--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ionflow/ionflow.xml	Mon Aug 09 09:41:22 2021 +0000
@@ -0,0 +1,437 @@
+<!--
+wl-10-08-2020, Mon: commence
+wl-24-08-2020, Mon: first version
+wl-16-11-2020, Mon: second version
+wl-23-03-2021, Tue: third version
+wl-08-06-2021, Tue: fourth version: new stuff from Jacopo
+-->
+
+<tool id="ionfow" name="IonFlow" version="0.4.0">
+  <description>
+    Pipeline for processing and analysis of ionomics data
+  </description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+
+  <!-- =============================================================== -->
+  <command detect_errors="exit_code">
+    <![CDATA[
+
+      Rscript ${__tool_directory__}/ionflow.R
+        ## Input
+        --ion_file '$ion_file'
+        --var_id '$pre.var_id'
+        --batch_id '$pre.batch_id'
+        --data_id '$pre.data_id'
+        --method_norm '$pre.method_norm'
+        --batch_control '$pre.batch.batch_control'
+        #if $pre.batch.batch_control=='yes'
+          --control_lines '$pre.batch.control_lines'
+          --control_use '$pre.batch.control_use'
+        #end if
+        --method_outliers '$pre.method_outliers'
+        --thres_outl '$pre.thres_outl'
+        --stand_method '$pre.stand.stand_method'
+        #if $pre.stand.stand_method=='custom':
+          --std_file '$pre.stand.std_file'
+        #end if
+        --thres_symb '$pre.thres_symb'
+
+        ## Exploratory analysis
+        --thres_ion_corr '$expl.thres_ion_corr'
+
+        ## Clustering analysis
+        --min_clust_size '$clus.min_clust_size'
+        --h_tree '$clus.h_tree'
+        --filter_zero_string '$clus.filter_zero_string'
+
+        ## Enrichment analysis
+        --pval '$enri.pval'
+        --min_count '$enri.min_count'
+        --ont '$enri.ont'
+        --annot_pkg '$enri.annot_pkg'
+
+        ## Network analysis
+        --method_corr '$net.method_corr'
+        --thres_corr '$net.thres_corr'
+
+        ## output: pre-processing
+        --pre_proc_pdf  '$pre_proc_pdf'
+        --df_stats_out  '$df_stats_out'
+        --outl_out  '$outl_out'
+        --data_wide_out  '$data_wide_out'
+        --data_wide_symb_out  '$data_wide_symb_out'
+
+        ## output: exploratory analysis
+        --expl_anal_pdf  '$expl_anal_pdf'
+
+        ## output: clustering analysis
+        --clus_anal_pdf  '$clus_anal_pdf'
+
+        ## output: enrichment analysis
+        --go_en_out  '$go_en_out'
+
+        ## output: network analysis
+        --gene_net_pdf  '$gene_net_pdf'
+        --imbe_out  '$imbe_out'
+    ]]>
+  </command>
+
+  <!-- =============================================================== -->
+  <inputs>
+    <param name="ion_file" type="data" format="csv"
+           label="Ion data table"
+           help="Ion data table with columns of Ions and meta information." />
+
+    <!-- start of pre -->
+    <section name="pre" title="Pre Processing" >
+
+      <param name="var_id" type="integer" value="1"
+             label="Specify variable column index of input data"
+             help="Indicate which column will be the variable (ORF or SYMBOL)." />
+
+      <param name="batch_id" type="integer" value="3"
+             label="Specify batch ID column index of input data"
+             help="Indicate which column will be batch ID." />
+
+      <param name="data_id" type="integer" value="5"
+             label="Specify data start column index of input data"
+             help="Indicate which column will be the start of data matrix." />
+
+      <param name="method_norm" type="select"
+             label="Select a method for batch correction">
+      <option value="median" selected="true">Median</option>
+      <option value="median+std">Median plus std</option>
+      <option value="none">None</option>
+      </param>
+
+      <!-- batch control -->
+      <conditional name="batch">
+        <param name="batch_control" type="select"
+               label="Use control lines for batch correction or not" >
+        <option value="yes" selected="true">Yes</option>
+        <option value="no">No</option>
+        </param>
+
+        <when value="yes">
+          <param name="control_lines" type="text" value="BY4741"
+                 label="Specify batch control lines (rows)">
+          <sanitizer>
+            <valid initial="string.ascii_letters,string.digits"></valid>
+          </sanitizer>
+          </param>
+
