comparison flow-compensate.xml @ 1:ffc083c86d44 draft default tip

"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit fd7533e2c5c6c078bd2734c1ded95db9b74e450e"

0:ca7ba337b727

        mkdir -p input_dir;
        #for $fcs in $fcs_list:
          ln -s '$fcs' input_dir/'$fcs.element_identifier';
        #end for 
        mkdir -p output_dir;
        Rscript '$compensate_script' '$compensation_matrix' input_dir output_dir
      ]]></command>
    <configfiles>
      <configfile name="compensate_script"><![CDATA[
library(flowCore)

    </inputs>
    <outputs>
      <collection name="compensated_fcs" format="fcs" label="${tool.name} compensated FCS files on ${on_string}" type="list">
        <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" />
      </collection>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>

1:ffc083c86d44

        mkdir -p input_dir;
        #for $fcs in $fcs_list:
          ln -s '$fcs' input_dir/'$fcs.element_identifier';
        #end for 
        mkdir -p output_dir;
        Rscript '$compensate_script' '$compensation_matrix' input_dir output_dir &> '$log_file'
      ]]></command>
    <configfiles>
      <configfile name="compensate_script"><![CDATA[
library(flowCore)

    </inputs>
    <outputs>
      <collection name="compensated_fcs" format="fcs" label="${tool.name} compensated FCS files on ${on_string}" type="list">
        <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" />
      </collection>
      <data name="log_file" format="txt" label="Log for compensation by ${tool.name} on ${on_string}"/> 
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>