tassel5: tassel.xml annotate

annotate tassel.xml @ 7:e2608e112f2a draft

Uploaded

author	dereeper
date	Thu, 21 Dec 2023 16:00:45 +0000
parents	28c0efb3a226
children

rev	line source
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	1 <tool id="Tassel" name="Tassel" version="2.0.0">
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	2 <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
3 0eebff4180d9 Uploaded dereeper parents: diff changeset	3 <requirements>
7 e2608e112f2a Uploaded dereeper parents: 6 diff changeset	4 <requirement type="package" version="5.2.89">tassel</requirement>
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	5 <requirement type="package" version="1.8">openjdk</requirement>
3 0eebff4180d9 Uploaded dereeper parents: diff changeset	6 </requirements>
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	7
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	8 <stdio>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	9 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	10 <exit_code range="1:" level="fatal" />
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	11 </stdio>
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	12
28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	13 <command detect_errors="exit_code"><![CDATA[./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
3 0eebff4180d9 Uploaded dereeper parents: diff changeset	14 #if $analysis_opts.fonction_selector == "mlm":
0eebff4180d9 Uploaded dereeper parents: diff changeset	15 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
0eebff4180d9 Uploaded dereeper parents: diff changeset	16 -fork2 -r $analysis_opts.trait
0eebff4180d9 Uploaded dereeper parents: diff changeset	17 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
0eebff4180d9 Uploaded dereeper parents: diff changeset	18 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
0eebff4180d9 Uploaded dereeper parents: diff changeset	19 #end if
0eebff4180d9 Uploaded dereeper parents: diff changeset	20 -fork4 -k $analysis_opts.kinship
0eebff4180d9 Uploaded dereeper parents: diff changeset	21 -combineA -input1 -input2
0eebff4180d9 Uploaded dereeper parents: diff changeset	22 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
0eebff4180d9 Uploaded dereeper parents: diff changeset	23 -input3
0eebff4180d9 Uploaded dereeper parents: diff changeset	24 #end if
0eebff4180d9 Uploaded dereeper parents: diff changeset	25 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2
0eebff4180d9 Uploaded dereeper parents: diff changeset	26 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
0eebff4180d9 Uploaded dereeper parents: diff changeset	27 -runfork3
0eebff4180d9 Uploaded dereeper parents: diff changeset	28 #end if
0eebff4180d9 Uploaded dereeper parents: diff changeset	29 -runfork4
0eebff4180d9 Uploaded dereeper parents: diff changeset	30
0eebff4180d9 Uploaded dereeper parents: diff changeset	31 #else if $analysis_opts.fonction_selector == "glm":
0eebff4180d9 Uploaded dereeper parents: diff changeset	32 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
0eebff4180d9 Uploaded dereeper parents: diff changeset	33 -fork2 -r $analysis_opts.trait
0eebff4180d9 Uploaded dereeper parents: diff changeset	34 #if $analysis_opts.add_file.additional_file_selector == "yes":
0eebff4180d9 Uploaded dereeper parents: diff changeset	35 -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
0eebff4180d9 Uploaded dereeper parents: diff changeset	36 #end if
0eebff4180d9 Uploaded dereeper parents: diff changeset	37 -combineA -input1 -input2
0eebff4180d9 Uploaded dereeper parents: diff changeset	38 #if $analysis_opts.add_file.additional_file_selector == "yes":
0eebff4180d9 Uploaded dereeper parents: diff changeset	39 -input3
0eebff4180d9 Uploaded dereeper parents: diff changeset	40 #end if
0eebff4180d9 Uploaded dereeper parents: diff changeset	41 -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
0eebff4180d9 Uploaded dereeper parents: diff changeset	42 #if $analysis_opts.add_file.additional_file_selector == "yes":
0eebff4180d9 Uploaded dereeper parents: diff changeset	43 -runfork3
0eebff4180d9 Uploaded dereeper parents: diff changeset	44 #end if
0eebff4180d9 Uploaded dereeper parents: diff changeset	45 #else if $analysis_opts.fonction_selector == "ld":
0eebff4180d9 Uploaded dereeper parents: diff changeset	46 -fork1 -h $hapmap
0eebff4180d9 Uploaded dereeper parents: diff changeset	47 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
0eebff4180d9 Uploaded dereeper parents: diff changeset	48 #else if $analysis_opts.fonction_selector == "ck":
0eebff4180d9 Uploaded dereeper parents: diff changeset	49 -fork1 -h $hapmap
0eebff4180d9 Uploaded dereeper parents: diff changeset	50 -ck -export tmpdir$$/kinship -runfork1
0eebff4180d9 Uploaded dereeper parents: diff changeset	51 #end if
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	52 ]]></command>
3 0eebff4180d9 Uploaded dereeper parents: diff changeset	53 <inputs>
0eebff4180d9 Uploaded dereeper parents: diff changeset	54 <param format="txt" name="hapmap" type="data" label="HapMap file"/>
0eebff4180d9 Uploaded dereeper parents: diff changeset	55 <conditional name="analysis_opts">
0eebff4180d9 Uploaded dereeper parents: diff changeset	56 <param name="fonction_selector" type="select" label="Type of analysis">
