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"

0:8e568997abda

<tool id="fcs_merge_downsample" name="Merge and downsample" version="1.0+galaxy1">
  <description>FCS files with FlowSOM</description>
  <requirements>
    <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement>
  </requirements>
  <stdio>
    <exit_code range="10" level="fatal" description="One or more FCS files is not valid. See stderr for more details." />
    <exit_code range="11" level="fatal" description="Please provide a numeric value [0,1] for the downsampling factor." />
    <exit_code range="12" level="fatal" description="There are inconsistencies in marker names between FCS files." />
  </stdio>
  <command><![CDATA[
      FCSMergeDownsample.R '${output_file}' '${outformat}' '${factorDS}'
  #for $f in $input
    '${f}'
  #end for
  ]]>
  </command>

1:04afe468b234

<tool id="fcs_merge_downsample" name="Merge and downsample" version="1.0+galaxy1" profile="18.01">
  <description>FCS files with FlowSOM</description>
  <requirements>
    <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:9" level="fatal" description="See stderr for more details." />
    <exit_code range="10" level="fatal" description="One or more FCS files is not valid. See stderr for more details." />
    <exit_code range="11" level="fatal" description="Please provide a numeric value [0,1] for the downsampling factor." />
    <exit_code range="12" level="fatal" description="There are inconsistencies in marker names between FCS files." />
    <exit_code range="13:" level="fatal" description="See stderr for more details." />
  </stdio>
  <command><![CDATA[
      Rscript --slave --vanilla '$__tool_directory__/FCSMergeDownsample.R' '${output_file}' '${outformat}' '${factorDS}'
  #for $f in $input
    '${f}'
  #end for
  ]]>
  </command>