--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_viz.xml	Thu Apr 25 13:48:59 2019 -0400
@@ -0,0 +1,433 @@
+<tool id="metaquantome_viz" name="metaQuantome: visualize" version="@GVERSION@">
+    <description>taxonomic analysis, functional analysis, and function-taxonomy analysis results</description>
+    <macros>
+        <import>macros.xml</import>
+        <xml name="barcol">
+          <param argument="--barcol" type="select" label="Color for the bar fill">
+            <option value="1">Blue</option>
+            <option value="2">Orange</option>
+            <option value="3">Yellow</option>
+            <option value="4">Red</option>
+            <option value="5">Violet</option>
+            <option value="6">Black</option>
+              <help>
+                These same colors are also used in the heatmap and PCA plot,
+                so the colors can be tweaked to match. Note that these colors
+                are coded as 1 through 6 in the command line tool.
+              </help>
+          </param>
+        </xml>
+        <xml name="common_bar_params">
+          <param argument="--meancol" type="text" label="Mean intensity column name"
+                  help="Mean intensity column name for desired experimental condition">
+                  <validator type="empty_field"/>
+          </param>
+          <param argument="--nterms" type="integer"
+            value="5" min="1" optional="true"
+            label="Number of terms to display"
+            help="leave blank for all terms"/>
+        </xml>
+        <xml name="common_volc_params">
+          <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe">
+                  <validator type="empty_field"/>
+          </param>
+          <param argument="--textannot" type="text" optional="true" label="Name of the annotation column"
+              help="Provides text annotatation for the plot.  Optional. If missing, no text will be plotted."/>
+          <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false"
+              label="Flip the fold change (i.e., multiply log fold change by -1)"/>
+        </xml>
+        <xml name="common_heatmap_params">
+          <conditional name="heatmap">
+            <param argument="--filter_to_sig" type="boolean" checked="false"
+              label="Only plot significant term" help="Necessitates use of results from `test`"/>
+            <when value="true">
+              <param argument="--alpha" type="float"
+              value="0.05" min="0.0" max="1.0"
+              label="The q-value significance level"/>
+            </when>
+            <when value="false">
+              <!-- do nothing -->
+            </when>
+          </conditional>
+        </xml>
+        <xml name="pca_calcsep">
+          <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false"
+              label="Calculate separation between groups and include in title?"/>
+        </xml>
+        <xml name="target_onto">
+          <param argument="--target_onto" type="select" optional="false"
+            label="GO category to restrict to">
+            <help>
+              Only the values from this category
+              of GO terms will be displayed.
+            </help>
+            <option value="bp">Biological Process</option>
+            <option value="mf">Molecular Function</option>
+            <option value="cc">Cellular Component</option>
+          </param>
+        </xml>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        metaquantome viz
+        --samps '$samps'
+        --mode '$mode_args.mode'
+        #if str($mode_args.mode) == 'f'
+            --ontology='$mode_args.ontology'
+        #end if
+        --infile='$infile'
+        --plottype='$mode_args.plot.plottype'
+        #if $mode_args.plot.plottype == 'bar':
+            #if str($mode_args.mode) == 't':
+                --target_rank='$mode_args.plot.target_rank'
+            #end if
+            --meancol='$mode_args.plot.meancol'
+            #if str($mode_args.plot.nterms) == '':
+                --nterms='all'
+            #else
+                --nterms=$mode_args.plot.nterms
+            #end if
+            #if str($mode_args.mode) == 'f':
+                --target_onto='$mode_args.plot.target_onto'
+            #end if
+            --barcol=$mode_args.plot.barcol
+        #elif $mode_args.plot.plottype == 'volcano':
+            --fc_name='$mode_args.plot.fc_name'
+            #if $mode_args.plot.textannot:
+                --textannot='$mode_args.plot.textannot'
+            #end if
+            $mode_args.plot.flip_fc
+            #if $mode_args.mode == 'f':
+              $mode_args.plot.gosplit
+            #end if
+        #elif $mode_args.plot.plottype == 'heatmap':
+            #if $mode_args.plot.heatmap.filter_to_sig:
+              --filter_to_sig
+              --alpha=$mode_args.plot.heatmap.alpha
+            #end if
+        #elif $mode_args.plot.plottype == 'pca':
+            $mode_args.plot.calculate_sep
+        #elif $mode_args.plot.plottype == 'ft_dist':
+            --barcol='$mode_args.plot.barcol'
+            --whichway='$mode_args.plot.margin.whichway'
+            --meancol='$mode_args.plot.meancol'
+            #if $mode_args.plot.margin.term.id_or_name == 'id':
+                --id='$mode_args.plot.margin.term.id'
+            #else:
+                --name='$mode_args.plot.margin.term.name'
+            #end if
+            #if $mode_args.plot.margin.whichway == 't_dist':
+                --target_rank='$mode_args.plot.margin.target_rank'
+            #end if
+            #if $mode_args.plot.margin.whichway == 'f_dist':
+                --target_onto=$mode_args.plot.margin.target_onto
+            #end if
+        #end if
+        #if $width:
+            --width=$width
+        #end if
+        #if $height:
+            --height=$height
+        #end if
+        --img='outfile.png'
+        --tabfile='plotdata.tab' &&
+        mkdir '${ wrapped_outfile.files_path }' &&
+        cp outfile.png '${ wrapped_outfile.files_path }' &&
+        echo "<!DOCTYPE html>
+        <html>
+          <body>
+            <img src=\"outfile.png\" width=600>
+            <br>
+            <p>To download the image, right-click and choose \"Save image as...\"</p>
+            <br>
+            <p>
+              If text is cut off or the plot is not displaying properly,
+              the easiest fix is to increase the plot dimensions
