view 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"

<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>
  <inputs>
    <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/>
    <param name="factorDS" type="text" label="Downsample by:" value="i.e.:0.1 or 10%" optional="true" help="By default 0.1"/>
    <param name="outformat" type="select" label="Output Format">
      <option value="flowFrame">R Data, flowFrame</option>
      <option value="FCS">FCS 3.0</option>
    </param>
  </inputs>
  <outputs>
    <data format="flowframe" name="output_file" label="Merged FCS from ${input.name} in ${outformat}">
      <change_format>
        <when input="outformat" value="FCS" format="fcs" />
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input">
        <collection type="list">
          <element name="input1.fcs" value="input1.fcs"/>
          <element name="input2.fcs" value="input2.fcs"/>
          <element name="input3.fcs" value="input3.fcs"/>
        </collection>
      </param>
      <param name="factorDS" value=".8"/>
      <param name="outformat" value="flowFrame"/>
      <output name="output_file" file="merge1.flowframe" compare="sim_size" delta="1000000"/>
    </test>
    <test>
      <param name="input">
        <collection type="list">
          <element name="input1.fcs" value="input1.fcs"/>
          <element name="input2.fcs" value="input2.fcs"/>
          <element name="input3.fcs" value="input3.fcs"/>
        </collection>
      </param>
      <param name="factorDS" value="i.e.:0.1 or 10%"/>
      <param name="outformat" value="FCS"/>
      <output name="output_file" file="merge2.fcs" compare="sim_size" delta="1000000"/>
    </test>
  </tests>
  <help><![CDATA[
Merge and downsample using FlowSOM
-------------------

This tool merges and downsamples multiple FCS files into one flowframe or FCS file using FlowSOM.

**Input files**

This tool requires a collection of FCS files as input.

.. class:: warningmark

Input files **MUST** have the same markers *and* channels. The following tools in the FCS Files tool section can help harmonize channels and/or markers in the FCS files collection:

- Get list of markers or channels in FCS files.
- Edit markers or channels in FCS files

**Downsampling**

By default, files are downsampled to 10% of the total number of events across input files. If a downsampling factor is provided, each file in the input dataset collection will be downsampled randomly without replacement as follows:

- If n is between 0 and 1, the size of the output will be n times that of the input files.
- If n is between 1 and 100, the size of the output will be n% that of the input files.

.. class:: infomark

Downsampling is implemented such that each file will contribute an equal number of event to the aggregate.

.. class:: warningmark

At this time, up-sampling is not supported. If the number provided is greater than 100, the tool will exit.

**Output file**

The output file contains an aggregation of events from the input files provided all are valid FCS files. If a downsampling factor is provided, the corresponding proportion of each input file ONLY will be read in. Output can be provided in FCS format or in a RData object containing a flowFrame.

.. class:: infomark

The output generated contains data for all markers present in the original files. No information is added, or removed.

-----

**Example**

*File1*: 20K events::

   Marker1 Marker2 Marker3 ...
   34      45      12      ...
   33      65      10      ...
   87      26      76      ...
   24      56      32      ...
   95      83      53      ...
   ...     ...     ...     ...

*File2*: 20K events::

   Marker1 Marker2 Marker3 ...
   19      62      98      ...
   12      36      58      ...
   41      42      68      ...
   76      74      53      ...
   62      34      45      ...
   ...     ...     ...     ...

*Output*: 4K events::

   Marker1 Marker2 Marker3 ...
   34      45      12      ...
   87      26      76      ...
   12      36      58      ...
   62      34      45      ...
   ...     ...     ...     ...

.. class:: infomark

With a downsampling factor of 0.5: 20K events::

   Marker1 Marker2 Marker3 ...
   34      45      12      ...
   24      56      32      ...
   95      83      53      ...
   19      62      98      ...
   12      36      58      ...
   62      34      45      ...
   ...     ...     ...     ...
 ]]>
  </help>
  <citations>
    <citation type="doi">10.1002/cyto.a.22625</citation>
  </citations>
</tool>