Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/rgToolFactory2.xml @ 56:68fbdbe35f08 draft

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Uploaded
author fubar
date Tue, 20 Oct 2020 03:20:32 +0000
parents dcf59d4e4515
children d21517a36db8
comparison
equal deleted inserted replaced
55:dcf59d4e4515 56:68fbdbe35f08
1 <tool id="rgTF2" name="toolfactory" version="3.00" profile="16.04" > 1 <tool id="rgTF2" name="toolfactory" version="2.00" profile="16.04" >
2 <description>Scripts into tools</description> 2 <description>Scripts into tools v2</description>
3 <macros> 3 <macros>
4 <xml name="tool_metadata"> 4 <xml name="tool_metadata">
5 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01" 5 <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
6 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/> 6 help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
7 <param name="tool_desc" label="Tool Description" type="text" value="" 7 <param name="tool_desc" label="Tool Description" type="text" value=""
128 <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed" 128 <param name="param_CLprefixed" type="text" label="Override the generated default argparse name prefix if not empty - eg ----foo if needed"
129 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" /> 129 help="Some targets like Planemo expect an unadorned action like 'test' before --galaxy_root." value="" />
130 </repeat> 130 </repeat>
131 </xml> 131 </xml>
132 </macros> 132 </macros>
133
133 <requirements> 134 <requirements>
134 <requirement type="package">planemo</requirement> 135 <requirement type="package" version="0.72.0" >planemo</requirement>
135 <requirement type="package">galaxyxml</requirement> 136 <requirement type="package" >bioblend</requirement>
136 <requirement type="package">lxml</requirement> 137 <requirement type="package" >galaxyxml</requirement>
137 <requirement type="package">ephemeris</requirement> 138 <requirement type="package" >ephemeris</requirement>
138 <requirement type="package">bioblend</requirement>
139 </requirements> 139 </requirements>
140
140 <command ><![CDATA[ 141 <command ><![CDATA[
141 #import os 142 #import os
142 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1' 143 #set dev_env = os.environ.get('GALAXY_DEVELOPMENT_ENVIRONMENT', '0') == '1'
143 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ): 144 #if not $dev_env and ( $__user_email__ not in $__admin_users__ ):
144 python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__ 145 python3 $__tool_directory__/rgToolFactory2.py --bad_user $__user_email__
183 --input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help" 184 --input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats~~~$intab.input_label~~~$intab.input_help"
184 #end for 185 #end for
185 #for $otab in $ppass.history_outputs: 186 #for $otab in $ppass.history_outputs:
186 --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test" 187 --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test"
187 #end for 188 #end for
189 --galaxy_root="$__root_dir__"
188 #end if 190 #end if
189 ]]></command> 191 ]]></command>
190 <configfiles> 192 <configfiles>
191 <configfile name="runme"> 193 <configfile name="runme">
192 $usescript.dynScript 194 $usescript.dynScript