+            </p>
+          </body>
+        </html>" > wrapped_outfile.html
+    ]]></command>
+    <inputs>
+      <param argument="--infile" type="data"
+        format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
+      <expand macro="SAMPS"/>
+      <conditional name="mode_args">
+        <param argument="--mode" type="select" label="Mode">
+            <option value="f">Functional analysis</option>
+            <option value="t">Taxonomic analysis</option>
+            <option value="ft">Functional-taxonomic interaction analysis</option>
+        </param>
+        <when value="f">
+          <param name="ontology" type="select" label="Ontology">
+            <option value="go">Gene Ontology (GO terms)</option>
+            <option value="ec">Enzyme Commission (EC) numbers</option>
+            <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
+          </param>
+          <conditional name="plot">
+            <param argument="--plottype" type="select" label="Plot type">
+              <option value="bar">Bar Chart (bar)</option>
+              <option value="volcano">Volcano Plot (volcano)</option>
+              <option value="heatmap">Heatmap (heatmap)</option>
+              <option value="pca">Principal Components Analysis (pca)</option>
+            </param>
+            <when value="bar">
+              <expand macro="common_bar_params"/>
+              <expand macro="target_onto"/>
+              <expand macro="barcol"/>
+            </when>
+            <when value="volcano">
+              <expand macro="common_volc_params"/>
+              <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false"
+                  label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/>
+            </when>
+            <when value="heatmap">
+              <expand macro="common_heatmap_params"/>
+            </when>
+            <when value="pca">
+              <expand macro="pca_calcsep"/>
+            </when>
+          </conditional>
+        </when>
+        <when value="t">
+          <conditional name="plot">
+            <param argument="--plottype" type="select" label="Plot type">
+              <option value="bar">Bar Chart (bar)</option>
+              <option value="volcano">Volcano Plot (volcano)</option>
+              <option value="heatmap">Heatmap (heatmap)</option>
+              <option value="pca">Principal Components Analysis (pca)</option>
+            </param>
+            <when value="bar">
+              <param argument="--target_rank" type="select"
+                label="Taxonomic rank to restrict to in the plot"
+                      help="possibilities are taken from the input dataset.">
+                  <options from_dataset="infile">
+                    <column name="value" index="2"/>
+                    <filter type="unique_value" name="unique_taxon" column="2"/>
+                    <!-- <filter type="remove_value" value="rank" column="2"/> -->
+                  </options>
+              </param>
+              <expand macro="common_bar_params"/>
+              <expand macro="barcol"/>
+            </when>
+            <when value="volcano">
+              <expand macro="common_volc_params"/>
+            </when>
+            <when value="heatmap">
+              <expand macro="common_heatmap_params"/>
+            </when>
+            <when value="pca">
+              <expand macro="pca_calcsep"/>
+            </when>
+          </conditional>
+        </when>
+        <when value="ft">
+          <conditional name="plot">
+            <param argument="--plottype" type="select" label="Plot type">
+              <option value="ft_dist" selected="true">Functional Taxonomic Distribution (ft_dist)</option>
+            </param>
+            <when value="ft_dist">
+              <param argument="--meancol" type="text" label="Mean intensity column name"
+                      help="Mean intensity column name for desired experimental condition">
+                      <validator type="empty_field"/>
+              </param>
+              <conditional name="margin">
+                <param argument="--whichway" type="select" label="which distribution">
+                  <option value="f_dist">functional distribution for a taxon (f_dist)</option>
+                  <option value="t_dist">taxonomic distribution for a function (t_dist)</option>
+                </param>
+                <when value="f_dist">
+                  <conditional name="term">
+                    <param name="id_or_name" type="select" label="">
+                      <option value="id" selected="true">Taxon ID</option>
+                      <option value="name">Taxon name</option>
+                    </param>
+                    <when value="id">
+                        <param argument="--id" type="select" label="Taxon id">
+                            <options from_dataset="infile">
+                              <column name="value" index="3"/>
+                              <filter type="unique_value" column="3"/>
+                              <!-- <filter type="remove_value" value="tax_id"/> -->
+                            </options>
+                        </param>
+                    </when>
+                    <when value="name">
+                      <param argument="--name" type="select" label="Taxon name">
+                          <options from_dataset="infile">
+                            <column name="value" index="4"/>
+                            <filter type="unique_value" column="4"/>
+                            <!-- <filter type="remove_value" value="taxon_name"/> -->
+                          </options>
+                      </param>
+                    </when>
+                  </conditional>
+                  <expand macro="target_onto"/>
+                </when>
+                <when value="t_dist">
+                  <conditional name="term">
+                    <param name="id_or_name" type="select" label="">
+                      <option value="id" selected="true">Functional term ID</option>
+                      <option value="name">Functional term name</option>
+                    </param>
+                    <when value="id">
+                        <param argument="--id" type="select" label="Functional term id">
+                            <options from_dataset="infile">
+                              <column name="value" index="0"/>
