Mercurial > repos > melpetera > generic_filter
diff GalFilter/generic_filter.xml @ 0:2c9afaf849ad draft
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author | melpetera |
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date | Thu, 23 Feb 2017 04:39:36 -0500 |
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children | b1fa45bd2b44 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GalFilter/generic_filter.xml Thu Feb 23 04:39:36 2017 -0500 @@ -0,0 +1,257 @@ +<tool id="generic_filter" name="Generic_Filter" version="2016.03.03"> + <description>Removes elements according to numerical or qualitative values</description> + <command interpreter="Rscript"> + filter_wrap.R + dataMatrix_in "$dataMatrix_in" + sampleMetadata_in "$sampleMetadata_in" + variableMetadata_in "$variableMetadata_in" + + Numeric "${numeric_condition.Factors}" + #if str($numeric_condition.Factors) == 'TRUE': + #for $i in $numeric_condition.numeric_repeat: + num_file "${i.num_file}" + parm_col "${i.parm_col_num}" + Interval "${i.interval_condition.interval}" + #if str($i.interval_condition.interval) == 'lower': + low_value "${i.interval_condition.low_value}" + #elif str($i.interval_condition.interval) == 'upper': + up_value "${i.interval_condition.up_value}" + #elif str($i.interval_condition.interval) == 'between': + low_value "${i.interval_condition.low_value}" + up_value "${i.interval_condition.up_value}" + #elif str($i.interval_condition.interval) == 'extremity': + low_value "${i.interval_condition.low_value}" + up_value "${i.interval_condition.up_value}" + #end if + #end for + #end if + + Factors "${qualitative_condition.Factors}" + #if str($qualitative_condition.Factors) == 'TRUE': + #for $i in $qualitative_condition.qualitative_repeat: + qual_file "${i.qual_file}" + factor_col "${i.factor_col}" + factors_value "${i.factors_value}" + #end for + #end if + + dataMatrix_out "$dataMatrix_out" + sampleMetadata_out "$sampleMetadata_out" + variableMetadata_out "$variableMetadata_out" + </command> + + <inputs> + <param name="dataMatrix_in" type="data" label="Data Matrix file" help="" format="tabular" /> + <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" /> + <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" /> + + <conditional name="numeric_condition"> + <param name="Factors" type="select" label="Deleting samples and/or variables according to Numerical values" help=""> + <option value="FALSE">no</option> + <option value="TRUE">yes</option> + </param> + <when value="TRUE"> + <repeat name="numeric_repeat" title="Identify the parameter to filter " min="1"> + <param name="num_file" label="On file" type="select" display="radio" help=""> + <option value="sample">Sample metadata</option> + <option value="variable">Variable metadata</option> + </param> + <param name="parm_col_num" label="Name of the column to filter" type="text" value="" help="" /> + <conditional name="interval_condition"> + <param name="interval" type="select" label="Interval of values to remove" help=""> + <option value="lower">lower</option> + <option value="upper">upper</option> + <option value="between">between</option> + <option value="extremity">extremity</option> + </param> + <when value="lower"> + <param name="low_value" type="float" label="Remove all values lower than" optional="true" value="0" help=""/> + </when> + <when value="upper"> + <param name="up_value" type="float" label="Remove all values upper than" optional="true" value="0" help=""/> + </when> + <when value="between"> + <param name="low_value" type="float" label="Remove all values between" optional="true" value="0" help=""/> + <param name="up_value" type="float" label="And" optional="true" value="1" help=""/> + </when> + <when value="extremity"> + <param name="low_value" type="float" label="Remove all values lower than" optional="true" value="0" help=""/> + <param name="up_value" type="float" label="And upper than" optional="true" value="1" help=""/> + </when> + </conditional> + </repeat> + </when> + <when value="FALSE"> + </when> + </conditional> + + <conditional name="qualitative_condition"> + <param name="Factors" type="select" label="Deleting samples and/or variables according to Qualitative values" help=""> + <option value="FALSE">no</option> + <option value="TRUE">yes</option> + </param> + <when value="TRUE"> + <repeat name="qualitative_repeat" title="Removing a level in factor" min="1"> + <param name="qual_file" label="On file" type="select" display="radio" help=""> + <option value="sample">Sample metadata</option> + <option value="variable">Variable metadata</option> + </param> + <param name="factor_col" label="Name of the column to filter" type="text" value="" help="" /> + <param name="factors_value" type="text" label="Remove factor when" help="" value="" /> + </repeat> + </when> + <when