gait_gm: sPLS.xml annotate

annotate sPLS.xml @ 2:2c218a253d56 draft default tip

"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"

author	malex
date	Thu, 29 Jul 2021 20:48:10 +0000
parents	ec9ee8edb84d
children

rev	line source
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	1 <tool id="secimtools_spls" name="Metabolite - Gene Integration" version="@WRAPPER_VERSION@">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	2 <description></description>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	3 <macros>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	4 <import>macros.xml</import>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	5 </macros>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	6 <expand macro="requirements" />
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	7 <stdio>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	8 <exit_code range="2" level="fatal" description="Not enough metabolites for the Analysis."/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	9 </stdio>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	10 <command detect_errors="exit_code"><![CDATA[
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	11 sPLS.py
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	12 -g=$metsOption.geneDataset
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	13 -gid=$metsOption.geneId
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	14 #if $metsOption.useGeneAnnoCond.useGeneAnno == "y":
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	15 -ga=$metsOption.useGeneAnnoCond.geneAnno
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	16 -gn=$metsOption.useGeneAnnoCond.geneName
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	17 #end if
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	18 -go=$metsOption.genesOption.allGenes
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	19 #if $metsOption.genesOption.allGenes == "geneList":
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	20 -gl=$metsOption.genesOption.relatedGeneList
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	21 #end if
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	22 #if $metsOption.genesOption.allGenes == "path":
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	23 -gkp=$metsOption.genesOption.geneKeggPath
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	24 -mkp=$metsOption.genesOption.metKeggPath
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	25 #end if
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	26 #if $metsOption.genesOption.allGenes == "pana":
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	27 -gka=$metsOption.genesOption.geneKeggAnno
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	28 -gkn=$metsOption.genesOption.geneKeggName
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	29 -p2g=$metsOption.genesOption.path2genes
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	30 -cu=$metsOption.genesOption.cutoff
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	31 -f=$metsOption.genesOption.facSel
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	32 #if $metsOption.genesOption.PANAAnno.usePANAAnno == "yes":
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	33 -p2n=$metsOption.genesOption.PANAAnno.path2names
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	34 #end if
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	35 -o3=$panaOut
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	36 #end if
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	37 -k=$keepX
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	38 -t=$threshold
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	39 -m=$metDataset
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	40 -mid=$metId
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	41 #if $useMetAnnoCond.useMetAnno == "y":
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	42 -ma=$useMetAnnoCond.metAnno
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	43 -mn=$useMetAnnoCond.metName
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	44 #end if
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	45 -mo=$metsOption.allMets
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	46 -mka=$metsOption.metKeggAnno
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	47 #if $metsOption.allMets == "mmc":
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	48 -d=$metsOption.design
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	49 -c=$metsOption.corr
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	50 -sl=$metsOption.sigmaLow
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	51 -sh=$metsOption.sigmaHigh
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	52 -sn=$metsOption.sigmaNum
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	53 -f2=$figure2
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	54 -o2=$mmcOut
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	55 #end if
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	56 #if $metsOption.allMets == "both":
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	57 -d=$metsOption.design
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	58 -c=$metsOption.corr
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	59 -sl=$metsOption.sigmaLow
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	60 -sh=$metsOption.sigmaHigh
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	61 -sn=$metsOption.sigmaNum
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	62 -f2=$figure2
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	63 -o2=$mmcOut
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	64 #end if
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	65 -f1=$figure1
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	66 -o1=$splsOut
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	67 ]]></command>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	68 <inputs>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	69 <param name="metDataset" type="data" format="tabular" label="Metabolite Wide Dataset for Integration" help="Select the Metabolite Wide Dataset from your history"/>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	70 <param name="metId" type="text" size="30" value="" label="Unique Metabolite FeatureID" help="Name of the column in your Metabolite Wide Dataset that contains unique identifiers."/>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	71 <conditional name="useMetAnnoCond">
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	72 <param name="useMetAnno" type="select" label="Use Metabolite Annotation File?" help="You can choose to input a file containing metabolite annotation information (e.g. metabolite names, identifiers, etc.) to use for labeling the output files.">
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	73 <option value="n">No</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	74 <option value="y">Yes</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	75 </param>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	76 <when value="y">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	77 <param name="metAnno" type="data" format="tabular" label="Metabolomic Annotation File" help="Select the Metabolomic Annotation File from your history."/>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	78 <param name="metName" type="text" size="30" value="" label="Metabolite Names" help="Name of the column in your Metabolomic Annotation Dataset that contains metabolite annotation information."/>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	79 </when>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	80 <when value="n" />
