Mercurial > repos > fubar > tool_factory_2
diff rgToolFactory2.xml @ 9:ce5ec1d989fd draft
Uploaded
author | fubar |
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date | Wed, 14 Jan 2015 19:17:11 -0500 |
parents | 6a3c292412fa |
children |
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--- a/rgToolFactory2.xml Mon Jan 12 05:27:52 2015 -0500 +++ b/rgToolFactory2.xml Wed Jan 14 19:17:11 2015 -0500 @@ -1,15 +1,17 @@ -<tool id="rgTF2" name="Tool Factory Two" version="1.15"> +<tool id="rgTF2" name="Tool Factory Two" version="1.16"> <description>Scripts into tools</description> <requirements> <requirement type="package" version="9.10">ghostscript</requirement> <requirement type="package" version="1.3.20">graphicsmagick</requirement> </requirements> + <code file="getlocalrpackages.py"/> <command interpreter="python"> #if ( $__user_email__ not in $__admin_users__ ): rgToolFactory2.py --bad_user $__user_email__ #else: - rgToolFactory2.py --script_path "$runme" --interpreter "$interpreter" + rgToolFactory2.py --script_path "$runme" --interpreter "$interp.interpreter" --tool_name "$tool_name" --user_email "$__user_email__" --citations "$citeme" + --envshpath "$interp.envpath" #if $make_TAB.value=="yes": --output_tab "$output1" @@ -96,7 +98,7 @@ </param> <when value="doi"> <param name="doi" label="DOI" type="text" value="" - 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." /> + 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." /> </when> <when value="bibtex"> <param name="bibtex" label="BibTex" type="text" area="true" size="8x120" @@ -135,6 +137,7 @@ <column name="value" index="0"/> </options> </param> + <conditional name="interp"> <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host"> <option value="Rscript" selected="true">Rscript</option> <option value="python">python</option> @@ -142,6 +145,19 @@ <option value="bash">bash</option> <option value="sh">sh</option> </param> + <when value="Rscript"> + <param name="envpath" type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_r_')" + help = "Select the R interpreter to use when running this code - should show all installed tool shed package_r_..." /> + </when> + <when value="python"> + <param name="envpath" type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_python_')" + help = "Select the python dependency to use when running this code - should show all installed tool shed package_python_..." /> + </when> + <when value="perl"> + <param name="envpath" type="select" label="Interpreter to use" dynamic_options="find_packages(prefix='package_perl_')" + help = "Select the Perl interpreter to use when running this code - should show all installed tool shed package_perl_..." /> + </when> + </conditional> <param name="edit_params" type="select" label="Add all additional parameters to the generated tool form so they are user editable?" 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"> <option value="yes">Yes, allow user to edit all additional parameters on the generated tool form</option> @@ -244,6 +260,7 @@ <param name="output_format" value="tabular" /> <param name="input_formats" value="tabular" /> <param name="interpreter" value='python' /> + <param name="envpath" value='system' /> <param name="runme" value="tf2_test_runme.py"/> <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/> <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/> @@ -418,7 +435,7 @@ </help> <citations> - <citation type="doi">doi: 10.1093/bioinformatics/bts573</citation> + <citation type="doi">10.1093/bioinformatics/bts573</citation> </citations> </tool>