Mercurial > repos > fubar > tool_factory_2

comparison rgToolFactory2.xml @ 9:ce5ec1d989fd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Wed, 14 Jan 2015 19:17:11 -0500
parents 6a3c292412fa
children
comparison
equal deleted inserted replaced
8:9d58cc32a12d 9:ce5ec1d989fd
1 <tool id="rgTF2" name="Tool Factory Two" version="1.15"> 1 <tool id="rgTF2" name="Tool Factory Two" version="1.16">
2 <description>Scripts into tools</description> 2 <description>Scripts into tools</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="9.10">ghostscript</requirement> 4 <requirement type="package" version="9.10">ghostscript</requirement>
5 <requirement type="package" version="1.3.20">graphicsmagick</requirement> 5 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
6 </requirements> 6 </requirements>
7 <code file="getlocalrpackages.py"/>
7 <command interpreter="python"> 8 <command interpreter="python">
8 #if ( $__user_email__ not in $__admin_users__ ): 9 #if ( $__user_email__ not in $__admin_users__ ):
9 rgToolFactory2.py --bad_user $__user_email__ 10 rgToolFactory2.py --bad_user $__user_email__
10 #else: 11 #else:
11 rgToolFactory2.py --script_path "$runme" --interpreter "$interpreter" 12 rgToolFactory2.py --script_path "$runme" --interpreter "$interp.interpreter"
12 --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" 13 --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme"
14 --envshpath "$interp.envpath"
13 15
14 #if $make_TAB.value=="yes": 16 #if $make_TAB.value=="yes":
15 --output_tab "$output1" 17 --output_tab "$output1"
16 --output_format "$output_format" 18 --output_format "$output_format"
17 #end if 19 #end if
94 <option value="doi">DOI</option> 96 <option value="doi">DOI</option>
95 <option value="bibtex">BibTeX</option> 97 <option value="bibtex">BibTeX</option>
96 </param> 98 </param>
97 <when value="doi"> 99 <when value="doi">
98 <param name="doi" label="DOI" type="text" value="" 100 <param name="doi" label="DOI" type="text" value=""
99 help="Supply a DOI (e.g. 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." /> 101 help="Supply a DOI (e.g. doi: 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." />
100 </when> 102 </when>
101 <when value="bibtex"> 103 <when value="bibtex">
102 <param name="bibtex" label="BibTex" type="text" area="true" size="8x120" 104 <param name="bibtex" label="BibTex" type="text" area="true" size="8x120"
103 help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" > 105 help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
104 <sanitizer> 106 <sanitizer>
133 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml"> 135 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
134 <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> 136 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
135 <column name="value" index="0"/> 137 <column name="value" index="0"/>
136 </options> 138 </options>
137 </param> 139 </param>
140 <conditional name="interp">
138 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host"> 141 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
139 <option value="Rscript" selected="true">Rscript</option> 142 <option value="Rscript" selected="true">Rscript</option>
140 <option value="python">python</option> 143 <option value="python">python</option>
141 <option value="perl">perl</option> 144 <option value="perl">perl</option>
142 <option value="bash">bash</option> 145 <option value="bash">bash</option>
143 <option value="sh">sh</option> 146 <option value="sh">sh</option>
144 </param> 147 </param>
148 <when value="Rscript">
149 <param name="envpath" type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_r_')"
150 help = "Select the R interpreter to use when running this code - should show all installed tool shed package_r_..." />
151 </when>
152 <when value="python">
153 <param name="envpath" type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_python_')"
154 help = "Select the python dependency to use when running this code - should show all installed tool shed package_python_..." />
155 </when>
156 <when value="perl">
157 <param name="envpath" type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_perl_')"
158 help = "Select the Perl interpreter to use when running this code - should show all installed tool shed package_perl_..." />
159 </when>
160 </conditional>
145 <param name="edit_params" type="select" label="Add all additional parameters to the generated tool form so they are user editable?" 161 <param name="edit_params" type="select" label="Add all additional parameters to the generated tool form so they are user editable?"
146 help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing"> 162 help="If no (default), users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
147 <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option> 163 <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option>
148 <option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option> 164 <option value="no" selected="true">No - use the fixed values for all additional parameters - no user editing</option>
149 </param> 165 </param>
242 <param name="make_HTML" value="yes" /> 258 <param name="make_HTML" value="yes" />
243 <param name="make_TAB" value="yes" /> 259 <param name="make_TAB" value="yes" />
244 <param name="output_format" value="tabular" /> 260 <param name="output_format" value="tabular" />
245 <param name="input_formats" value="tabular" /> 261 <param name="input_formats" value="tabular" />
246 <param name="interpreter" value='python' /> 262 <param name="interpreter" value='python' />
263 <param name="envpath" value='system' />
247 <param name="runme" value="tf2_test_runme.py"/> 264 <param name="runme" value="tf2_test_runme.py"/>
248 <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/> 265 <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/>
249 <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/> 266 <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/>
250 <output name='new_tool' file="tf2_test.toolshed.gz" compare="sim_size" delta="20" /> 267 <output name='new_tool' file="tf2_test.toolshed.gz" compare="sim_size" delta="20" />
251 </test> 268 </test>
416 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&amp;keytype=ref 433 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&amp;keytype=ref
417 434
418 435
419 </help> 436 </help>
420 <citations> 437 <citations>
421 <citation type="doi">doi: 10.1093/bioinformatics/bts573</citation> 438 <citation type="doi">10.1093/bioinformatics/bts573</citation>
422 </citations> 439 </citations>
423 </tool> 440 </tool>
424 441
425 442