value="FALSE"> + </when> + </conditional> + </inputs> + + <outputs> + <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data> + <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data> + <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> + </outputs> + + <help> + +.. class:: infomark + +**Authors** Marion Landi and Melanie Petera + +--------------------------------------------------- + +============== +Generic_Filter +============== + +----------- +Description +----------- + + | Allows to remove all samples and/or variables corresponding to specific values regarding designated factors or numerical variables. + | + + +----------------- +Workflow position +----------------- + + +.. image:: filter.png + :width: 800 + + + +----------- +Input files +----------- + ++----------------------------+------------+ +| Parameter : num + label | Format | ++============================+============+ +| 1 : Data Matrix file | tabular | ++----------------------------+------------+ +| 2 : Sample metadata file | tabular | ++----------------------------+------------+ +| 3 : Variable metadata file | tabular | ++----------------------------+------------+ + +| +| Missing values in numerical columns of data must be coded NA if you want to use the Numerical filter on them. + + +---------- +Parameters +---------- + +Deleting samples and/or variables according to Numerical values: + | If 'yes' (not default): execution deletes all samples or variables (according to selection) for which the designated + | numerical parameter ("Name of the column to remove" field) equals the selected range of values (depending on the "Interval of values to remove" chosen). + | To delete multiple independent intervals of value from the same parameter, it is necessary to add as many times as necessary + | the corresponding column via the button "Add new Identify the parameter to filter". + +| *On file (only if 'yes')* +| Choice between sample and variable filtering (referring to the input file containing the factor). +| + +| *Name of the column to filter (only if 'yes')* +| Column name of the numerical parameter from which we want to remove a range of values. +| + +| *Interval of values to remove (only if 'yes')* +| Allows to choose which type of interval should be removed: +| - lower: removes all values below a specified value +| - upper: removes all values above a specified value +| - between: removes all values both greater than a specified value and lower than another (upper) one +| - extremity: removes all values that are either lower than a specified value or greater than another (upper) one +| + +| *'Remove all values' + interval chosen (only if 'yes')* +| Numerical value(s) used as threshold, depending on the type of interval chosen above. +| Only one value for 'lower' and 'upper'; two values for 'between' and 'extremity'. +| + +| *Notes:* +| - these parameters can be used several times using the "Add new Identify the parameter to filter" button +| - Numerical filter does not remove NA values; if you want to suppress them, use the Qualitative filter below +| + + +Deleting samples and/or variables according to Qualitative values + | If 'yes' (not default): execution deletes all data samples or variables (according to selection) for which the designated + | factor ("Name of the column to remove" field) equals the selected level ("Remove factor when" field). + | To delete multiple values of the same factor, it is necessary to add as many times as necessary the corresponding factor + | via the button "Add new Removing a level in factor". + +| *On file (only if 'yes')* +| Choice between sample and variable filtering (referring to the input file containing the factor). +| + +| *Name of the column to filter (only if 'yes')* +| Column name of the factor from which we want to remove a level. +| + +| *Remove factor when (only if 'yes')* +| Value that you want to delete from the selected column. +| Each line with that value of designated factor will be deleted. +| + +| *Notes:* +| - these parameters can be used several times using the "Add new Removing a level in factor" button +| - this filter can be used to filter NA in numerical parameters, or to remove a specific numerical value +| + + +------------ +Output files +------------ + + +dataMatrix + | tabular output + | Identical to the input Data Matrix file with the sample columns and variable lines deleted according to specified filters + | + +sampleMetadata + | tabular output + | Identical to the input Sample metadata file with the sample lines deleted according to specified filters + | + +variableMetadata + | tabular output + | Identical to the input Variable metadata file with the variable lines deleted according to specified filters + | + + +--------------------------------------------------- + +--------------- +Working example +--------------- + + +.. class:: warningmark + +Soon see the corresponding "Page" + + </help> +</tool> \ No newline at end of file