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	81 </conditional>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	82 <conditional name="metsOption">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	83 <param name="allMets" type="select" display="radio" label="Select which option to use for subsetting the Metabolite Wide Dataset" help="Select one of the options above.">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	84 <option value="generic">By metabolite class -- Uses the 'Name_in_KEGG' column generated from the 'Link Name to KEGGID' tool to subset.</option>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	85 <option value="mmc">By MMC pattern -- Runs the SECIMTools MMC tool and uses the tool-generated pattern blocks for subsetting.</option>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	86 <option value="both">By both metabolite class AND by MMC pattern.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	87 </param>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	88 <when value="generic">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	89 <param name="metKeggAnno" type="data" format="tabular" label="'Metabolite to KEGGID Link' File." help="Select the 'Metabolite to KEGGID Link' File from your history. This file can be generated using the 'Link Name to KEGGID' tool."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	90 <param name="geneDataset" type="data" format="tabular" label="Gene Expression Wide Dataset for Integration" help="Select the Gene Expression Wide Dataset from your history"/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	91 <param name="geneId" type="text" size="30" value="" label="Unique Gene FeatureID" help="Name of the column in your Gene Expression Wide Dataset that contains unique identifiers."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	92 <conditional name="useGeneAnnoCond">
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	93 <param name="useGeneAnno" type="select" label="Use a Gene Annotation File?" help="You can choose to input a file containing gene annotation information (e.g. gene names, identifiers, etc.) for labeling the output files.">
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	94 <option value="n">No</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	95 <option value="y">Yes</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	96 </param>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	97 <when value="y">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	98 <param name="geneAnno" type="data" format="tabular" label="Gene Expression Annotation File" help="Select the Gene Expression Annotation File from your history."/>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	99 <param name="geneName" type="text" size="30" value="" label="Gene Names" help="Name of the column in your Gene Expression Annotation Dataset that contains gene annotation information."/>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	100 </when>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	101 <when value="n" />
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	102 </conditional>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	103 <conditional name="genesOption">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	104 <param name="allGenes" type="select" display="radio" label="Select which option to use for subsetting the Gene Expression Wide Dataset" help="Select one of the options above.">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	105 <option value="all">Include all genes in the Gene Expression Wide Dataset -- no subsetting.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	106 <option value="geneList">Use a custom tsv file containing specific genes of interest.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	107 <option value="path">Include genes linked to each metabolite class through common KEGG pathways.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	108 <option value="pana">Use Metagenes from PANA (PAthway Network Analysis from gene expression data).</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	109 </param>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	110 <when value="all" />
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	111 <when value="geneList">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	112 <param name="relatedGeneList" type="data" format="tabular" label="Select a Custom Gene List from your history" help="This custom list must consist of a single column of Gene Symbols."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	113 </when>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	114 <when value="path">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	115 <param name="geneKeggPath" type="data" format="tabular" label="Gene Expression KEGG Pathway File" help="Select the Gene Expression KEGG Pathway File from your history. This file can be generated using the 'Add KEGG Pathway Information' tool."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	116 <param name="metKeggPath" type="data" format="tabular" label="Metabolomic KEGG Pathway File" help="Select the Metabolomic KEGG Pathway File from your history. This file can be generated using the 'Add KEGG Pathway Information' tool."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	117 </when>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	118 <when value="pana">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	119 <param name="geneKeggAnno" type="data" format="tabular" label="Gene to KEGGID Link File" help="Select the Gene to KEGGID Link File from your history. This file can be generated from the 'Link Name to KEGGID' tool."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	120 <param name="geneKeggName" type="text" label="Gene Symbol" help="Name of the column in your 'Gene to KEGGID Link File' that contains Gene Symbols."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	121 <param name="path2genes" type="data" format="tabular" label="GeneKEGGID2PathwayID" help="Select the File from your history containing the list of ALL Gene KEGGIDs to Pathway IDs. This file can be generated from the 'Add KEGG Pathway Information' tool."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	122 <param name="facSel" type="select" display="radio" label="Criterion to select components" help="Choose the criterion to select components. Default: single%.">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	123 <option value="single">single% -- Percent of variability for a given principle component.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	124 <option value="accum">%accum -- Percent of accumulated variability.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	125 <option value="abs.val">abs.val -- Absolute value of the variabily for a given principle component.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	126 <option value="rel.abs">rel.abs -- Fold variability of tot.var/rank(X).</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	127 </param>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	128 <param name="cutoff" type="float" value="0.20" label="Variability cut-off value" help="Select the variability cut-off value. Default: 0.20"/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	129 <conditional name="PANAAnno">