0eebff4180d9 Uploaded dereeper parents: diff changeset	57 <option value="mlm" selected="True">MLM</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	58 <option value="glm">GLM</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	59 <option value="ld">Linkage Disequilibrium</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	60 <option value="ck">Kinship</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	61 </param>
0eebff4180d9 Uploaded dereeper parents: diff changeset	62 <when value="glm">
0eebff4180d9 Uploaded dereeper parents: diff changeset	63 <param format="txt" name="trait" type="data" label="Trait file"/>
0eebff4180d9 Uploaded dereeper parents: diff changeset	64 <conditional name="add_file">
0eebff4180d9 Uploaded dereeper parents: diff changeset	65 <param name="additional_file_selector" type="select" label="Add structure file">
0eebff4180d9 Uploaded dereeper parents: diff changeset	66 <option value="no" selected="True">no</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	67 <option value="yes">yes</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	68 </param>
0eebff4180d9 Uploaded dereeper parents: diff changeset	69 <when value="yes">
0eebff4180d9 Uploaded dereeper parents: diff changeset	70 <param format="txt" name="structure" type="data" label="Structure file"/>
0eebff4180d9 Uploaded dereeper parents: diff changeset	71 </when>
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	72 <when value="no">
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	73 </when>
3 0eebff4180d9 Uploaded dereeper parents: diff changeset	74 </conditional>
0eebff4180d9 Uploaded dereeper parents: diff changeset	75 </when>
0eebff4180d9 Uploaded dereeper parents: diff changeset	76 <when value="mlm">
0eebff4180d9 Uploaded dereeper parents: diff changeset	77 <param format="txt" name="trait" type="data" label="Trait file"/>
0eebff4180d9 Uploaded dereeper parents: diff changeset	78 <param format="txt" name="kinship" type="data" label="Kinship file"/>
0eebff4180d9 Uploaded dereeper parents: diff changeset	79 <conditional name="add_structure_file">
0eebff4180d9 Uploaded dereeper parents: diff changeset	80 <param name="additional_file_selector" type="select" label="Add structure file">
0eebff4180d9 Uploaded dereeper parents: diff changeset	81 <option value="no" selected="True">no</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	82 <option value="yes">yes</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	83 </param>
0eebff4180d9 Uploaded dereeper parents: diff changeset	84 <when value="yes">
0eebff4180d9 Uploaded dereeper parents: diff changeset	85 <param format="txt" name="structure" type="data" label="Structure file"/>
0eebff4180d9 Uploaded dereeper parents: diff changeset	86 </when>
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	87 <when value="no">
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	88 </when>
3 0eebff4180d9 Uploaded dereeper parents: diff changeset	89 </conditional>
0eebff4180d9 Uploaded dereeper parents: diff changeset	90 <param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
0eebff4180d9 Uploaded dereeper parents: diff changeset	91 <option value="P3D" selected="True">P3D</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	92 <option value="EachMarker">EachMarker</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	93 </param>
0eebff4180d9 Uploaded dereeper parents: diff changeset	94 <param name="mlmCompressionLevel" type="select" label="Compression Level">
0eebff4180d9 Uploaded dereeper parents: diff changeset	95 <option value="Optimum" selected="True">Optimum</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	96 <option value="Custom">Custom</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	97 <option value="None">None</option>
0eebff4180d9 Uploaded dereeper parents: diff changeset	98 </param>
0eebff4180d9 Uploaded dereeper parents: diff changeset	99 </when>
0eebff4180d9 Uploaded dereeper parents: diff changeset	100 <when value="ld"></when>
0eebff4180d9 Uploaded dereeper parents: diff changeset	101 <when value="ck"></when>
0eebff4180d9 Uploaded dereeper parents: diff changeset	102 </conditional>
0eebff4180d9 Uploaded dereeper parents: diff changeset	103 <param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
0eebff4180d9 Uploaded dereeper parents: diff changeset	104 </inputs>
0eebff4180d9 Uploaded dereeper parents: diff changeset	105 <outputs>
0eebff4180d9 Uploaded dereeper parents: diff changeset	106 <data format="txt" name="output1" label="Tassel output">
0eebff4180d9 Uploaded dereeper parents: diff changeset	107 <change_format>
0eebff4180d9 Uploaded dereeper parents: diff changeset	108 <when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
0eebff4180d9 Uploaded dereeper parents: diff changeset	109 </change_format>
0eebff4180d9 Uploaded dereeper parents: diff changeset	110 </data>
0eebff4180d9 Uploaded dereeper parents: diff changeset	111
0eebff4180d9 Uploaded dereeper parents: diff changeset	112 <data format="txt" name="output2" label="Allele effects">
0eebff4180d9 Uploaded dereeper parents: diff changeset	113 <filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
0eebff4180d9 Uploaded dereeper parents: diff changeset	114 </data>
0eebff4180d9 Uploaded dereeper parents: diff changeset	115
