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comparison FlowSOMGenerateTree.xml @ 1:6c1721e7d0d6 draft

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_tree commit 6a60b44dd06df7be2eb851a5328cfc9e76c1d44e"
author azomics
date Mon, 06 Jul 2020 19:50:37 -0400
parents 54a25f1139b4
children 0efc47dba930
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0:54a25f1139b4 1:6c1721e7d0d6
1 <tool id="flowsom_tree" name="Generate a reference Self Organizing Map" version="1.0+galaxy1"> 1 <tool id="flowsom_tree" name="Generate a reference Self Organizing Map" version="1.0+galaxy1" profile="18.01">
2 <description>using FlowSOM.</description> 2 <description>using FlowSOM.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement> 4 <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:9" level="fatal" description="See stderr for more details." />
7 <exit_code range="10" level="fatal" description="Please provide a valid input (FCS or flowFrame)." /> 8 <exit_code range="10" level="fatal" description="Please provide a valid input (FCS or flowFrame)." />
8 <exit_code range="11" level="fatal" description="Please provide integers for columns you want to analyze, in a comma separated list." /> 9 <exit_code range="11" level="fatal" description="Please provide integers for columns you want to analyze, in a comma separated list." />
9 <exit_code range="12" level="fatal" description="Provided indices are out of range in the FCS file / flowframe given as input." /> 10 <exit_code range="12" level="fatal" description="Provided indices are out of range in the FCS file / flowframe given as input." />
10 <exit_code range="13" level="fatal" description="Please provide integers for the number of expected clusters." /> 11 <exit_code range="13" level="fatal" description="Please provide integers for the number of expected clusters." />
11 <exit_code range="14" level="fatal" description="Please provide integers for the grid size." /> 12 <exit_code range="14" level="fatal" description="Please provide integers for the grid size." />
12 <exit_code range="15" level="fatal" description="Please provide an integer to set the seed." /> 13 <exit_code range="15" level="fatal" description="Please provide an integer to set the seed." />
14 <exit_code range="16:" level="fatal" description="See stderr for more details." />
13 </stdio> 15 </stdio>
14 <command><![CDATA[ 16 <command><![CDATA[
15 Rscript $__tool_directory__/FlowSOMGenerateTree.R '${input}' '${output}' '${cols}' '${cluster}' '${xdim}' '${ydim}' '${seed}' 17 Rscript $__tool_directory__/FlowSOMGenerateTree.R '${input}' '${output}' '${cols}' '${cluster}' '${xdim}' '${ydim}' '${seed}'
16 #if $plotoutput.plot == "TRUE" 18 #if $plotoutput.plot == "TRUE"
17 '${treeplot}' '${plotoutput.plotformat}' '${plotoutput.nodesize}' 19 '${treeplot}' '${plotoutput.plotformat}' '${plotoutput.nodesize}'