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author | melpetera |
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date | Fri, 03 Jan 2020 04:09:28 -0500 |
parents | 12cf1eed21f4 |
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<tool id="generic_filter" name="Generic_Filter" version="2020.01"> <description>Removes elements according to numerical or qualitative values</description> <requirements> <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> <command> Rscript '$__tool_directory__/filter_wrap.R' dataMatrix_in "$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> <tests> <test> <param name="dataMatrix_in" value="in_DM1.tabular"/> <param name="sampleMetadata_in" value="in_SM1.tabular"/> <param name="variableMetadata_in" value="in_VM1.tabular"/> <conditional name="numeric_condition"> <param name="Factors" value="TRUE"/> <param name="numeric_repeat_0|num_file" value="variable"/> <param name="numeric_repeat_0|parm_col_num" value="rt"/> <param name="numeric_repeat_0|interval_condition|interval" value="lower"/> <param name="numeric_repeat_0|interval_condition|low_value" value="1.2"/> </conditional> <conditional name="qualitative_condition"> <param name="Factors" value="TRUE"/> <param name="qualitative_repeat_0|qual_file" value="sample"/> <param name="qualitative_repeat_0|factor_col" value="Time"/> <param name="qualitative_repeat_0|factors_value" value="3"/> </conditional> <output name="dataMatrix_out" file="out_DM1.tabular"/> <output name="sampleMetadata_out" file="out_SM1.tabular"/> <output name="variableMetadata_out" file="out_VM1.tabular"/> </test> </tests> <help> .. class:: infomark **Authors:** Melanie Petera for original R code - Marion Landi and Melanie Petera for original Galaxy wrapper **Maintainer:** Melanie Petera (PFEM - INRAE - MetaboHUB) --------------------------------------------------- ============== 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: 700 ----------- 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 "Insert Identify the parameter to filter" button. | *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 "Insert 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 "Insert Removing a level in factor" button. | *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 "Insert 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 | --------------------------------------------------- ---------------------- Additional information ---------------------- .. class:: warningmark For more information about input files, refer to the corresponding "W4M HowTo" page: | `W4M table format for Galaxy <http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf>`_ | </help> <citations> <citation type="doi">10.1093/bioinformatics/btu813</citation> </citations> </tool>