0eebff4180d9 Uploaded dereeper parents: diff changeset	116 <data format="txt" name="output3" label="Compression file">
0eebff4180d9 Uploaded dereeper parents: diff changeset	117 <filter>analysis_opts['fonction_selector'] == "mlm"</filter>
0eebff4180d9 Uploaded dereeper parents: diff changeset	118 </data>
0eebff4180d9 Uploaded dereeper parents: diff changeset	119
0eebff4180d9 Uploaded dereeper parents: diff changeset	120 <data format="txt" name="log" label="Log file"/>
0eebff4180d9 Uploaded dereeper parents: diff changeset	121 </outputs>
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	122
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	123 <tests>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	124 <test>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	125 <param name="hapmap" value="input_hapmap.txt"/>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	126 <conditional name="analysis_opts">
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	127 <param name="fonction_selector" value="glm"/>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	128 <param name="trait" value="phenotyping_DRB.csv"/>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	129 <conditional name="add_structure_file">
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	130 <param name="additional_file_selector" value="yes"/>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	131 <param name="structure" value="Best_K_Output"/>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	132 </conditional>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	133 </conditional>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	134 <param name="filterAlignMinFreq" value="0.05"/>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	135 <output name="output1" value="Tassel_output.txt"/>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	136 <output name="output2" value="Allele_effects.txt"/>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	137 </test>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	138 </tests>
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	139
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	140 <help><![CDATA[
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	141
28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	142
3 0eebff4180d9 Uploaded dereeper parents: diff changeset	143 .. class:: infomark
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	144
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	145 Tassel5 version 5.2.40
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	146
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	147 .. class:: infomark
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	148
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	149 Galaxy integration Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	150
3 0eebff4180d9 Uploaded dereeper parents: diff changeset	151 .. class:: infomark
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	152
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	153 Support For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	154
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	155 ---------------------------------------------------
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	156
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	157 =======
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	158 Tassel5
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	159 =======
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	160
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	161 -----------
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	162 Description
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	163 -----------
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	164
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	165 \| Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	166 \| For further informations on tassel, please visit the website_.
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	167
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	168 .. _website: http://www.maizegenetics.net/tassel/
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	169
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	170 ------------
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	171 Dependencies
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	172 ------------
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	173 Tassel5
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	174 tassel_ 5.2.40, Conda version
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	175
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	176 .. _tassel: https://anaconda.org/bioconda/tassel
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	177
4 652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	178 ]]></help>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	179 <citations>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	180 <citation type="doi">10.1093/bioinformatics/btm308</citation>
652aafd88060 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 3 diff changeset	181 </citations>
6 28c0efb3a226 Uploaded dereeper parents: 4 diff changeset	182 </tool>

Mercurial > repos > dereeper > tassel5

annotate tassel.xml @ 7:e2608e112f2a draft