+          <param name="control_use" type="select"
+                 label="Select lines for batch correction">
+          <option value="control">Use control lines for batch correction</option>
+          <option value="all" selected="true">Use all lines for batch correction</option>
+          <option value="control.out">Use all lines except control lines for batch correction</option>
+          </param>
+        </when>
+
+        <when value="no">
+        </when>
+      </conditional>
+
+      <param name="method_outliers" type="select"
+             label="Select a method for outlier detection">
+      <option value="IQR">IQR</option>
+      <option value="mad">MAD</option>
+      <option value="log.FC.dist" selected="true">log FC dist</option>
+      <option value="none">none</option>
+      </param>
+
+      <param name="thres_outl" type="float" value="3.0"
+             label="Specify outlier detection threshold" />
+
+      <!-- standardisation method -->
+      <conditional name="stand">
+        <param name="stand_method" type="select"
+              label="Select a method for standardisation">
+        <option value="std" selected="true">STD</option>
+        <option value="mad">MAD</option>
+        <option value="custom">Custom</option>
+        </param>
+
+        <when value="custom">
+          <param name="std_file" type="data"  format="tabular"
+                 label="STD file"
+                 help="A data matrix with only two columns. The fisrt
+                       column is the names of ion and the second one is std
+                       values. " />
+        </when>
+      </conditional>
+
+      <param name="thres_symb" type="float" value="2.0"
+             label="Specify symbolisation threshold" />
+
+    </section>
+    <!-- end of pre -->
+
+    <section name="expl" title="Exploratory analysis" >
+      <param name="thres_ion_corr" type="float" value="0.15"
+             label="Threshold for Ion correlation (0 - 1)" />
+    </section>
+
+    <section name="clus" title="Clustering analysis" >
+      <param name="min_clust_size" type="float" value="10.0"
+             label="Specify minimal cluster center number" />
+      <param name="h_tree" type="float" value="0.0"
+             label="Cutting height for hierarchical clustering" />
+      <param name="filter_zero_string" type="boolean" truevalue="True"
+             falsevalue="False" checked="True"
+             label="Filter the zero string?" />
+    </section>
+
+    <section name="enri" title="Enrichment analysis" >
+      <param name="pval" type="float" value="0.05"
+             label="Specify p-value threshold for enrichment analysiss" />
+      <param name="min_count" type="float" value="3.0"
+             label="Minimal count number for enrichment analysis" />
+      <param name="ont" type="select"
+             label="Select gene ontology for GO Terms">
+      <option value="BP" selected="true">BP</option>
+      <option value="MF">MF</option>
+      <option value="CC">CC</option>
+      </param>
+      <param name="annot_pkg" type="select"
+            label="Select an annotation package">
+      <option value="org.Sc.sgd.db" selected="true">Yeast(org.Sc.sgd.db)</option>
+      <option value="org.Hs.eg.db">Human(org.Hs.eg.db)</option>
+      <option value="org.Mm.eg.db">Mouse(org.Mm.eg.db)</option>
+      </param>
+    </section>
+
+    <section name="net" title="Network analysis" >
+      <param name="method_corr" type="select"
+             label="Select a method for similarity measure">
+      <option value="pearson">Pearson</option>
+      <option value="spearman">Spearman</option>
+      <option value="kendall">Kendall</option>
+      <option value="cosine" selected="true">Cosine</option>
+      <option value="mahal_cosine">Mahalanobis Cosine</option>
+      <option value="hybrid_mahal_cosine">Hybrid Mahalanobis Cosine</option>
+      </param>
+      <param name="thres_corr" type="float" value="0.7" min="0" max="1"
+             label="Specify similarity threshold (0 - 1)" />
+    </section>
+
+  </inputs>
+
+
+  <!-- =============================================================== -->
+  <outputs>
+    <data format="pdf" name="pre_proc_pdf"
+          label="Pre-processing plots for Ions on ${on_string}" />
+    <data format="tabular" name="df_stats_out"
+          label="Statistical summary of data set on ${on_string}"/>
