Mercurial > repos > jjohnson > eggnog_mapper

comparison data_manager/data_manager_eggnog.xml @ 4:ea9772670fb5 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit ab8f3af4dd052475db01f8120df0f9da6e8fff29
author jjohnson
date Wed, 06 Nov 2019 14:06:45 -0500
parents 9d94fe7ce8b9
children
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3:9d94fe7ce8b9 4:ea9772670fb5
14 #if $dbs: 14 #if $dbs:
15 #set $eggnogdbs = ' '.join(str($dbs).split(',')) 15 #set $eggnogdbs = ' '.join(str($dbs).split(','))
16 #else 16 #else
17 #set $eggnogdbs = 'none' 17 #set $eggnogdbs = 'none'
18 #end if 18 #end if
19 #if $test == 'false' 19 #if $test == 'true'
20 #import os.path
21 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally')
22 echo $install_path >> /Users/jj/gxt/gxt/eggnog_install_path &&
23 #end if
20 mkdir -p '${install_path}' && 24 mkdir -p '${install_path}' &&
21 download_eggnog_data.py 25 download_eggnog_data.py
22 $diamond_database -y -q --data_dir $install_path $eggnogdbs 26 $diamond_database -y -q
23 ' '.join(dbs.split(',')) && 27 #if $test == 'true'
24 #else 28 -s
25 #set $install_path = '/Users/jj/gx/gh/jj/tools-galaxyp/tools/eggnog_mapper/test-data/cached_locally'
26 #end if 29 #end if
30 --data_dir '$install_path'
31 $eggnogdbs &&
27 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs' 32 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs'
28 ]]></command> 33 ]]></command>
29 <inputs> 34 <inputs>
30 <param name="test" type="hidden" value="false" /> 35 <param name="test" type="hidden" value="false" />
31 <param name="target_path" type="text" label="Download Destination (full path)" /> 36 <param name="target_path" type="text" label="Download Destination (full path)" />
148 </outputs> 153 </outputs>
149 <tests> 154 <tests>
150 <test> 155 <test>
151 <param name="test" value="true"/> 156 <param name="test" value="true"/>
152 <param name="diamond_database" value="false"/> 157 <param name="diamond_database" value="false"/>
158 <param name="dbs" value="thaNOG"/>
153 <output name="out_file"> 159 <output name="out_file">
154 <assert_contents> 160 <assert_contents>
155 <has_text text="eggnog_mapper_db" /> 161 <has_text text="eggnog_mapper_db" />
156 </assert_contents> 162 </assert_contents>
157 </output> 163 </output>