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	130 <param name="usePANAAnno" type="select" label="Include Pathway Names in results files and figures?" help="You can choose to input a file containing annotations for the KEGG pathwayIDs.">
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	131 <option value="no">No</option>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	132 <option value="yes">Yes</option>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	133 </param>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	134 <when value="yes">
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	135 <param name="path2names" type="data" format="tabular" label="Pathway Names File" help="Select the Pathway Names File from your history. This file can be generated from the 'Add KEGG Pathway Information' tool."/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	136 </when>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	137 <when value="no" />
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	138 </conditional>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	139 </when>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	140 </conditional>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	141 </when>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	142 <when value="mmc">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	143 <param name="metKeggAnno" type="data" format="tabular" label="Metabolite to KEGGID Link File to Input into MMC" help="Select the Metabolite KEGGID Link File from your history. This file can be generated from the 'Link Name to KEGGID' tool."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	144 <param name="design" type="data" format="tabular" label="Design Dataset" help="Select the Design file to use with your Metabolite KEGGID Link File. This file can be generated using the 'Create: Design, Wide, and Annotation datasets' tool. Note that you need a column called 'sampleID' that contains the names of your samples."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	145 <param name="sigmaLow" type="float" size="6" value="0.05" label="Lower sigma bound" help="Default: 0.05." />
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	146 <param name="sigmaHigh" type="float" size="6" value="0.50" label="Upper sigma bound" help="Default: 0.50." />
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	147 <param name="sigmaNum" type="integer" size="6" value="451" label="Number of Sigma values" help="Number of values of sigma to search. Default: 451." />
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	148 <param name="corr" type="select" value="pearson" label="Correlation method" help="Select correlation method for preliminary correlation before clustering. Default: Pearson." >
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	149 <option value="pearson" selected="true">Pearson</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	150 <option value="kendall" selected="true">Kendall</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	151 <option value="spearman" selected="true">Spearman</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	152 </param>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	153 <param name="geneDataset" type="data" format="tabular" label="Gene Expression Wide Dataset for Integration" help="Select the Gene Expression Wide Dataset from your history."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	154 <param name="geneId" type="text" size="30" value="" label="Unique Gene FeatureID" help="Name of the column in your Gene Expression Annotation File that contains unique identifiers."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	155 <conditional name="useGeneAnnoCond">
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	156 <param name="useGeneAnno" type="select" label="Use Gene Annotation File?" help="You can choose to input a file containing gene annotations (e.g. gene names, identifiers, etc.) for labeling output files.">
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	157 <option value="n">No</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	158 <option value="y">Yes</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	159 </param>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	160 <when value="y">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	161 <param name="geneAnno" type="data" format="tabular" label="Gene Expression Annotation File" help="Select the Gene Expression Annotation File from your history."/>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	162 <param name="geneName" type="text" size="30" value="" label="Gene Names" help="Name of the column in your Gene Expression Annotation Dataset that contains gene annotations."/>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	163 </when>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	164 <when value="n"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	165 </conditional>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	166 <conditional name="genesOption">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	167 <param name="allGenes" type="select" display="radio" label="Select which option to use for subsetting the Gene Dataset" help="Select one of the options above.">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	168 <option value="all">Include all genes in the Gene Expression Wide Dataset -- no subsetting.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	169 <option value="geneList">Use a custom tsv file containing specific genes of interest.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	170 <option value="pana">Use Metagenes from PANA (PAthway Network Analysis from gene expression data).</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	171 </param>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	172 <when value="all" />
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	173 <when value="geneList">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	174 <param name="relatedGeneList" type="data" format="tabular" label="Select a Custom Gene List from your history" help="This custom list must contain Gene Symbol IDs and must be a single column."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	175 </when>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	176 <when value="pana">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	177 <param name="geneKeggAnno" type="data" format="tabular" label="Gene to KEGGID Link File" help="Select Gene to KEGGID Link File from your history. This file can be generated from the 'Link Name to KEGGID' tool."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	178 <param name="geneKeggName" type="text" label="Gene Symbol" help="Name of the column in your 'Gene to KEGGID Link File' that contains Gene Symbols."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	179 <param name="path2genes" type="data" format="tabular" label="GeneKEGGID2PathwayID" help="Select the File from your history containing the list of ALL Gene KEGGIDs to Pathway IDs. This file can be generated from the 'Add KEGG Pathway Information' tool."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	180 <param name="facSel" type="select" display="radio" label="Criterion to select components" help="Choose the criterion to select components. Default: single%.">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	181 <option value="single">single% -- Percent of variability for a given principle component.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	182 <option value="accum">%accum -- Percent of accumulated variability.</option>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	183 <option value="abs.val">abs.val -- Absolute value of the variability for a given principle component.</option>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	184 <option value="rel.abs">rel.abs -- Fold variability of tot.var/rank(X).</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	185 </param>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	186 <param name="cutoff" type="float" value="0.23" label="Variability cut-off value" help="Select the variability cut-off value. Default: 0.23"/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	187 <conditional name="PANAAnno">