+                              <filter type="unique_value" column="0"/>
+                              <!-- <filter type="remove_value" value="go_id"/> -->
+                            </options>
+                        </param>
+                    </when>
+                    <when value="name">
+                      <param argument="--name" type="select" label="Functional term name">
+                          <options from_dataset="infile">
+                            <column name="value" index="1"/>
+                            <filter type="unique_value" column="1"/>
+                            <!-- <filter type="remove_value" value="name"/> -->
+                          </options>
+                      </param>
+                    </when>
+                  </conditional>
+                  <param argument="--target_rank" type="select"
+                    label="Taxonomic rank to restrict to in the plot"
+                    help="possibilities are taken from the input dataset.">
+                    <options from_dataset="infile">
+                      <column name="value" index="5"/>
+                      <filter type="unique_value" name="unique_taxon" column="5"/>
+                      <!-- <filter type="remove_value" value="rank" column="5"/> -->
+                    </options>
+                  </param>
+                </when>
+              </conditional>
+              <expand macro="barcol"/>
+            </when>
+          </conditional>
+        </when>
+      </conditional>
+      <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/>
+      <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/>
+    </inputs>
+    <outputs>
+      <data format="html" name="wrapped_outfile"
+          label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html"
+          from_work_dir="wrapped_outfile.html"/>
+      <data format="tabular" name="plotdata"
+        label="${tool.name} ${on_string} ${mode_args.plot.plottype}: plot data"
+        from_work_dir="plotdata.tab">
+        <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
+      </data>
+    </outputs>
+    <tests>
+        <test>
+             <param name="infile" value="tax_filt_out.tab" ftype="tabular"/>
+             <param name="mode" value="t" />
+             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+             <param name="plottype" value="bar" />
+             <param name="target_rank" value="genus" />
+             <param name="meancol" value="NS_mean" />
+             <output name="wrapped_outfile">
+                <assert_contents>
+                    <has_text text="To download the image" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+             <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
+             <param name="mode" value="t" />
+             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+             <param name="plottype" value="volcano" />
+             <param name="target_rank" value="genus" />
+             <param name="fc_name" value="log2fc_NS_over_WS" />
+             <param name="textannot" value="taxon_name" />
+             <output name="wrapped_outfile">
+                <assert_contents>
+                    <has_text text="To download the image" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+             <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
+             <param name="mode" value="t" />
+             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+             <param name="plottype" value="heatmap" />
+             <output name="wrapped_outfile">
+                <assert_contents>
+                    <has_text text="To download the image" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+             <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
+             <param name="mode" value="t" />
+             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+             <param name="plottype" value="pca" />
+             <output name="wrapped_outfile">
+                <assert_contents>
+                    <has_text text="To download the image" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+             <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
+             <param name="mode" value="f" />
+             <param name="ontology" value="go" />
+             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+             <param name="plottype" value="bar" />
+             <param name="meancol" value="NS_mean" />
+             <param name="target_onto" value="bp"/>
+             <output name="wrapped_outfile">
+                <assert_contents>
+                    <has_text text="To download the image" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+             <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
+             <param name="mode" value="f" />
+             <param name="ontology" value="go"/>
+             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+             <param name="plottype" value="volcano" />
+             <param name="fc_name" value="log2fc_NS_over_WS" />
+             <output name="wrapped_outfile">
+                <assert_contents>
+                    <has_text text="To download the image" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+             <param name="infile" value="tf_filt_out.tab" ftype="tabular"/>
+             <param name="mode" value="ft" />
+             <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
+             <param name="plottype" value="ft_dist" />
+             <param name="meancol" value="NS_mean" />
+             <param name="whichway" value="f_dist" />
+             <param name="id_or_name" value="id" />
+             <param name="id" value="1301" />
+             <param name="target_onto" value="bp" />
+             <output name="wrapped_outfile">
+                <assert_contents>
+                    <has_text text="To download the image" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+metaQuantome viz
+===================
+
+The *viz* module is the final step in the metaQuantome analysis workflow.
+The available visualizations are:
+
+- bar plot
+- volcano plot
+- heatmap
+- PCA plot
+
+Please consult the manuscript for full details on each of these plots.
+
+Questions, Comments, Problems, Kudos
+--------------------------------------
+
+Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
+    ]]></help>
+    <expand macro="citations" />
+</tool>