Mercurial > repos > azomics > fcs_merge_downsample
comparison FCSMergeDownsample.xml @ 1:04afe468b234 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit d62d7d86dafd09575d91ddb6d07a8dd6a6dc4a27"
author | azomics |
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date | Mon, 06 Jul 2020 19:22:44 -0400 |
parents | 8e568997abda |
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0:8e568997abda | 1:04afe468b234 |
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1 <tool id="fcs_merge_downsample" name="Merge and downsample" version="1.0+galaxy1"> | 1 <tool id="fcs_merge_downsample" name="Merge and downsample" version="1.0+galaxy1" profile="18.01"> |
2 <description>FCS files with FlowSOM</description> | 2 <description>FCS files with 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="One or more FCS files is not valid. See stderr for more details." /> | 8 <exit_code range="10" level="fatal" description="One or more FCS files is not valid. See stderr for more details." /> |
8 <exit_code range="11" level="fatal" description="Please provide a numeric value [0,1] for the downsampling factor." /> | 9 <exit_code range="11" level="fatal" description="Please provide a numeric value [0,1] for the downsampling factor." /> |
9 <exit_code range="12" level="fatal" description="There are inconsistencies in marker names between FCS files." /> | 10 <exit_code range="12" level="fatal" description="There are inconsistencies in marker names between FCS files." /> |
11 <exit_code range="13:" level="fatal" description="See stderr for more details." /> | |
10 </stdio> | 12 </stdio> |
11 <command><![CDATA[ | 13 <command><![CDATA[ |
12 FCSMergeDownsample.R '${output_file}' '${outformat}' '${factorDS}' | 14 Rscript --slave --vanilla '$__tool_directory__/FCSMergeDownsample.R' '${output_file}' '${outformat}' '${factorDS}' |
13 #for $f in $input | 15 #for $f in $input |
14 '${f}' | 16 '${f}' |
15 #end for | 17 #end for |
16 ]]> | 18 ]]> |
17 </command> | 19 </command> |