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	188 <param name="usePANAAnno" type="select" label="Include Pathway Names in results files and figures?" help="You can choose to input a file containing annotations for the KEGG pathway IDs.">
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	189 <option value="no">No</option>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	190 <option value="yes">Yes</option>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	191 </param>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	192 <when value="yes">
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	193 <param name="path2names" type="data" format="tabular" label="Pathway Names File" help="Select the Pathway Names File from your history. This file can be generated from the 'Add KEGG Pathway Information' tool."/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	194 </when>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	195 <when value="no" />
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	196 </conditional>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	197 </when>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	198 </conditional>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	199 </when>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	200 <when value="both">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	201 <param name="metKeggAnno" type="data" format="tabular" label="Metabolite to KEGGID Link File" help="Select the Metabolite KEGGID Link File from your history.his file can be generated from the 'Link Name to KEGGID' tool."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	202 <param name="design" type="data" format="tabular" label="Design File" help="Select the Design file to use with your Metabolite KEGGID Link File. This file can be generated using the 'Create: Design, Wide, and Annotation datasets' tool. Note that you need a 'sampleID' column."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	203 <param name="sigmaLow" type="float" size="6" value="0.05" label="Lower sigma bound" help="Default: 0.05." />
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	204 <param name="sigmaHigh" type="float" size="6" value="0.50" label="Upper sigma bound" help="Default: 0.50." />
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	205 <param name="sigmaNum" type="integer" size="6" value="451" label="Number of Sigma values" help="Number of values of sigma to search. Default: 451." />
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	206 <param name="corr" type="select" value="pearson" label="Correlation method" help="Select correlation method for preliminary correlation prior to clustering. Default: Pearson." >
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	207 <option value="pearson" selected="true">Pearson</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	208 <option value="kendall" selected="true">Kendall</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	209 <option value="spearman" selected="true">Spearman</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	210 </param>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	211 <param name="geneDataset" type="data" format="tabular" label="Gene Expression Wide Dataset for Integration" help="Select Gene Expression Wide Dataset from your history"/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	212 <param name="geneId" type="text" size="30" value="" label="Unique Gene FeatureID" help="Name of the column in your Gene Expression Annotation File that contains unique identifiers."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	213 <conditional name="useGeneAnnoCond">
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	214 <param name="useGeneAnno" type="select" label="Use a Gene Annotation File?" help="You can choose to input a file containing gene annotations (e.g. gene names, identifiers, etc.) to use for labeling output files.">
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	215 <option value="n">No</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	216 <option value="y">Yes</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	217 </param>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	218 <when value="y">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	219 <param name="geneAnno" type="data" format="tabular" label="Gene Expression Annotation File" help="Select the Gene Expression Annotation File from your history."/>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	220 <param name="geneName" type="text" size="30" value="" label="Gene Names" help="Name of the column in your Gene Expression Annotation Dataset that contains gene annotations."/>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	221 </when>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	222 <when value="n" />
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	223 </conditional>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	224 <conditional name="genesOption">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	225 <param name="allGenes" type="select" display="radio" label="Gene Dataset Subsetting Option" help="Select one of the following.">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	226 <option value="all">Include all genes in the Gene Expression Wide Dataset -- no subsetting.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	227 <option value="geneList">Upload a custion list containing specific genes of interest.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	228 <option value="pana">Use Metagenes (PANA Approach).</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	229 </param>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	230 <when value="all" />
