diff abims_sartools_deseq2.xml @ 4:05c9b1a7f44e draft default tip

Uploaded new release 1.7.3
author lgueguen
date Thu, 07 Jan 2021 11:12:01 +0000
parents de6d0b7c17af
children
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--- a/abims_sartools_deseq2.xml	Mon Oct 01 05:07:56 2018 -0400
+++ b/abims_sartools_deseq2.xml	Thu Jan 07 11:12:01 2021 +0000
@@ -1,114 +1,96 @@
-<tool id="sartools_deseq2" name="SARTools DESeq2" version="@WRAPPER_VERSION@.0">
+<tool id="sartools_deseq2" name="SARTools DESeq2" version="@TOOL_VERSION@+galaxy0">
     
-    <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description>Compare two or more biological conditions in a RNA-Seq framework with DESeq2</description>
     
     <macros>
-    	<import>macros.xml</import>
+        <import>macros.xml</import>
     </macros>
     
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     
-    <!-- [REQUIRED] The command to execute -->
-    <command interpreter="python"><![CDATA[
-	
-	abims_sartools_deseq2_wrapper.py
-	## parameters
-	@COMMAND_BASIC_PARAMETERS@
-    	#if str( $advanced_parameters.adv_param ) == "show":
-            @COMMAND_BATCH_PARAM@
-            --fitType $advanced_parameters.fitType
-            --cooksCutoff $advanced_parameters.cooksCutoff
-            --independentFiltering $advanced_parameters.independentFiltering
-	    --alpha $advanced_parameters.alpha
-	    --pAdjustMethod $advanced_parameters.pAdjustMethod
-	    --typeTrans $advanced_parameters.typeTrans
-	    --locfunc $advanced_parameters.locfunc
-	    --colors $advanced_parameters.colors
-            --forceCairoGraph $advanced_parameters.forceCairoGraph
-    	#end if
-	## ouputs
-	@COMMAND_OUTPUTS@
+    <command><![CDATA[
+ 
+python '$__tool_directory__/abims_sartools_deseq2_wrapper.py'
+## parameters
+@COMMAND_BASIC_PARAMETERS@
+@COMMAND_BATCH_PARAM@
+--fitType '$advanced_parameters.fitType'
+--cooksCutoff '$advanced_parameters.cooksCutoff'
+--independentFiltering '$advanced_parameters.independentFiltering'
+--alpha '$advanced_parameters.alpha'
+--pAdjustMethod '$advanced_parameters.pAdjustMethod'
+--typeTrans '$advanced_parameters.typeTrans'
+--locfunc '$advanced_parameters.locfunc'
+--colors "'$advanced_parameters.colors'"
+--forceCairoGraph '$advanced_parameters.forceCairoGraph'
+## ouputs
+@COMMAND_OUTPUTS@
        
     ]]></command>
     
-    <!-- [REQUIRED] Input files and tool parameters -->
     <inputs>
         
         <expand macro="basic_parameters" />
- 
-        <conditional name="advanced_parameters" >
-            <param name="adv_param" type="select" label="Advanced Parameters" help="" >
-                <option value="hide" selected="true">Hide</option>
-                <option value="show">Show</option>
+
+        <section name="advanced_parameters" title="Advanced Parameters" expanded="false">
+            <expand macro="batch_param" />
+            <param type="select" label="Mean-variance relationship" argument="--fitType" help="Type of model for the mean-dispersion relationship. Parametric by default." >
+                <option value="parametric" selected="true">parametric</option>
+                <option value="local">local</option>
+                <option value="mean">mean</option>
             </param>
-            <when value="hide" />
-            <when value="show">
-		<expand macro="batch_param" />
-                <param type="select" label="Mean-variance relationship" argument="--fitType" help="Type of model for the mean-dispersion relationship. Parametric by default." >
-          		<option value="parametric" selected="true">parametric</option>
-			<option value="local">local</option>
-			<option value="mean">mean</option>
-		</param>
-		<param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" argument="--cooksCutoff" help="Checked by default."/>
-		<param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" argument="--independentFiltering" help="Checked by default."/>
-		<expand macro="alpha_param" />
-		<expand macro="padjustmethod_param" />
-            	<param type="select" label="Transformation for PCA/clustering" argument="--typeTrans" help="Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." >
-                	<option value="VST" selected="true">VST</option>
-                	<option value="rlog">rlog</option>
-            	</param>
-            	<param type="select" label="Estimation of the size factors" argument="--locfunc" help="'median' (default) or 'shorth' from the genefilter package." >
-                	<option value="median" selected="true">median</option>
-                	<option value="shorth">shorth</option>
-            	</param>
-		<expand macro="colors_param" />
-		<expand macro="forceCairoGraph_param" />
-            </when>
-        </conditional>
+            <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" argument="--cooksCutoff" help="Checked by default."/>
+            <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" argument="--independentFiltering" help="Checked by default."/>
+            <expand macro="alpha_param" />
+            <expand macro="padjustmethod_param" />
+            <param type="select" label="Transformation for PCA/clustering" argument="--typeTrans" help="Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." >
+                <option value="VST" selected="true">VST</option>
+                <option value="rlog">rlog</option>
+            </param>
+            <param type="select" label="Estimation of the size factors" argument="--locfunc" help="'median' (default) or 'shorth' from the genefilter package." >
+                <option value="median" selected="true">median</option>
+                <option value="shorth">shorth</option>
+            </param>
+            <expand macro="colors_param" />
+            <expand macro="forceCairoGraph_param" />
+        </section>
 