+    <data format="tabular" name="outl_out"
+          label="Outlier table on ${on_string}"/>
+    <data format="tabular" name="data_wide_out"
+          label="Pre-processed data in wide format on ${on_string}"/>
+    <data format="tabular" name="data_wide_symb_out"
+          label="Symbolization data in wide format on ${on_string}"/>
+    <data format="pdf" name="expl_anal_pdf"
+          label="Explanatation analysis plots for Ions on ${on_string}" />
+    <data format="pdf" name="clus_anal_pdf"
+          label="Explanatation analysis plots for Ions on ${on_string}" />
+    <data format="tabular" name="go_en_out"
+          label="GO enrichment table on ${on_string}"/>
+    <data format="pdf" name="gene_net_pdf"
+          label="Gene network plots on ${on_string}" />
+    <data format="tabular" name="imbe_out"
+          label="Impact and betweenness table on ${on_string}"/>
+  </outputs>
+
+  <!-- =============================================================== -->
+  <tests>
+    <test>
+      <param name="ion_file" value="Dataset_IonFlow_Ionome_KO_short.csv" />
+      <param name="var_id" value="1" />
+      <param name="batch_id" value="3" />
+      <param name="data_id" value="5" />
+      <param name="method_norm" value="median" />
+      <param name="batch_control" value="yes" />
+      <param name="control_lines" value="BY4741" />
+      <param name="control_use" value="all" />
+      <param name="method_outliers" value="log.FC.dist" />
+      <param name="thres_outl" value="3.0" />
+      <param name="stand_method" value="std" />
+      <param name="thres_symb" value="2" />
+      <param name="thres_ion_corr" value="0.15" />
+      <param name="min_clust_size" value="10.0" />
+      <param name="h_tree" value="0.0" />
+      <param name="filter_zero_string" value="TRUE" />
+      <param name="pval" value="0.05" />
+      <param name="min_count" value="3" />
+      <param name="ont" value="BP" />
+      <param name="annot_pkg" value="org.Sc.sgd.db" />
+      <param name="method_corr" value="cosine" />
+      <param name="thres_corr" value="0.7" />
+      <output name="pre_proc_pdf" file="res/pre_proc.pdf" compare="sim_size" />
+      <output name="df_stats_out" file="res/df_stats.tsv" compare="diff" />
+      <output name="outl_out" file="res/outl.tsv" compare="diff" />
+      <output name="data_wide_out" file="res/data_wide.tsv" compare="diff" />
+      <output name="data_wide_symb_out" file="res/data_wide_symb.tsv" compare="diff" />
+      <output name="expl_anal_pdf" file="res/expl_anal.pdf" compare="sim_size" />
+      <output name="clus_anal_pdf" file="res/clus_anal.pdf" compare="sim_size" />
+      <output name="go_en_out" file="res/go_en.tsv" compare="diff" />
+      <output name="gene_net_pdf" file="res/gene_net.pdf" compare="sim_size" />
+      <output name="imbe_out" file="res/impact_betweenness.tsv" compare="diff" />
+    </test>
+  </tests>
+
+  <!-- =============================================================== -->
+<help>
+IonFlow  Pipeline
+=================
+
+Description
+-----------
+
+This galaxy tool wraps R package IonFlow_ with modification to process
+ionomics data to aid reproducible data sharing and big data initiatives.
+
+The pipeline includes:
+
+Pre-Processing
+  This procedure performs batch correction with or without control lines,
+  outlier detection and data standardisation. The processed concentration
+  data and a symbolisation profile data are returned for further analysis.
+
+Exploratory Analysis
+  This procedure performs correlation analysis and PCA analysis in terms of
+  ions. The heatmap with hierarchical clustering and network graph are based
+  on the correlation analysis.
+
+Clustering Analysis
+  This step performs hierarchical clustering based on symbolised profile.
+  The selected cluster centres (control by the threshold of minimal cluster
+  centre number) are applied to enrichment and network analysis.
+
+Enrichment Analysis
+  This step uses the clustering results for enrichment analysis. Current suports
+  three annotation packages:
+
+  - Yeast(org.Sc.sgd.db)
+  - Human(org.Hs.eg.db)
+  - Mouse(org.Mm.eg.db)
+
+Network Analysis
+  This part uses hierarchical clustering of the symbolised profile
+  for network analysis. Genes with correlation coefficient large than a
+  threshold are then used. Some network analysis stats such as impact and
+  betweenness are also returned.