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	231 <when value="geneList">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	232 <param name="relatedGeneList" type="data" format="tabular" label="Select a Custom Gene List from your history" help="The list must consist of a single column of Gene Symbols."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	233 </when>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	234 <when value="pana">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	235 <param name="geneKeggAnno" type="data" format="tabular" label="Gene to KEGGID Link File" help="Select Gene to KEGGID Link File from your history. This file can be generated from the 'Link Name to KEGGID' tool."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	236 <param name="geneKeggName" type="text" label="Gene Symbol" help="Name of the column in your 'Gene to KEGGID Link File' that contains Gene Symbols."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	237 <param name="path2genes" type="data" format="tabular" label="Gene Expression KEGG Pathway File" help="Select the File from your history that contains the list of ALL Gene KEGGIDs to PathwayIDs. This file can be generated from the 'Add KEGG Pathway Information' tool."/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	238 <param name="facSel" type="select" display="radio" label="Criterion to select components" help="Choose the criterion to select components. Default: single%.">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	239 <option value="single">single% -- Percent of variability for a given principle component.</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	240 <option value="accum">%accum -- Percent of accumulated variability.</option>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	241 <option value="abs.val">abs.val -- Absolute value of the variability for a given principle componenet.</option>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	242 <option value="rel.abs">rel.abs -- Fold variability of tot.var/rank(X).</option>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	243 </param>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	244 <param name="cutoff" type="float" value="0.23" label="Variability cut-off value" help="Select the variability cut-off value. Default: 0.23"/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	245 <conditional name="PANAAnno">
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	246 <param name="usePANAAnno" type="select" label="Include Pathway Names in results files and figures?" help="You can choose to input a file containing annotations for the KEGG pathwayIDs.">
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	247 <option value="no">No</option>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	248 <option value="yes">Yes</option>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	249 </param>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	250 <when value="yes">
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	251 <param name="path2names" type="data" format="tabular" label="Pathway Names File" help="Select the Pathway Names File from your history. This file can be generated from the 'Add KEGG Pathway Information' tool."/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	252 </when>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	253 <when value="no" />
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	254 </conditional>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	255 </when>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	256 </conditional>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	257 </when>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	258 </conditional>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	259 <param name="keepX" type="integer" size="30" value="10" label="Number of Genes to Keep in the Model" help="Enter the number of genes to keep for each component in the sPLS analysis."/>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	260 <param name="threshold" type="float" size="30" value="0.8" label="Threshold" help="Correlations under this threshold will NOT be included in the output file."/>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	261 </inputs>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	262 <outputs>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	263 <data format="pdf" name="figure1" label="${tool.name} on ${on_string}: sPLS Figure"/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	264 <data format="tabular" name="splsOut" label="${tool.name} on ${on_string}: sPLS Correlation Table"/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	265 <data format="pdf" name="figure2" label="${tool.name} on ${on_string}: MMC Figure">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	266 <filter>(metsOption['allMets'] == 'mmc') or (metsOption['allMets'] == 'both')</filter>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	267 </data>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	268 <data format="tabular" name="mmcOut" label="${tool.name} on ${on_string}: MMC Output Table">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	269 <filter>(metsOption['allMets'] == 'mmc') or (metsOption['allMets'] == 'both')</filter>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	270 </data>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	271 <data format="tabular" name="panaOut" label="${tool.name} on ${on_string}: PANA Output Table">
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	272 <filter>(metsOption['genesOption']['allGenes'] == 'pana')</filter>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	273 </data>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	274 </outputs>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	275 <tests>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	276 <!-- sPLS_lzh -->
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	277 <test>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	278 <param name="metDataset" value="metabolite_wide_dataset.tsv"/>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	279 <param name="metId" value="UniqueID"/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	280 <param name="allMets" value="generic"/>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	281 <param name="metKeggAnno" value="metabolite_to_keggId_link.tsv"/>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	282 <param name="metName" value="MetName"/>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	283 <param name="geneDataset" value="gene_wide_dataset.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	284 <param name="geneId" value="UniqueID"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	285 <param name="allGenes" value="pana"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	286 <param name="geneKeggAnno" value="gene_to_keggId_link.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	287 <param name="geneKeggName" value="GeneSymbol"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	288 <param name="path2names" value="pathwayId2pathwayNames.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	289 <param name="path2genes" value="geneKeggId2pathwayId.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	290 <param name="keepX" value="10"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	291 <param name="threshold" value="0.8"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	292 <param name="cutoff" value="0.23" />
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	293 <param name="facSel" value="single" />
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	294 <output name="splsOut" file="spls_correlation.tsv" compare="diff" lines_diff="1000"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	295 <output name="figure1" file="spls_figure.pdf" compare="sim_size" delta="1000000"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	296 <output name="panaOut" file="spls_pana_outputTable.tsv" compare="diff" lines_diff="30000"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	297 </test>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	298 <!-- sPLS_met_generic_gene_all -->
