--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metacyto_search_clr.xml	Wed Jul 28 22:02:38 2021 +0000
@@ -0,0 +1,108 @@
+<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>