Mercurial > repos > ebi-gxa > scanpy_regress_variable
diff scanpy-regress-variable.xml @ 1:203fac3b1ba3 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1cc5d2101b8b14fa99e11b01714e5544704e669f
| author | ebi-gxa |
|---|---|
| date | Tue, 15 Oct 2019 05:21:49 -0400 |
| parents | 6c990f8ccad3 |
| children | b174cb4cb89e |
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--- a/scanpy-regress-variable.xml Mon Sep 16 08:22:16 2019 -0400 +++ b/scanpy-regress-variable.xml Tue Oct 15 05:21:49 2019 -0400 @@ -1,22 +1,31 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_regress_variable" name="Scanpy RegressOut" version="@TOOL_VERSION@+galaxy0"> +<tool id="scanpy_regress_variable" name="Scanpy RegressOut" version="@TOOL_VERSION@+galaxy1"> <description>variables that might introduce batch effect</description> <macros> <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ -ln -s '${input_obj_file}' input.h5 && -PYTHONIOENCODING=utf-8 scanpy-regress - --keys '${variable_keys}' - @INPUT_OPTS@ - @OUTPUT_OPTS@ +#if $variable_keys + ln -s '${input_obj_file}' input.h5 && + PYTHONIOENCODING=utf-8 scanpy-regress + --keys '${variable_keys}' + @INPUT_OPTS@ + @OUTPUT_OPTS@ +#else + echo "No regression variables passed, simply passing original input as output unchanged."; + cp '${input_obj_file}' '${output_h5}' +#end if ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> - <param name="variable_keys" type="text" label="Variables to regress out" help="Use comma to separate multiple variables"/> + <param name="variable_keys" type="text" label="Variables to regress out" help="Use comma to separate multiple variables. Not supplying variables will simply pass the input data as output unchanged."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> </inputs> <outputs>