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	299 <test>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	300 <param name="metDataset" value="metabolite_wide_dataset.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	301 <param name="metId" value="UniqueID"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	302 <param name="allMets" value="generic"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	303 <param name="metKeggAnno" value="metabolite_to_keggId_link.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	304 <param name="metName" value="MetName"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	305 <param name="geneDataset" value="gene_wide_dataset.tsv"/>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	306 <param name="geneId" value="UniqueID"/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	307 <param name="allGenes" value="all"/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	308 <param name="keepX" value="10"/>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	309 <param name="threshold" value="0.8"/>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	310 <param name="cutoff" value="0.20" />
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	311 <param name="facSel" value="single" />
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	312 <output name="splsOut" file="spls_correlation_generic_all.tsv" compare="diff" lines_diff="1000"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	313 <output name="figure1" file="spls_figure_generic_all.pdf" compare="sim_size" delta="1000000"/>
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	314 </test>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	315 <!-- sPLS_met_mmc_gene_pana -->
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	316 <test>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	317 <param name="metDataset" value="metabolite_wide_dataset.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	318 <param name="metId" value="UniqueID"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	319 <param name="allMets" value="mmc"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	320 <param name="metAnno" value="metabolite_annotation.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	321 <param name="metKeggAnno" value="metabolite_to_keggId_link.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	322 <param name="metName" value="MetName"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	323 <param name="design" value="gene_design.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	324 <param name="corr" value="pearson"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	325 <param name="sigmaLow" value="0.05"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	326 <param name="sigmaHigh" value="0.50"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	327 <param name="sigmaNum" value="451"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	328 <param name="geneDataset" value="gene_wide_dataset.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	329 <param name="geneId" value="UniqueID"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	330 <param name="allGenes" value="pana"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	331 <param name="geneKeggAnno" value="gene_to_keggId_link.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	332 <param name="geneKeggName" value="GeneSymbol"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	333 <param name="path2genes" value="geneKeggId2pathwayId.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	334 <param name="path2names" value="gene_kegg_pathway.tsv"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	335 <param name="keepX" value="5"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	336 <param name="threshold" value="0.8"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	337 <param name="cutoff" value="0.20" />
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	338 <output name="splsOut" file="integration_mmc_pana_genes_sPLS_output.tsv" compare="diff" lines_diff="100000"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	339 <output name="figure1" file="integration_mmc_pana_genes_sPLS_fig.pdf" compare="sim_size" delta="10000000"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	340 <output name="figure2" file="integration_mmc_pana_genes_MMC_heatmap.pdf" compare="sim_size" delta="10000000"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	341 <output name="mmcOut" file="integration_mmc_pana_genes_MMC_output.tsv" compare="diff" lines_diff="100000"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	342 <output name="panaOut" file="integration_mmc_pana_genes_PANA_output.tsv" compare="diff" lines_diff="100000"/>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	343 </test>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	344
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	345 </tests>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	346 <help><![CDATA[
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	347
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	348 Tool Description
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	349
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	350 NOTE: The parameters you select are data dependent.
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	351
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	352 This tool carries out the integrated analysis of metabolite and gene expression data. Here, metabolite data are considered the dependent variable
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	353 and genes the explanatory variable. The tool allows for several combinations of metabolite and gene models. A note of caution: a complete metabolite
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	354 and gene expression dataset with no filtering will be challenging to interpret using this tool.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	355
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	356 We recommend that both gene expression and metabolite datasets be reduced to reflect a common biological hypothesis before running this tool. For example,
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	357 metabolite data can be subset by class (i.e. using the 'Name_in_KEGG' column generated from the 'Link Name to KEGGID' tool). Users who want to include
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	358 similarly behaving compounds without regard to identification or type of compound can estimate modules with the Modulated Modularity Clustering (MMC) tool
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	359 (Stone and Ayroles 2009). Each module can be examined separately. Finally, metabolite data can be reduced by using both metabolite class and the MMC tool.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	360 Similarly, gene expression data can be reduced in scope by uploading and using a custom list of genes of interest or by using metagenes as implemented in PANA
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	361 (Ponzoni et al. 2014).
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	362
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	363 1) Classes of metabolites can be modeled as a function of metagenes.
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	364 2) Classes of metabolites can be modeled as a function of a set of individual genes.
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	365 3) Unbiased clusters of metabolites can be modeled as a function of metagenes
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	366 4) Unbiased clusters of metabolites can be modeled as a function of a set of individual genes.
