Mercurial > repos > iuc > pick_value
changeset 0:bf793b71559a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value commit ef564483fa8dc267c599af8745aab4e03b0c57e0
| author | iuc |
|---|---|
| date | Tue, 07 Nov 2023 09:02:42 +0000 |
| parents | |
| children | b19e21af9c52 |
| files | pick_value.xml test-data/simple_line.txt test-data/simple_line_alternative.txt |
| diffstat | 3 files changed, 375 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pick_value.xml Tue Nov 07 09:02:42 2023 +0000 @@ -0,0 +1,373 @@ +<tool name="Pick parameter value" id="pick_value" version="0.1.0" profile="21.01" tool_type="expression"> + <macros> + <xml name="booleans"> + <repeat name="pick_from" title="Pick from"> + <param name="value" type="boolean" optional="true" label="Value" /> + </repeat> + </xml> + <xml name="integers"> + <repeat name="pick_from" title="Pick from"> + <param name="value" type="integer" label="Value" optional="true" /> + </repeat> + </xml> + <xml name="floats"> + <repeat name="pick_from" title="Pick from"> + <param name="value" type="float" label="Value" optional="true" /> + </repeat> + </xml> + <xml name="texts"> + <repeat name="pick_from" title="Pick from"> + <param name="value" type="text" optional="true" label="Value" /> + </repeat> + </xml> + <xml name="datas"> + <repeat name="pick_from" title="Pick from"> + <param name="value" type="data" format="data" optional="true" label="Value" /> + </repeat> + </xml> + <xml name="param_type"> + <param name="param_type" type="select" label="Select type of parameter to select from"> + <option value="data">Dataset</option> + <option value="text">Text</option> + <option value="integer">Integer</option> + <option value="float">Float</option> + <option value="boolean">Boolean</option> + </param> + </xml> + <xml name="param_pick_style"> + <param name="pick_style" type="select" label="Picking behavior" help="How should the case when not exactly one value is non-null be handled?"> + <option value="first">Pick first value</option> + <option value="first_or_default">Pick first value (or provide default)</option> + <option value="first_or_error">Pick first value (or fail)</option> + <option value="only">Pick only value</option> + </param> + </xml> + <xml name="type_conditional"> + <conditional name="type_cond"> + <expand macro="param_type" /> + <when value="text"> + <expand macro="texts" /> + </when> + <when value="integer"> + <expand macro="integers" /> + </when> + <when value="float"> + <expand macro="floats" /> + </when> + <when value="boolean"> + <expand macro="booleans" /> + </when> + <when value="data"> + <expand macro="datas" /> + </when> + </conditional> + </xml> + <xml name="type_conditional_with_default"> + <conditional name="type_cond"> + <expand macro="param_type" /> + <when value="text"> + <expand macro="texts" /> + <param name="default_value" type="text" label="Default Value" /> + </when> + <when value="integer"> + <expand macro="integers" /> + <param name="default_value" type="integer" optional="true" label="Default Value" /> + </when> + <when value="float"> + <expand macro="floats" /> + <param name="default_value" type="float" optional="true" label="Default Value" /> + </when> + <when value="boolean"> + <expand macro="booleans" /> + <param name="default_value" type="boolean" label="Default Value" /> + </when> + <when value="data"> + <expand macro="datas" /> + <param name="default_value" type="data" format="data" label="Default Value" /> + </when> + </conditional> + </xml> + <xml name="style_conditional"> + <conditional name="style_cond"> + <expand macro="param_pick_style" /> + <when value="first"> + <expand macro="type_conditional" /> + </when> + <when value="first_or_default"> + <expand macro="type_conditional_with_default" /> + </when> + <when value="first_or_error"> + <expand macro="type_conditional" /> + </when> + <when value="only"> + <expand macro="type_conditional" /> + </when> + </conditional> + </xml> + </macros> + <expression type="ecma5.1"><![CDATA[{ +var out = null; +var pickStyle = $job.style_cond.pick_style; +var paramType = $job.style_cond.type_cond.param_type; +var pickFrom = $job.style_cond.type_cond.pick_from; +for ( var i = 0; i < pickFrom.length; i++ ) { + if ( pickFrom[i].value !== null ) { + if ( pickStyle == 'only' && out !== null ) { + return { '__error_message': 'Multiple null values found, only one allowed.' }; + } else if ( out == null ) { + out = pickFrom[i].value; + } + } +} +if ( out == null && pickStyle == 'first_or_default' ) { + out = $job.style_cond.type_cond.default_value; +} +if ( paramType == "data" && out ) { + out = out.src; +} +if ( out == null && ( pickStyle == "first_or_error" || pickStyle == "only" ) ) { + return { '__error_message': 'No non-null values found among tool inputs.' }; +} +return { 'output': out }; +}]]></expression> + <inputs> + <expand macro="style_conditional" /> + </inputs> + <outputs> + <output type="text" name="text_param" from="output"> + <filter>style_cond['type_cond']['param_type'] == 'text'</filter> + </output> + <output type="integer" name="integer_param" from="output"> + <filter>style_cond['type_cond']['param_type'] == 'integer'</filter> + </output> + <output type="float" name="float_param" from="output"> + <filter>style_cond['type_cond']['param_type'] == 'float'</filter> + </output> + <output type="boolean" name="boolean_param" from="output"> + <filter>style_cond['type_cond']['param_type'] == 'boolean'</filter> + </output> + <output type="data" name="data_param" from="output"> + <filter>style_cond['type_cond']['param_type'] == 'data'</filter> + </output> + </outputs> + <help> +A "null" value is an empty value, it means some input wasn't specified or some tool produced +an empty value or was skipped entirely. This can be thought of as an NA in Excel or a None value +in Python. This expression tool can be fed multiple values - from parameter inputs or the +outputs or other tools or workflows - and pick one. This allows building workflows which can +skip steps and branch in complex ways. + +There are