conditional>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
398 <section name="output_options">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
399 <param name="report_orthologs" value="true"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
400 <param name="no_file_comments" value="true"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
401 <param name="md5" value="true"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
402 </section>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
403 <expand macro="seed_orthologs_assertion"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
404 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
405 <expand macro="annotations_orthologs_assertion"/>
10
3d30526975d7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
galaxyp
parents: 9
diff changeset
406 <expand macro="stdout_assertion"/>
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
diff changeset
407 </test>
11
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
408
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
409 <!-- test using chached annotations from previous run -->
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
410 <test expect_num_outputs="2">
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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parents: 5
diff changeset
411 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
11
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
412 <conditional name="ortho_method">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
413 <param name="m" value="cache"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
414 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
415 <param name="cache" value="DIA_nlim.emapper.annotations_cached" ftype="tabular"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
416 </conditional>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
417 <section name="output_options">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
418 <param name="report_orthologs" value="true"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
419 <param name="no_file_comments" value="true"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
420 <param name="md5" value="true"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
421 </section>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
422 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
423 <output name="no_annotations" ftype="fasta">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
424 <assert_contents>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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parents: 10
diff changeset
425 <has_n_lines n="0"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
426 </assert_contents>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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parents: 10
diff changeset
427 </output>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
428 <expand macro="stdout_assertion"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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parents: 10
diff changeset
429 </test>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
430
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
431 <!-- test setting tax scope-->
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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parents: 10
diff changeset
432 <test expect_num_outputs="3">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
433 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
434 <conditional name="ortho_method">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
435 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
436 </conditional>
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
diff changeset
437 <section name="annotation_options">
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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parents: 5
diff changeset
438 <param name="tax_scope" value="651137" />
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
diff changeset
439 </section>
11
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
440 <section name="output_options">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
441 <param name="report_orthologs" value="true"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
442 <param name="no_file_comments" value="true"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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parents: 10
diff changeset
443 </section>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
444 <expand macro="seed_orthologs_assertion"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
445 <expand macro="annotations_assertion"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
446 <expand macro="annotations_orthologs_assertion"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
447 <expand macro="stdout_assertion">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
448 <has_text text="--tax_scope=651137"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
449 </expand>
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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450 </test>
11
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galaxyp
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diff changeset
451
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
452 <!-- test setting a diamond option-->
10
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453 <test expect_num_outputs="3">
7
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
454 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
11
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galaxyp
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diff changeset
455 <conditional name="ortho_method">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
456 <param name="m" value="diamond" />
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
457 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
458 <param name="sensmode" value="fast" />
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
459 </conditional>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
460 <section name="output_options">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
461 <param name="report_orthologs" value="true"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
462 <param name="no_file_comments" value="true"/>
7
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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diff changeset
463 </section>
11
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
464 <expand macro="seed_orthologs_assertion"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
465 <expand macro="annotations_assertion"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
466 <expand macro="annotations_orthologs_assertion"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
467 <expand macro="stdout_assertion">
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
parents: 10
diff changeset
468 <has_text text="--sensmode fast"/>
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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diff changeset
469 </expand>
7
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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diff changeset
470 </test>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
471 <!-- not enabled as it requires a specific .db file, hard to minimize -->
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
472 <!--test>
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diff changeset
473 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
7
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
474 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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diff changeset
475 <section name="seed_ortho_options">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
476 <conditional name="ortho_method">
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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diff changeset
477 <param name="m" value="mmseqs" />
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
478 <param name="start_sens" value="4" />
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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479 </conditional>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
480 </section>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
481 <param name="report_orthologs" value="true"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
482 <param name="no_file_comments" value="true"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
483 <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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diff changeset
484 <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
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diff changeset
485 <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
9d426cb7823b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit e45c15081260025e470d23975ef5a734d3f8fc66"
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diff changeset
486 </test-->
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
487 </tests>
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
488 <help><![CDATA[
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
489
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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diff changeset
490 eggnog-mapper
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
491 =============
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
492 Overview
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
493 --------
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
494
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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diff changeset
495 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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diff changeset
496 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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diff changeset
497 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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498 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
499
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
500 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
501
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
502 Outputs
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
503 -------
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
504
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
505 **seed_orthologs**
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
506
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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diff changeset
507 each line in the file provides the best match of each query within the best Orthologous Group (OG)
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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diff changeset
508 reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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diff changeset
509 The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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diff changeset
510 If using the diamond search mode, seed orthologs are directly
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
511 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
512
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
513 **annotations**
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
514
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
515 This file provides final annotations of each query. Tab-delimited columns in the file are:
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
516
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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517 - ``query_name``: query sequence name
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
518 - ``seed_eggNOG_ortholog``: best protein match in eggNOG
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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diff changeset
519 - ``seed_ortholog_evalue``: best protein match (e-value)
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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520 - ``seed_ortholog_score``: best protein match (bit-score)
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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diff changeset
521 - ``predicted_taxonomic_group``
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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diff changeset
522 - ``predicted_protein_name``: Predicted protein name for query sequences
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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523 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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diff changeset
524 - ``EC_number``
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
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525 - ``KEGG_KO``
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
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526 - ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
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527 - ``KEGG_Module``
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
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528 - ``KEGG_Reaction``
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
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529 - ``KEGG_rclass``
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
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530 - ``BRITE``
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
diff changeset
531 - ``KEGG_TC``
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
diff changeset
532 - ``CAZy``
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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533 - ``BiGG_Reactions``
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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534 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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535 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
6
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
diff changeset
536 - ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs)
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents: 5
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537 - ``COG_functional_categories``: COG functional category inferred from best matching OG
1d6c4af4b7bc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
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538 - ``eggNOG_free_text_description``
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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539
11
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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540 **Recommentation for large input data**
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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541
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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diff changeset
542 EggNOG-mapper consists of two phases
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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543
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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544 1. finding seed orthologous sequences (compute intensive)
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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545 2. expanding annotations (IO intensive)
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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546
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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547 by default (i.e. if *Method to search seed orthologs* is not *Skip search stage...* and *Annotate seed orthologs* is *Yes*)
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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548 both phases are executed within one tool run.
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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549
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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550 For large input FASTA datasets in can be favourable to split this in two separate
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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551 tool runs as follows:
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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552
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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553 1. Split the FASTA (e.g. 1M seqs per data set)
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
galaxyp
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554 2. Run the search phase only (set *Annotate seed orthologs* to *No*) on the separate FASTA files.
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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555 3. Run the annotation phase (set *Method to search seed orthologs* to *Skip search stage...*)
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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556
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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557 See [also](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs)
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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558
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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559 Another alternative is to use cached annotations (produced in a run with --md5 enabled).
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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560
1f2be4ae431f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
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561
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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562 ]]></help>
5
59501122d153 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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563 <expand macro="citations"/>
0
2354d9b43a91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
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564 </tool>