     </inputs>
     
-    <!-- [REQUIRED] Output files -->
     <outputs>
         
         <expand macro="outputs" /> 
               
     </outputs>
     
-    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
     <tests>
-        <!-- [HELP] Test files have to be in the ~/test-data directory -->
         <test>
         <!-- Test with 2 conditions, 2 replicates, 8217 features -->
             <param name="targetFile" dbkey="?" value="target.txt" />
             <param name="rawDir"   value="raw.zip" dbkey="?" ftype="zip"/>
-	        <param name="adv_param" value="show"/>
             <output name="log">
                 <assert_contents>
-                    <has_text text="KO vs WT    0.1       171" />
+                    <has_text text="KO vs WT    0.1                171" />
                     <has_text text="KO vs WT    2583   2663 5246" />
                     <has_text text="HTML report created" />
                 </assert_contents>
             </output>
         </test>
-<!--        <test>
+<!--    <test>
 -->        <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect -->
-<!--            <param name="targetFile" dbkey="?" value="targetT048.txt" />
+<!--        <param name="targetFile" dbkey="?" value="targetT048.txt" />
             <param name="rawDir"   value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/>
-	    <param name="condRef" value="T0"/>
-	    <param name="adv_param" value="show"/>
-	    <param name="condition" value="true"/>
+            <param name="condRef" value="T0"/>
+            <param name="condition" value="true"/>
             <output name="tables_html" file="SARTools_DESeq2_targetT048_tables.html" lines_diff="14">
-            	<extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_DESeq2_T4vsT0.complete.txt"/>
-            	<extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_DESeq2_T8vsT0.complete.txt"/>
-            	<extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_DESeq2_T8vsT4.complete.txt"/>
-	    </output>
+                <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_DESeq2_T4vsT0.complete.txt"/>
+                <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_DESeq2_T8vsT0.complete.txt"/>
+                <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_DESeq2_T8vsT4.complete.txt"/>
+            </output>
         </test>
--->    </tests>
+--> </tests>
     
-    <!-- [OPTIONAL] Help displayed in Galaxy -->
     <help><![CDATA[
 
 @HELP_AUTHORS@
@@ -135,17 +117,17 @@
 Parameters
 ----------
 
-	@HELP_BASIC_PARAMETERS@
-	* **batch:** adjustment variable to use as a batch effect, must be a column of the target file (NULL if no batch effect needs to be taken into account);
-	* **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);
-	* **fitType:** type of model for the mean-dispersion relationship ("parametric" by default, or "local");
-	* **cooksCutoff:** TRUE (default) of FALSE to execute or not the detection of the outliers [4];
-	* **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5];
-	* **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods);
-	* **typeTrans:** method of transformation of the counts for the clustering and the PCA (default is "VST" for Variance Stabilizing Transformation, or "rlog" for Regularized Log Transformation);
-	* **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package);
-	* **colors:** colors used for the figures (one per biological condition), 8 are given by default.
-	* **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo").
+ @HELP_BASIC_PARAMETERS@
+ * **batch:** adjustment variable to use as a batch effect, must be a column of the target file (NULL if no batch effect needs to be taken into account);
+ * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);
+ * **fitType:** type of model for the mean-dispersion relationship ("parametric" by default, or "local");
+ * **cooksCutoff:** TRUE (default) of FALSE to execute or not the detection of the outliers [4];
+ * **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5];
+ * **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods);
+ * **typeTrans:** method of transformation of the counts for the clustering and the PCA (default is "VST" for Variance Stabilizing Transformation, or "rlog" for Regularized Log Transformation);
+ * **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package);
+ * **colors:** colors used for the figures (one per biological condition), 8 are given by default.
+ * **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo").
 
 
 ------------
@@ -154,7 +136,7 @@
 
 @HELP_OUTPUT_FILES@
 
-		
+  
 ---------------------------------------------------
 
 [1] G.-K. Smyth. Limma: linear models for microarray data. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber, editors, Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pages 397–420. Springer, New York, 2005.
@@ -172,27 +154,27 @@
 [7] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165–1188, 2001.
 
 
-   ]]></help>
+    ]]></help>
 
-   <citations>
-    <expand macro="common_citations" /> 
-    <citation type="bibtex">@ARTICLE{Cook77,
-    author = {R.-D. Cook},
-    title = {Detection of Influential Observation in Linear Regression},
-    journal = {Technometrics},
-    year = {1977},
-    month = {February}
-    }</citation>
-    <citation type="bibtex">@ARTICLE{Bourgon10,
-    author = {R. Bourgon, R. Gentleman, and W. Huber},
-    title = {Independent filtering increases detection power for high-throughput experiments},
-    journal = {PNAS},
-    year = {2010},
-    volume = {107},
-    number = {21},
-    pages = {9546–9551},
-    note = {URL: http://www.pnas.org/content/107/21/9546.long}
-    }</citation>
-   </citations>
+    <citations>
+        <expand macro="common_citations" /> 
+        <citation type="bibtex">@ARTICLE{Cook77,
+            author = {R.-D. Cook},
+            title = {Detection of Influential Observation in Linear Regression},
+            journal = {Technometrics},
+            year = {1977},
+            month = {February}
+        }</citation>
+        <citation type="bibtex">@ARTICLE{Bourgon10,
+            author = {R. Bourgon, R. Gentleman, and W. Huber},
+            title = {Independent filtering increases detection power for high-throughput experiments},
+            journal = {PNAS},
+            year = {2010},
+            volume = {107},
+            number = {21},
+            pages = {9546–9551},
+            note = {URL: http://www.pnas.org/content/107/21/9546.long}
+        }</citation>
+    </citations>
     
 </tool>