proteomicsr_msigdb_workflow: msigdb

annotate msigdb_workflow.xml @ 0:0fbb062e0cf5 draft default tip

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty

author	mbernt
date	Tue, 19 Dec 2023 15:51:04 +0000
parents
children

rev	line source
0 0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	1 <tool id="proteomicsr_msigdb_workflow" name="proteomicsr: enrichment using MSigDB gene sets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	2 <macros>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	3 <import>macros.xml</import>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	4 </macros>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	5 <expand macro="requirements"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	6 <stdio>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	7 <regex source="stdout" level="fatal" match="ERROR: Timeout" description="The ENSEMBL server timed out. A retry may help."/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	8 </stdio>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	10 Rscript '$rscript'
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	11 && mv Rdata/Summary_ALL.csv .
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	12 ]]></command>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	13 <configfiles>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	14 <configfile name="rscript"><![CDATA[
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	15 library(proteomicsr)
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	16
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	17 #if $dat_calculated.ext == 'csv'
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	18 dat_calculated <- read.csv("$dat_calculated", row.names = 1)
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	19 #else
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	20 dat_calculated <- read.delim("$dat_calculated", header = TRUE, row.names = 1, sep = "\t")
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	21 #end if
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	22 @READ_SAMPLE_GENES_MAPPING@
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	23
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	24 null <- run_msigdb_workflow(
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	25 dat_calculated,
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	26 msigdb_category = "$msigdb_category",
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	27 #if $msigdb_subcategory
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	28 msigdb_subcategory = "$msigdb_subcategory",
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	29 #end if
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	30 ## knowledgebase = NULL, not needed
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	31 sampleGenes = NULL,
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	32 sampleMapping = NULL,
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	33 pvalue_decision = "$pvalue_decision",
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	34 significance_cutoff_candidates = $significance_cutoff_candidates,
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	35 get_ID_to_map = NULL,
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	36 ID_provided = "$ID_provided",
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	37 organism = "$organism",
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	38 padjust_method = "$padjust_method",
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	39 significance_cutoff_terms = $significance_cutoff_terms,
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	40 direction_calculation = "$direction_calculation",
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	41 topx = $topx,
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	42 topx_per_comparison = $topx_per_comparison,
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	43 #if $plot_term_candidates
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	44 plot_term_candidates = "$plot_term_candidates",
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	45 #end if
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	46 color_up = "${color_up}FF",
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	47 color_down = "${color_down}FF"
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	48 )
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	49 ]]></configfile>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	50 </configfiles>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	51 <inputs>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	52
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	53 <param argument="dat_calculated" type="data" format="csv,tabular" label="Sample table" help="Rows: unique identifiers (e.g. uniprot accessions), Columns: samples. Replicates should be indicated using _1, _2, .... Content should be numeric."/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	54 <param argument="msigdb_category" type="select" label="Gene set knowledgebase" help="Visit https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp to get more information on MSigDB categories and if the chosen category needs the definition of a subcategory. MEDICUS and LEGACY gene sets seem to be not supported yet.">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	55 <option value="H">Hallmark gene sets</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	56 <option value="C1">Positional gene sets</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	57 <option value="C2">Curated gene sets</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	58 <option value="C3">Regulatory target gene sets</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	59 <option value="C4">Computational gene sets</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	60 <option value="C5">Ontology gene sets</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	61 <option value="C6">Oncogenic signature gene sets</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	62 <option value="C7">Immunologic signature gene sets</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	63 <option value="C8">Cell type signature gene sets</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	64 </param>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	65 <param argument="msigdb_subcategory" type="select" optional="true" label="Gene set knowledgebase subcategory" help="Visit https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp to get more information on MSigDB categories and if the chosen category needs the definition of a subcategory. MEDICUS and LEGACY gene sets seem to be not supported yet.">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	66 <option value="CGP">C2 subcategory: chemical and genetic perturbations</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	67 <option value="CP">C2 subcategory: canonical pathways</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	68 <option value="CP:BIOCARTA">C2 subcategory: BioCarta canonical pathways</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	69 <option value="CP:KEGG">C2 subcategory: KEGG canonical pathways (KEGG_MEDICUS and KEGG_LEGACY seem to be not supported yet)</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	70 <option value="CP:PID">C2 subcategory: PID canonical pathways</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	71 <option value="CP:REACTOME">C2 subcategory: Reactome canonical pathways</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	72 <option value="MIR:MIRDB">C3 subcategory: gene sets containing high-confidence gene-level predictions of human miRNA targets as catalogued by miRDB v6.0 algorithm (MIR_LEGACY seems to be not supported yet)</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	73 <option value="TFT:GTRD">C3 subcategory: genes that share GTRD predicted transcription factor binding sites in the region -1000,+100 bp around the TSS for the indicated transcription factor.