+
+.. _IonFlow: https://github.com/AlinaPeluso/MetaboFlow
+
+Inputs
+------
+
+Ionomics data
+~~~~~~~~~~~~~
+
+The input file is an ionomics data table in tubular format. The following is
+an example with the first two columns of knockout name and batch ID and
+other columns are ion data. To use this input data in ``Pre-processing`` , the
+user must indicate ``var_id`` as ``1`` (``Knockout``), ``batch_id`` as ``2``
+(``Batch_ID``) and ``data_id`` as ``3``. If the file has the batch control
+information in the first column, ``control_lines`` should indicate. For
+example, if ``YDL227C`` will be used as batch control, ``control_lines =
+"YDL227C"``.
+
+
+ +----------+----------+---------+-------+-------+--------+----------+---------+-------+---------+-------+----------+----------+
+ | Knockout | Batch_ID | Ca      | Cd    | Cu    | Fe     | K        | Mg      | Mo    | Na      | Ni    | P        | S        |
+ +----------+----------+---------+-------+-------+--------+----------+---------+-------+---------+-------+----------+----------+
+ | YDL227C  | 14       | 59.549  | 0.953 | 2.202 | 10.942 | 3448.070 | 693.992 | 1.603 | 259.816 | 1.573 | 4963.315 | 556.397  |
+ +----------+--+-------+---------+-------+-------+--------+----------+---------+-------+---------+-------+----------+----------+
+ | YDL227C  | 14       | 62.258  | 0.927 | 2.067 | 26.262 | 3493.741 | 705.008 | 2.691 | 273.640 | 4.443 | 4874.101 | 553.229  |
+ +----------+--+-------+---------+-------+-------+--------+----------+---------+-------+---------+-------+----------+----------+
+ | YDL227C  | 14       | 65.075  | 0.875 | 2.048 | 10.244 | 3317.611 | 691.411 | 1.878 | 278.167 | 1.448 | 4608.300 | 535.609  |
+ +----------+--+-------+---------+-------+-------+--------+----------+---------+-------+---------+-------+----------+----------+
+ | YDL227C  | 14       | 56.886  | 0.985 | 2.203 |  9.206 | 3330.854 | 702.734 | 1.396 | 268.609 | 1.640 | 5119.736 | 546.230  |
+ +----------+----------+---------+-------+-------+--------+----------+---------+-------+---------+-------+----------+----------+
+
+|
+
+Custom STD data
+~~~~~~~~~~~~~~~
+
+Standard derivation values can be provide by user if standardisation method
+``stand_method`` in pre-processing procedure is selected as ``custom``. The
+user defined std file has tabular format such as:
+
+  +------+----------+
+  |  Ion |   sd     |
+  +------+----------+
+  |  Ca  | 0.150    |
+  +------+----------+
+  |  Fe  | 0.163    |
+  +------+----------+
+  |  K   | 0.094    |
+  +------+----------+
+  |  Mg  | 0.059    |
+  +------+----------+
+  |  Na  | 0.107    |
+  +------+----------+
+  |  Ni  | 0.078    |
+  +------+----------+
+  |  Zn  | 0.067    |
+  +------+----------+
+
+|
+
+Outputs
+-------
+
+Pre-processing
+~~~~~~~~~~~~~~
+
+The output includes:
+
+- A PDF file for the plots:  dot-plot with ion vs batch and distribution
+  plot of ions.
+- A tabular file for statistical summary of data set
+- A tabular file for outlier table
+- A tabular file for processed data set
+- A tabular file for the symbolisation data set
+
+Exploratory analysis
+~~~~~~~~~~~~~~~~~~~~
+
+A single PDF file with plots:
+
+- Correlation map
+- Heatmap with dendrogram
+- PCA plot
+- Correlation network graph
+
+Clustering analysis
+~~~~~~~~~~~~~~~~~~~
+
+A single PDF file with clustering plots.
+
+Enrichment analysis
+~~~~~~~~~~~~~~~~~~~
+
+A tabular file for GO Terms enrichment table.
+
+Network analysis
+~~~~~~~~~~~~~~~~
+
+Two files are returned:
+
+- A PDF file for plots
+  - network graph
+  - impact scatter plot
+- A tabular file for impact and betweenness table
+
+
+</help>
+  <citations>
+  </citations>
+</tool>