<tool id="metacyto_search_clr" name="Guided identification of clusters" version="1.0+galaxy0" profile="18.01">
  <description>using MetaCyto</description>
  <requirements>
    <requirement type="package" version="1.4.0">bioconductor-metacyto</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:9" />
    <exit_code range="10" level="fatal" description="Please provide valid input FCS files." />
    <exit_code range="11" level="fatal" description="Please provide FCS files pre-processed for MetaCyto." />
    <exit_code range="12" level="fatal" description="Pre-processing summary doesn't match the set of FCS files." />
    <exit_code range="13" level="fatal" description="The pre-processing summary is in the wrong format." />
    <exit_code range="14" level="fatal" description="Please provide a cluster definition" />
    <exit_code range="15:" />
  </stdio>
  <command><![CDATA[
    Rscript --slave --vanilla '$__tool_directory__/metacyto_search_clr.R' '${summary}' 'fcs_stats' '${first_def}' '${unused}' '${cluster_list}'
  #for $r in $cl_df
    '${r.cluster_def}'
  #end for
  'FCS_FILES'
  #for $f in $group
    '${f}' '${f.name}'
  #end for
  ]]>
  </command>
  <inputs>
    <param format="metacyto_summary.txt" name="summary" type="data" label="MetaCyto preprocessing summary"/>
    <param format="fcs" name="group" type="data_collection" collection_type="list" label="FCS files Collection pre-processed for MetaCyto"/>
    <param name="first_def" type="text" label="Cluster definition" help="i.e.:CD3+,CD4-,CD8+,CCR7+"/>
    <repeat name="cl_df" title="Cluster">
      <param name="cluster_def" type="text" label="Additional cluster definition" help="i.e.:CD3+,CD4-,CD8+,CCR7+"/>
    </repeat>
  </inputs>
  <outputs>
    <data format="tabular" name="unused" label="List of clusters not found in all files from ${group.name}"/>
    <data format="metacyto_clr.txt" name="cluster_list" label="List of clusters from guided clustering analysis of ${group.name}"/>
    <collection type="list" label="Guided cluster identification analysis in ${group.name}" name="output">
      <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="fcs_stats" format="metacyto_stats.txt" />
    </collection>
  </outputs>
  <tests>
    <test>
      <param name="summary" value="preprocess.metacyto_summary.txt"/>
      <param name="group">
        <collection type="list">
          <element name="Group1" value="Group1.fcs"/>
          <element name="Group2" value="Group2.fcs"/>
        </collection>
      </param>
      <param name="first_def" value="CD3+,CD4-,CD8+" />
      <repeat name="cl_df">
        <param name="cluster_def" value="CD8+,CCR7+" />
      </repeat>
      <output name="unused" >
        <assert_contents>
          <has_n_lines n="2"/>
        </assert_contents>
      </output>
      <output_collection name="output">
        <element name="Group2_cluster_stats.txt">
          <assert_contents>
            <has_n_lines n="9"/>
          </assert_contents>
        </element>
      </output_collection>
    </test>
  </tests>
  <help><![CDATA[
This tool uses MetaCyto to search for clusters of cells corresponding to provided gate definitions
--------------------------------------------------------------------------------------------------

**Input files**

This tool requires the pre-processing summary generated for MetaCyto as well as the pre-processed FCS files.

*Cluster definitions*

Please provide gate definitions as comma-separated lists of marker names, for instance "CD3+, CD4+, CD25+, Foxp3+".

**Output**

This tool generates a list of provided clusters definitions, as well as a table of the MFI for each marker in each cluster in each file, and proportion of each cluster in each file. A list of unused cluster definitions, if any, is also generated.

**Example**

*Input* - Pre-Processing Summary Table

========  ===========================  =========
study_id  antibodies                   filenames
========  ===========================  =========
group1    Marker1|Marker2|Marker3|...  file1.fcs
group2    Marker1|Marker2|Marker3|...  file2.fcs
...       ...                          ...
========  ===========================  =========


*Output* - Clustering Summary Tables

========== ================ ========== ========================== ================ ======= ======= === ========
group_name fcs_files        cluster_id label                      fcs_names        Marker1 Marker2 ... fraction
========== ================ ========== ========================== ================ ======= ======= === ========
group1     file1_group1.fcs cluster1   Marker1+|Marker2+|Marker3+ file1_group1.fcs 1.9815  0.2024  ... 0.373
group1     file2_group1.fcs cluster1   Marker1+|Marker2+|Marker3+ file2_group1.fcs 2.3739  0.3377  ... 0.26
   ...        ...              ...        ...                        ...              ...     ...  ... ...
========== ================ ========== ========================== ================ ======= ======= === ========
  ]]>
  </help>
</tool>