</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	74 <option value="CGN">C4 subcategory: cancer gene neighborhoods</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	75 <option value="CM">C4 subcategory: cancer modules</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	76 <option value="GO:BP">C5 subcategory: gene sets derived from the GO Biological Process ontology</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	77 <option value="GO:CC">C5 subcategory: gene sets derived from the GO Cellular Component ontology</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	78 <option value="GO:MF">C5 subcategory: gene sets derived from the GO Molecular Function ontology</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	79 <option value="HPO">C5 subcategory: Human Phenotype Ontology</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	80 <option value="IMMUNESIGDB">C7 subcategory: gene sets representing chemical and genetic perturbations of the immune system generated by manual curation of published studies in human and mouse immunology</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	81 <option value="VAX">C7 subcategory: gene sets curated by the Human Immunology Project Consortium (HIPC) describing human transcriptomic immune responses to vaccinations</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	82 </param>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	83 <!-- <param argument="knowledgebase" type="text" value="" label="Pattern to add to ouput, i.e. the database used for enrichment" help="Default is NULL, thus nothing is added to the output."/> -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	84 <expand macro="sample_genes_mapping"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	85 <param argument="ID_provided" type="text" value="uniprotswissprot" label="Define provided identifier" help="Define the ID type used in your dataframe of average Log2(FCs) and (adjusted) p-values. The ID should relate to attributes available using attributes = biomaRt::listAttributes(biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl")) or the attributes specific for the defined organism (e.g. "mmusculus_gene_ensembl" or "rnorvegicus_gene_ensembl")."/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	86 <!-- set of supported species can be determined with msigdbr::msigdbr_species()
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	87 TODO commented species require input to get_ID_to_map -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	88 <param argument="organism" type="select" label="Organism used" help="">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	89 <!-- <option value="Anolis carolinensis"/> -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	90 <option value="Bos taurus"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	91 <option value="Caenorhabditis elegans"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	92 <option value="Canis lupus familiaris"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	93 <option value="Danio rerio"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	94 <option value="Drosophila melanogaster"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	95 <!-- <option value="Equus caballus"/> -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	96 <!-- <option value="Felis catus"/> -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	97 <option value="Gallus gallus"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	98 <option value="Homo sapiens" selected="true"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	99 <!-- <option value="Macaca mulatta"/> -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	100 <!-- <option value="Monodelphis domestica"/> -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	101 <option value="Mus musculus"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	102 <!-- <option value="Ornithorhynchus anatinus"/> -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	103 <!-- <option value="Pan troglodytes"/> -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	104 <option value="Rattus norvegicus"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	105 <option value="Saccharomyces cerevisiae"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	106 <!-- <option value="Schizosaccharomyces pombe 972h-"/> -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	107 <option value="Sus scrofa"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	108 <!-- <option value="Xenopus tropicalis"/> -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	109 </param>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	110 <!-- should be pvalue pvalueadj if used downstream of fc_workflow or intensity_workflow -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	111 <param argument="pvalue_decision" type="text" value="pvalueadj" label="Pattern to select columns containing p-values to use" help="Examples: When pvalue, all columns ending on _pvalue are used to filter for significantly altered candidates, whereas the pattern pvalueadj will use all columns ending with this pattern"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	112 <param argument="significance_cutoff_candidates" type="float" value="0.05" min="0" max="1" label="Significance cutoff to filter for candidates used for enrichment" help="All candidates with (adjusted) p-value below this threshold will be subjected to enrichment analysis"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	113 <param argument="significance_cutoff_terms" type="float" value="0.05" min="0" max="1" label="Significance cutoff to identify significantly enriched terms" help="All terms with (adjusted) p-value below this threshold will be considered significantly enriched"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	114 <param argument="padjust_method" type="select" label="Method for p-value adjustment during enrichment analysis" help="">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	115 <option value="holm">Holm</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	116 <option value="hochberg">Hochberg</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	117 <option value="hommel">Hommel</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	118 <option value="bonferroni">Bonferroni</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	119 <option value="BY">Benjamini & Yekutieli (BY)</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	120 <option value="fdr" selected="true">Benjamini & Hochberg (BH/fdr)</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	121 <option value="none">None</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	122 </param>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	123 <param argument="direction_calculation" type="select" label="Decide how to calculate the direction of the term regulation" help="Decide whether to use median or mean values of the Log2(fold changes) of the candidates used for enrichment and assigned to the term.">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	124 <option value="median">Hallmark gene sets</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	125 <option value="mean">Positional gene sets</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	126 </param>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	127 <param argument="topx" type="integer" min="1" value="10" label="Number of top enriched pathways to return and visualize" help="In addition to exporting and visualizing all enriched terms and the significantly enriched terms, the top enriched terms will be exported and visualized based on the value defined here."