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	367
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	368 The tool executes a partial least squares regression with variable selection (sparse PLS, sPLS) as implemented in the 'mixOmics' package (Rohart F., Gautier, B, Singh,
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	369 A and Lê Cao, K. A. mixOmics: an R package for ‘omics feature selection and multiple data integration. On bioRxiv). The mixomics sPLS function is run in ‘classic mode’
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	370 (http://mixomics.org/methods/spls/) with the number of components included in the model set to 2. In addition, the user selects the number of variables (genes) for
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	371 each component to use in model construction.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	372
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	373 This tool needs at least 1 subset with a minimum number of 3 metabolites to run properly. If the user selects subset metabolites by class and no metabolite groups are
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	374 identified or small metabolite groups with less than 3 members are found, the tool will stop and a warning message will be generated to try the MMC option instead.
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	375 Similarly, if the user selects subset metabolites using MMC clusters and there are no clusters with at least 3 metabolites, the tool will stop and a warning message
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	376 will be generated to try the 'by class’ option instead.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	377
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	378 --------------------------------------------------------------------------------
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	379
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	380 INPUT
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	381
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	382 Please see the UserGuide for more details regarding tool inputs and options.
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	383
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	384 Metabolite Wide Dataset
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	385 A wide formatted dataset that contains measurements for each sample (samples are in columns):
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	386
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	387 +-----------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	388 \| FeatureID \| sample1 \| sample2 \| sample3 \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	389 +===========+=========+=========+=========+=====+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	390 \| met_one \| 10 \| 20 \| 10 \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	391 +-----------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	392 \| met_two \| 5 \| 22 \| 30 \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	393 +-----------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	394 \| met_three \| 30 \| 27 \| 2 \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	395 +-----------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	396 \| met_four \| 32 \| 17 \| 8 \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	397 +-----------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	398 \| ... \| ... \| ... \| ... \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	399 +-----------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	400
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	401 Unique Metabolite FeatureID
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	402 Name of the column in your Metabolite Wide Dataset that contains unique identifiers.
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	403
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	404 Optional - Metabolite Annotation File
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	405 A wide format dataset containing metabolite descriptor information (e.g. metabolite names, m/z ratios). The user can choose a column in the Annotation File for labeling output files.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	406
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	407 Optional - Metabolite Names
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	408 Column name in the Metabolite Annotation File to use for labeling output files.
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	409
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	410 Data reduction (subsetting) of Metabolite Data
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	411 1) By metabolite class - uses a pre-defined grouping of metabolites based on the 'Name_in_KEGG' column in the Metabolite to KEGGID Link File.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	412 2) By MMC pattern - runs the SECIMTools MMC tool and uses the tool-generated pattern blocks for subsetting. Please see Stone and Ayroles (2009) for MMC options.
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	413 3) By both metabolite class AND MMC pattern
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	414
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	415 Metabolite to KEGGID Link File
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	416 This file MUST contain a column called 'Name_in_KEGG' and can be generated using the 'Link Name to KEGGID' tool.
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	417
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	418 Gene Expression Wide Dataset
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	419 A wide formatted gene expression dataset that contains measurements for each sample:
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	420
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	421 +------------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	422 \| FeatureID \| sample1 \| sample2 \| sample3 \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	423 +============+=========+=========+=========+=====+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	424 \| one \| 10 \| 20 \| 10 \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	425 +------------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	426 \| two \| 5 \| 22 \| 30 \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	427 +------------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	428 \| three \| 30 \| 27 \| 2 \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	429 +------------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	430 \| four \| 32 \| 17 \| 8 \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	431 +------------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	432 \| ... \| ... \| ... \| ... \| ... \|
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	433 +------------+---------+---------+---------+-----+
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	434
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	435 Unique Gene FeatureID
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	436 Name of the column in your Gene Expression Wide Dataset that contains unique gene identifiers.
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	437
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	438 Optional - Gene Annotation File
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	439 A wide format dataset containing gene annotation information (e.g. gene names). The user can choose a column in the Annotation File for labeling output files.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	440
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	441 Optional - Gene Names
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	442 Column name in the Gene Annotation File to use for labeling output files.
