comparison Intchecks/xml_intensity_check.xml @ 6:ec75de7f1e08 draft default tip

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5:a31f3f802b2b

<tool id="intens_check" name="Intensity Check" version="1.2.8">
	<description>Statistical measures, number of missing values and mean fold change</description>
	<requirements>
	    <requirement type="package" version="1.1_5">r-batch</requirement>
	</requirements>
	<command interpreter="Rscript">
  
		wrapper_intensity_check.R
	

					<validator type="no_options" message="Please choose at least one statistic representation" />
				</param>
			</when>
			
			<when value="each_class">
				<param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" label="Class column" help="Class column in Sample metadata" />
				<param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics">
					<option value="mean">Mean</option>
                    <option value="sd">Standard deviation</option>
                    <option value="median">Median</option>
                    <option value="quartile">Quartile</option>

							<option value="none">none </option>
							<option value="log2">log2 </option>
							<option value="log10">log10 </option>
						</param>
					</when>
				</conditional>
			</when>
			
			<when value="one_class">
				<param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" label="Class column" help="Class column in Sample metadata" />
				<param name="class1" type="text" label="Selected class" help="Name of the class to test versus all the remaining samples." />
				<param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics">
					<option value="mean">Mean</option>
                    <option value="sd">Standard deviation</option>
                    <option value="median">Median</option>

							<option value="none">none </option>
							<option value="log2">log2 </option>
							<option value="log10">log10 </option>
						</param>
					</when>
				</conditional>
			</when>
		</conditional>
	</inputs>
					

		<data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" />
		<data name="graphs_out" label="IC_Graphs" format="pdf" />
	</outputs>
	
	

	
	<help>

.. class:: infomark

	
**Statistics**
	|  Select the statistical measures you want to add in the variable metadata table. If the method is "each class" or "one class", you can choose to leave this section blank if you only want to calculate the mean fold change (see below).

**Class column** (*only if "each class" or "one class"*)
	| Select the class column in sample metadata table.

**Selected class** (*only if "one class"*)
	| If the method is "one class", specify it. Remaining samples will be named "Other".
	
**Calculate the mean fold change** (*only if "each class" or "one class"*)

.. 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>`_
 |

6:ec75de7f1e08

<tool id="intens_check" name="Intensity Check" version="1.3.0">
	<description>Statistical measures, number of missing values and mean fold change</description>
	<requirements>
	    <requirement type="package" version="4.2.1">r-base</requirement>
	</requirements>
	<command interpreter="Rscript">
  
		wrapper_intensity_check.R
	

					<validator type="no_options" message="Please choose at least one statistic representation" />
				</param>
			</when>
			
			<when value="each_class">
				<param name="class_col" type="text" label="Class column" help="Name of the column in Sample metadata" />
				<param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics">
					<option value="mean">Mean</option>
                    <option value="sd">Standard deviation</option>
                    <option value="median">Median</option>
                    <option value="quartile">Quartile</option>

							<option value="none">none </option>
							<option value="log2">log2 </option>
							<option value="log10">log10 </option>
						</param>
					</when>
					<when value="No">
					</when>
				</conditional>
			</when>
			
			<when value="one_class">
				<param name="class_col" type="text" label="Class column" help="Name of the column in Sample metadata" />
				<param name="class1" type="text" label="Selected class" help="Name of the class to test versus all the remaining samples." />
				<param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics">
					<option value="mean">Mean</option>
                    <option value="sd">Standard deviation</option>
                    <option value="median">Median</option>

							<option value="none">none </option>
							<option value="log2">log2 </option>
							<option value="log10">log10 </option>
						</param>
					</when>
					<when value="No">
					</when>
				</conditional>
			</when>
		</conditional>
	</inputs>
					

		<data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" />
		<data name="graphs_out" label="IC_Graphs" format="pdf" />
	</outputs>
	
	
  <tests>
	<test>
      <param name="dataMatrix_in" value="input_IC_DM.txt"/>
      <param name="sampleMetadata_in" value="input_IC_SM.txt"/>
      <param name="variableMetadata_in" value="input_IC_VM.txt"/>
	  <param name="method" value="one_class"/>
	  <param name="chosen_stat" value="mean,sd,NA"/>
	  <param name="class_col" value="uv"/>
	  <param name="class1" value="s"/>
	  <param name="test_fold" value="Yes"/>
	  <param name="fold_frac" value="Bottom"/>
	  <param name="logarithm" value="log2"/>
      <output name="variableMetadata_out" file="output_IC_VM.tabular"/>
	</test>
  </tests>
	
	<help>

.. class:: infomark

	
**Statistics**
	|  Select the statistical measures you want to add in the variable metadata table. If the method is "each class" or "one class", you can choose to leave this section blank if you only want to calculate the mean fold change (see below).

**Class column** (*only if "each class" or "one class"*)
	| Fill the name of the class column in sample metadata table; it is case-sensitive.

**Selected class** (*only if "one class"*)
	| If the method is "one class", specify it. Remaining samples will be named "Other".
	
**Calculate the mean fold change** (*only if "each class" or "one class"*)

.. class:: warningmark

For more information about input files, refer to the corresponding "W4M HowTo" page:
 | `W4M table format for Galaxy <https://workflow4metabolomics.org/sites/default/files/fichiers/documents/w4m_TableFormatForGalaxy_150908.pdf>`_
 |