/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	128 <param argument="topx_per_comparison" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Extract the top enriched terms condition-wise" help="Decide whether to extract the top enriched terms condition-wise or based on their summed enrichment over all conditions"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	129 <param argument="plot_term_candidates" type="select" optional="true" label="Decide whether to visualize candidates assigned to enriched terms" help="">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	130 <option value="significant">Candidates of significantly enriched terms</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	131 <option value="all">Candidates of all enriched terms</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	132 </param>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	133 <param argument="color_up" type="color" value="#DC0000" label="Color for up-regulated candidates"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	134 <param argument="color_down" type="color" value="#3C5488" label="Color for down-regulated candidates"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	135 <param name="out_select" type="select" multiple="true" optional="true" label="Optional outputs">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	136 <option value="tables" selected="true">Detailed tables</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	137 <option value="plots" selected="true">Plots</option>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	138 </param>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	139 </inputs>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	140 <outputs>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	141 <data name="summary" format="csv" from_work_dir="Summary_ALL.csv"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	142 <collection name="output" type="list" label="${tool.name} on ${on_string}: additional tables">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	143 <discover_datasets pattern="__name_and_ext__" directory="Rdata"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	144 <filter>out_select and "tables" in out_select</filter>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	145 </collection>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	146 <collection name="plots" type="list" label="${tool.name} on ${on_string}: plots">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	147 <discover_datasets pattern="__name_and_ext__" directory="Plots"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	148 <filter>out_select and "plots" in out_select</filter>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	149 </collection>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	150
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	151 <collection name="sig_output" type="list" label="${tool.name} on ${on_string}: additional tables for significantly enriched terms">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	152 <discover_datasets pattern="__name_and_ext__" directory="CandidatesSignificantTerms/Rdata"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	153 <filter>"significant" in plot_term_candidates</filter>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	154 <filter>out_select and "tables" in out_select</filter>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	155 </collection>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	156 <collection name="sig_plots" type="list" label="${tool.name} on ${on_string}: plots for significantly enriched terms">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	157 <discover_datasets pattern="__name_and_ext__" directory="CandidatesSignificantTerms/Plots"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	158 <filter>"significant" in plot_term_candidates</filter>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	159 <filter>out_select and "plots" in out_select</filter>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	160 </collection>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	161
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	162 <collection name="all_output" type="list" label="${tool.name} on ${on_string}: additional tables for all enriched terms">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	163 <discover_datasets pattern="__name_and_ext__" directory="CandidatesAllTerms/Rdata"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	164 <filter>"all" in plot_term_candidates</filter>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	165 <filter>out_select and "tables" in out_select</filter>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	166 </collection>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	167 <collection name="all_plots" type="list" label="${tool.name} on ${on_string}: plots for all enriched terms">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	168 <discover_datasets pattern="__name_and_ext__" directory="CandidatesAllTerms/Plots"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	169 <filter>"all" in plot_term_candidates</filter>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	170 <filter>out_select and "plots" in out_select</filter>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	171 </collection>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	172 </outputs>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	173 <tests>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	174 <test expect_num_outputs="5">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	175 <param name="dat_calculated" value="dat_calculated.csv" ftype="csv"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	176 <param name="plot_term_candidates" value="significant"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	177 <output name="summary">
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0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	179 <has_n_lines n="89"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	180 <has_n_columns sep="," n="7"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	181 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	182 </output>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	183 <output_collection name="output" count="5" type="list">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	184 <element name="Enrichment_results_log.p.adjust_pvalueadj_0.05" ftype="csv">
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0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	186 <has_n_lines n="45"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	187 <has_n_columns sep="," n="3"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	188 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	189 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	190 <element name="Enrichment_results_long_pvalueadj_0.05_median_FC" ftype="csv">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	191 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	192 <has_n_lines n="70"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	193 <has_n_columns sep="," n="12"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	194 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	195 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	196 <element name="Enrichment_results_median_FC_pvalueadj_0.05" ftype="csv">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	197 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	198 <has_n_lines n="45"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	199 <has_n_columns sep="," n="3"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	200 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	201 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	202 <element name="MSigDB_gene_set_ID_mapping" ftype="csv">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	203 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	204 <has_n_lines n="8210"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	205 <has_n_columns sep="," n="2"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	206 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	207 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	208 <element name="Summary_Top10_combined" ftype="csv">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	209 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	210 <has_n_lines n="29"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	211 <has_n_columns sep="," n="7"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	212 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	213 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	214 </output_collection>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	215 <output_collection name="plots" count="9" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	216 <output_collection name="sig_output" count="8" type="list">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	217 <element name="Candidates_HALLMARK_COMPLEMENT" ftype="csv">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	218 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	219 <has_n_lines n="13"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	220 <has_n_columns sep="," n="8"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	221 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	222 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	223 <element name="Candidates_HALLMARK_INFLAMMATORY_RESPONSE" ftype="csv">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	224 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	225 <has_n_lines n="10"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	226 <has_n_columns sep="," n="8"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	227 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	228 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	229 <element name="Candidates_HALLMARK_TNFA_SIGNALING_VIA_NFKB" ftype="csv">