subtle but important distinctions between the selection style - though they all +essentially pick the first value that is non-null (i.e. the first input with a real value). + +- "Pick first value" is the default and will just return its own null value if none of the inputs +are non-null. +- "Pick first value (or provide default)" allows picking a default value that will be used if none of the +inputs are non-null. +- "Pick first value (or fail)" will cause the tool execution to fail if none of the selections are +non-null. This can be important because it provides a clearer indication that something went +wrong and can prevent the further evaluation of a workflow. +- "Pick only value" is like "First value (or fail)" in that it will cause an error if none of the +inputs are non-null but it will go further to ensure that exactly one value is non-null. When +building conditonal paths through a workflow this can ensure that at most one path is +taken. + </help> + <tests> + <test expect_num_outputs="1"> + <conditional name="style_cond"> + <param name="pick_style" value="first" /> + <conditional name="type_cond"> + <param name="param_type" value="data" /> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value="simple_line.txt" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value="simple_line_alternative.txt" /> + </repeat> + </conditional> + </conditional> + <output name="data_param" value="simple_line.txt" /> + </test> + <test expect_num_outputs="1"> + <conditional name="style_cond"> + <param name="pick_style" value="first" /> + <conditional name="type_cond"> + <param name="param_type" value="boolean" /> + <repeat name="pick_from"> + <param name="value" value_json="true" /> + </repeat> + </conditional> + </conditional> + <output name="boolean_param" value_json="true" /> + </test> + <test expect_num_outputs="1"> + <conditional name="style_cond"> + <param name="pick_style" value="first" /> + <conditional name="type_cond"> + <param name="param_type" value="boolean" /> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value_json="true" /> + </repeat> + </conditional> + </conditional> + <output name="boolean_param" value_json="true" /> + </test> + <test expect_num_outputs="1"> + <conditional name="style_cond"> + <param name="pick_style" value="first" /> + <conditional name="type_cond"> + <param name="param_type" value="boolean" /> + <repeat name="pick_from"> + <param name="value" value_json="false" /> + </repeat> + </conditional> + </conditional> + <output name="boolean_param" value_json="false" /> + </test> + <test expect_num_outputs="1"> + <conditional name="style_cond"> + <param name="pick_style" value="first" /> + <conditional name="type_cond"> + <param name="param_type" value="boolean" /> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value_json="false" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value_json="true" /> + </repeat> + </conditional> + </conditional> + <output name="boolean_param" value_json="false" /> + </test> + <test expect_num_outputs="1"> + <conditional name="style_cond"> + <param name="pick_style" value="first" /> + <conditional name="type_cond"> + <param name="param_type" value="boolean" /> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value_json="true" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value_json="false" /> + </repeat> + </conditional> + </conditional> + <output name="boolean_param" value_json="true" /> + </test> + <test expect_failure="true"> + <conditional name="style_cond"> + <param name="pick_style" value="only" /> + <conditional name="type_cond"> + <param name="param_type" value="boolean" /> + <repeat name="pick_from"> + <param name="value" value_json="true" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value_json="false" /> + </repeat> + </conditional> + </conditional> + </test> + <test expect_failure="true"> + <conditional name="style_cond"> + <param name="pick_style" value="first_or_error" /> + <conditional name="type_cond"> + <param name="param_type" value="boolean" /> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + </conditional> + </conditional> + </test> + <test expect_failure="true"> + <conditional name="style_cond"> + <param name="pick_style" value="only" /> + <conditional name="type_cond"> + <param name="param_type" value="boolean" /> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + </conditional> + </conditional> + </test> + <test expect_num_outputs="1"> + <conditional name="style_cond"> + <param name="pick_style" value="first" /> + <conditional name="type_cond"> + <param name="param_type" value="boolean" /> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + </conditional> + </conditional> + <output name="boolean_param" value_json="null" /> + </test> + <test expect_num_outputs="1"> + <conditional name="style_cond"> + <param name="pick_style" value="first_or_default" /> + <conditional name="type_cond"> + <param name="param_type" value="boolean" /> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <param name="default_value" value_json="true" /> + </conditional> + </conditional> + <output name="boolean_param" value_json="true" /> + </test> + <test expect_num_outputs="1"> + <conditional name="style_cond"> + <param name="pick_style" value="first_or_default" /> + <conditional name="type_cond"> + <param name="param_type" value="boolean" /> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <param name="default_value" value_json="false" /> + </conditional> + </conditional> + <output name="boolean_param" value_json="false" /> + </test> + <test expect_num_outputs="1"> + <conditional name="style_cond"> + <param name="pick_style" value="first_or_default" /> + <conditional name="type_cond"> + <param name="param_type" value="data" /> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <repeat name="pick_from"> + <param name="value" value_json="null" /> + </repeat> + <param name="default_value" value="simple_line.txt" /> + </conditional> + </conditional> + <output name="data_param" value="simple_line.txt" /> + </test> + </tests> +</tool> +