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	443
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	444 Data reduction (subsetting) of Gene Expression Data
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	445 1) No subsetting - include all genes in the Gene Expression Wide Dataset
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	446 2) Use a custom tsv file containing specific genes of interest - select a custom gene list from your history
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	447 3) Include genes linked to each metabolite class through common KEGG pathways
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	448 4) Use Metagenes from PANA (PAthway Network Analysis from gene expression data)
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	449
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	450 Gene Expression KEGG Pathway File
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	451 Contains links between gene symbols and KEGG Pathways. Can be generated using the 'Add KEGG Pathway Information' tool
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	452
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	453 Metabolomic KEGG Pathway File
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	454 Contains links between metabolites and KEGG Pathways. Can be generated using the 'Add KEGG Pathway Information' tool
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	455
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	456 Gene to KEGGID Link File
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	457 Contains links between gene symbols and KEGGIDs.
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	458
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	459 Gene Symbol
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	460 Name of the column in your Gene to KEGGID Link File that contains gene symbols
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	461
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	462 GeneKEGGID2PathwayID
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	463 Contains KEGG links between gene KEGGIDs and KEGG PathwayIDs. Can be generated from the 'Add KEGG Pathway Information' tool
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	464
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	465 Number of Genes to Keep in Model
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	466 Default: 10. This is the number of genes to keep for each principle component in the sPLS analysis.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	467
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	468 Threshold
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	469 Default: 0.8. Correlations less than this value will NOT be included in the output files.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	470
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	471 --------------------------------------------------------------------------------
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	472
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	473 OUTPUT
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	474
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	475 For metabolite reduction by metabolite class and all genes:
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	476 (1) A PDF containing a sPLS figure for each metabolite class.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	477 (2) A sPLS Correlation TSV file containing the correlations for each metabolite-gene pair and what subset (metabolite class) the pair locate to.
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	478
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	479 For metabolite reduction by MMC the following files will be output in addition to files (1) and (2) above
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	480 (3) A MMC PDF Figure containing unsorted, sorted and sorted-smoothed heatmaps of the variance-covariance matrices
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	481 (4) A MMC Output TSV file containing algorithm summaries in the following columns:
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	482
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	483 - Unique metabolite featureID
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	484 - Module: Contains the module number for each feature calculated by the MMC tool.
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	485 - Entry Index: Contains the original order of the names of the rows of the input Metabolite Wide Dataset.
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	486 - Degree: Average of the absolute values of correlations for the given element in a block to other elements within that block.
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	487 - Average Degree: Average values of the degrees computed above across all elements within the given block.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	488
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	489 For subsetting genes by generating metagenes using PANA the following files will be output in addition to files (1) and (2) above
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	490 (5) A PANA Output TSV table containing associations between gene symbols and KEGG pathways.
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	491
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	492 ]]>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	493 </help>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	494 <citations>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	495 <citation type="bibtex">@article{stone2009mmc,
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	496 title={Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	497 author={Stone, EA and Ayroles, JF},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	498 journal={PLOS Genetics},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	499 year={2009},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	500 }</citation>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	501 <citation type="bibtex">@article{ponzoni2014pathway,
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	502 title={Pathway network inference from gene expression data},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	503 author={Ponzoni, Ignacio and Nueda, Mar{\'\i}a Jos{\'e} and Tarazona, Sonia and G{\"o}tz, Stefan and Montaner, David and Dussaut, Julieta Sol and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	504 journal={BMC Systems Biology},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	505 volume={8},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	506 number={2},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	507 pages={S7},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	508 year={2014},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	509 publisher={BioMed Central}
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	510 }</citation>
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	511 <citation type="bibtex">@article{rohart2017mixomics,
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	512 title={mixOmics: an R package for Omics feature selection and multiple data integration},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	513 author={Rohart, F and Gautier, B and singh, A and L{\^e} Cao, K-A.},
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	514 journal={R package},
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	515 year={2017}
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	516 }</citation>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	517 <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	518 author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	519 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	520 journal = {BMC Bioinformatics},
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	521 year = {2018}
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	522 }</citation>
2 2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	523 <citation type="bibtex">@article{Mor2021GaitGM,
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	524 title={GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	525 author={Mor, DE and Huertas, F and Morse, AM and Kaletsky, R and Murphy, CT and Kalia, V and Miller, GW and Moskalenko, O and Conesa, A and McIntyre, LM},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	526 journal={BMC Genomics},
2c218a253d56 "planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b" malex parents: 1 diff changeset	527 year={submitted},
1 ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	528 }</citation>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	529 </citations>
ec9ee8edb84d Initial upload of 21.6.10 release. malex parents: diff changeset	530 </tool>

Mercurial > repos > malex > gait_gm

annotate sPLS.xml @ 2:2c218a253d56 draft default tip