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0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	231 <has_n_lines n="16"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	232 <has_n_columns sep="," n="8"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	233 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	234 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	235 <element name="Candidates_HALLMARK_UV_RESPONSE_UP" ftype="csv">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	236 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	237 <has_n_lines n="8"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	238 <has_n_columns sep="," n="8"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	239 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	240 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	241 <element name="Candidates_ggplot_HALLMARK_COMPLEMENT" ftype="csv">
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0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	243 <has_n_lines n="25"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	244 <has_n_columns sep="," n="8"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	245 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	246 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	247 <element name="Candidates_ggplot_HALLMARK_INFLAMMATORY_RESPONSE" ftype="csv">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	248 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	249 <has_n_lines n="19"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	250 <has_n_columns sep="," n="8"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	251 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	252 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	253 <element name="Candidates_ggplot_HALLMARK_TNFA_SIGNALING_VIA_NFKB" ftype="csv">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	254 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	255 <has_n_lines n="31"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	256 <has_n_columns sep="," n="8"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	257 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	258 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	259 <element name="Candidates_ggplot_HALLMARK_UV_RESPONSE_UP" ftype="csv">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	260 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	261 <has_n_lines n="15"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	262 <has_n_columns sep="," n="8"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	263 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	264 </element>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	265 </output_collection>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	266 <output_collection name="sig_plots" count="8" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	267 </test>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	268 <!-- same + sample genes -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	269 <test expect_num_outputs="5">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	270 <param name="dat_calculated" value="dat_calculated.csv" ftype="csv"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	271 <param name="sampleGenes" value="sampleGenes.csv" ftype="csv"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	272 <param name="plot_term_candidates" value="significant"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	273 <output name="summary">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	274 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	275 <has_n_lines n="89"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	276 <has_n_columns sep="," n="7"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	277 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	278 </output>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	279 <output_collection name="output" count="5" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	280 <output_collection name="plots" count="9" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	281 <output_collection name="sig_output" count="8" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	282 <output_collection name="sig_plots" count="8" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	283 </test>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	284 <!-- same + sample genes + sample mapping -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	285 <test expect_num_outputs="5">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	286 <param name="dat_calculated" value="dat_calculated.csv" ftype="csv"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	287 <param name="sampleGenes" value="sampleGenes.csv" ftype="csv"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	288 <param name="sampleMapping" value="sampleMapping.csv" ftype="csv"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	289 <param name="plot_term_candidates" value="significant"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	290 <output name="summary">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	291 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	292 <has_n_lines n="89"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	293 <has_n_columns sep="," n="7"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	294 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	295 </output>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	296 <output_collection name="output" count="5" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	297 <output_collection name="plots" count="9" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	298 <output_collection name="sig_output" count="8" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	299 <output_collection name="sig_plots" count="8" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	300 </test>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	301 <!-- same as 1st test but plot all candidates + only output tables -->
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	302 <test expect_num_outputs="3">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	303 <param name="dat_calculated" value="dat_calculated.csv" ftype="csv"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	304 <param name="plot_term_candidates" value="all"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	305 <param name="out_select" value="tables"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	306 <output name="summary">
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	307 <assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	308 <has_n_lines n="89"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	309 <has_n_columns sep="," n="7"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	310 </assert_contents>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	311 </output>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	312 <output_collection name="output" count="5" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	313 <output_collection name="all_output" count="88" type="list"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	314 </test>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	315 </tests>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	316 <help><![CDATA[
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	317 Enrichment analysis workflow using MSigDB gene sets
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	318
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	319 Providing a table with average Log2(FCs) and (adjusted) p-values, enrichment analysis is conducted against the gene sets provided by the MSigDB
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	320 ]]></help>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	321 <expand macro="citations"/>
0fbb062e0cf5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty mbernt parents: diff changeset	322 </tool>

Mercurial > repos > mbernt > proteomicsr_msigdb_workflow

annotate msigdb_workflow.xml @ 0:0fbb062e0cf5 draft default tip