# HG changeset patch
# User dereeper
# Date 1704274197 0
# Node ID 7ec8715bedc29ed5f1e4dd702daf05dbc7522fa2
# Parent  e2608e112f2a1a7b252b29ef5e6408139a3434b8
Deleted selected files

diff -r e2608e112f2a -r 7ec8715bedc2 tassel.xml
--- a/tassel.xml	Thu Dec 21 16:00:45 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,182 +0,0 @@
-<tool id="Tassel" name="Tassel" version="2.0.0">
-	<description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
-	<requirements>
-                <requirement type="package" version="5.2.89">tassel</requirement>
-				<requirement type="package" version="1.8">openjdk</requirement>
-        </requirements>
-​
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-​
-	<command detect_errors="exit_code"><![CDATA[./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
-#if $analysis_opts.fonction_selector == "mlm":
- -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
- -fork2 -r $analysis_opts.trait
- #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
-  -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
- #end if
- -fork4 -k $analysis_opts.kinship
- -combineA -input1 -input2 
- #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
-  -input3
- #end if
- -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2 
- #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
-  -runfork3
- #end if
- -runfork4
- 
-#else if $analysis_opts.fonction_selector == "glm":
- -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
- -fork2 -r $analysis_opts.trait
- #if $analysis_opts.add_file.additional_file_selector == "yes":
-  -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
- #end if
- -combineA -input1 -input2 
- #if $analysis_opts.add_file.additional_file_selector == "yes":
-  -input3
- #end if
- -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
- #if $analysis_opts.add_file.additional_file_selector == "yes":
-  -runfork3
- #end if 
-#else if $analysis_opts.fonction_selector == "ld":
- -fork1 -h $hapmap
- -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
-#else if $analysis_opts.fonction_selector == "ck":
- -fork1 -h $hapmap
- -ck -export tmpdir$$/kinship -runfork1
-#end if
-	]]></command>
-	<inputs>
-		<param format="txt" name="hapmap" type="data" label="HapMap file"/>
-		<conditional name="analysis_opts">
-			<param name="fonction_selector" type="select" label="Type of analysis">
-				<option value="mlm" selected="True">MLM</option>
-				<option value="glm">GLM</option>
-				<option value="ld">Linkage Disequilibrium</option>
-				<option value="ck">Kinship</option>
-			</param>
-			<when value="glm">
-                		<param format="txt" name="trait" type="data" label="Trait file"/>
-				<conditional name="add_file">
-					<param name="additional_file_selector" type="select" label="Add structure file">
-        	                	        <option value="no" selected="True">no</option>
-                	                	<option value="yes">yes</option>
-	                	        </param>
-					<when value="yes">
-						<param format="txt" name="structure" type="data" label="Structure file"/>
-					</when>
-                                        <when value="no">
-                                        </when>
-				</conditional>
-			</when>
-			<when value="mlm">
-                		<param format="txt" name="trait" type="data" label="Trait file"/>
-		                <param format="txt" name="kinship" type="data" label="Kinship file"/>
-				<conditional name="add_structure_file">
-					<param name="additional_file_selector" type="select" label="Add structure file">
-        	                	        <option value="no" selected="True">no</option>
-                	                	<option value="yes">yes</option>
-	                	        </param>
-					<when value="yes">
-						<param format="txt" name="structure" type="data" label="Structure file"/>
-					</when>
-                                        <when value="no">
-                                        </when>
-				</conditional>
-				<param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
-					<option value="P3D" selected="True">P3D</option>
-					<option value="EachMarker">EachMarker</option>
-				</param>
-				<param name="mlmCompressionLevel" type="select" label="Compression Level">
-					<option value="Optimum" selected="True">Optimum</option>
-					<option value="Custom">Custom</option>
-					<option value="None">None</option>
-				</param>
-                        </when>
-			<when value="ld"></when>
-			<when value="ck"></when>
-		</conditional>
-		<param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
-	</inputs>
-	<outputs>
-		<data format="txt" name="output1" label="Tassel output">
-			<change_format>
-				<when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
-			</change_format>
-		</data>
-		
-		<data format="txt" name="output2" label="Allele effects">
-			<filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
-		</data>
-		
-		<data format="txt" name="output3" label="Compression file">
-			<filter>analysis_opts['fonction_selector'] == "mlm"</filter>
-		</data>
-		
-		<data format="txt" name="log" label="Log file"/>
-	</outputs>
-​
-    <tests>
-        <test>
-            <param name="hapmap" value="input_hapmap.txt"/>
-            <conditional name="analysis_opts">
-                <param name="fonction_selector" value="glm"/>
-                <param name="trait" value="phenotyping_DRB.csv"/>
-                <conditional name="add_structure_file">
-                    <param name="additional_file_selector" value="yes"/>
-                    <param name="structure" value="Best_K_Output"/>
-                </conditional>
-            </conditional>
-            <param name="filterAlignMinFreq" value="0.05"/>
-            <output name="output1" value="Tassel_output.txt"/>
-            <output name="output2" value="Allele_effects.txt"/>
-        </test>
-    </tests>
-​
-    <help><![CDATA[
-​
-​
-.. class:: infomark
-​
-**Tassel5** version 5.2.40
-​
-.. class:: infomark
-​
-**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
-​
-.. class:: infomark
-​
-**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
-​
----------------------------------------------------
-​
-=======
-Tassel5
-=======
-​
------------
-Description
------------
-​
-  | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
-  | For further informations on tassel, please visit the website_.
-​
-.. _website: http://www.maizegenetics.net/tassel/
-​
-------------
-Dependencies
-------------
-Tassel5
-        tassel_ 5.2.40, Conda version
-​
-.. _tassel: https://anaconda.org/bioconda/tassel
-​
-    ]]></help>
-    <citations>
-       <citation type="doi">10.1093/bioinformatics/btm308</citation>
-    </citations>
-</tool>
\ No newline at end of file