--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_viz.xml	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,148 @@
+<tool id="metaquantome_viz" name="MetaQuantome Visualization Plots" version="@VERSION@.0">
+    <description>of taxonomic analysis, functional analysis, and function-taxonomy</description>
+    <macros>
+        <import>macros.xml</import>
+        <xml name="img_size">
+            <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/>       
+            <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/>       
+        </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" label="Number of taxa or functional terms to display"/>
+                <param argument="--barcolor" type="integer" value="1" min="1" max="6" label="Color for the bar fill">
+                    <help>
+                        The color vector in R is
+                        c("dodgerblue", "darkorange", "yellow2", "red2", "darkviolet", "black"), 
+                        so providing a 1 will give the "dodgerblue" color. 
+                        These same colors are also used in the heatmap and PCA plot, 
+                        so the colors can be tweaked to match.
+                    </help>
+                </param>
+        </xml>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @MAKE_SAMPS_TSV@
+        metaquantome viz
+        @COMMON_PARAMS@
+        --infile='$infile'
+        --plottype=$plot.plottype
+        #if $plot.plottype == 'bar':
+            --meancol='$plot.meancol'
+            --nterms=$plot.nterms
+            --barcolor=$plot.barcolor
+        #elif $plot.plottype == 'volcano':
+            --fc='$plot.fc'
+            #if $plot.textannot:
+                --textannot='$plot.textannot'
+            #end if
+            $plot.gosplit
+        #elif $plot.plottype == 'heatmap':
+            $plot.filter_to_sig
+            --alpha=$plot.alpha
+        #elif $plot.plottype == 'pca':
+            $plot.calculate_sep
+        #elif $plot.plottype == 'ft_dist':
+            --meancol='$plot.meancol'
+            --nterms=$plot.nterms
+            --barcolor=$plot.barcolor
+            --whichway=$plot.whichway
+            #if $plot.term.id_or_name == 'id':
+                --id='$plot.term.id'
+            #else:
+                --name='$plot.term.name'
+            #end if
+            #if $plot.target_onto:
+                --target_onto=$plot.target_onto
+            #end if
+        #end if
+        #if $plot.height:
+            --height=$plot.height
+        #end if
+        #if $plot.width1:
+            --width=$plot.width
+        #end if
+        --img='outfile.png'
+    ]]></command>
+    <inputs>
+        <expand macro="common_params"/>
+        <param argument="--infile" type="data" format="tabular" label="metaquantome stats or filtered file"
+                    help=""/>
+        <conditional name="plot">
+            <param argument="--plottype" type="select" label="Plot type">
+                <option value="bar">Bar Chart</option>
+                <option value="volcano">Volcano Plot</option>
+                <option value="heatmap">Heatmap</option>
+                <option value="pca">PCA - Principal Componets Analysis</option>
+                <option value="ft_dist">Bar Chart</option>
+            </param>
+            <when value="bar">
+                <expand macro="common_bar_params"/>
+                <expand macro="img_size"/>
+            </when>
+            <when value="volcano">
+                <param argument="--fc" 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 annoatation for the plot.  Optional, if missing, no text will be plotted."/>
+                <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false" 
+                    label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction"/>
+                <expand macro="img_size"/>
+            </when>
+            <when value="heatmap">
+                <param argument="--filter_to_sig" type="boolean" truevalue="--filter_to_sig" falsevalue="" checked="false" 
+                    label="Only plot significant term" help="Necessitates use of results from `test`"/>
+                <param argument="--aplha" type="float" value="0.05" min="0.0" max="1.0" label="If filter_to_sig, the q-value significance level"/>
+                <expand macro="img_size"/>
+            </when>
+            <when value="pca">
+                <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false" 
+                    label="Calculate separation between groups and include in title"/>
+                <expand macro="img_size"/>
+            </when>
+            <when value="ft_dist">
+                <expand macro="common_bar_params"/>
+                <param argument="--whichway" type="select" label="which distribution">
+                    <option value="f_dist">functional distribution for a taxon</option>
+                    <option value="t_dist">taxonomic distribution for a function</option>
+                </param>
+                <conditional name="term">
+                    <param argument="id_or_name" type="select" label="">
+                        <option value="id">Taxonomic or functional term ID</option>
+                        <option value="name">Taxonomic or functional term name</option>
+                    </param>
+                    <when value="id">
+                        <param argument="--id" type="text" label="Taxonomic or functional term id">
+                            <help>
+                                NCBI taxID or a GO term id (GO:XXXXXXX)
+                            </help>
+                        </param>
+                    </when>
+                    <when value="name">
+                       <param argument="--name" type="text" label="Taxonomic or functional term name">
+                           <help>
+                           </help>
+                       </param>
+                    </when>
+                </conditional>
+                <param argument="--target_onto" type="select" optional="true" label="Restrict to GO category">
+                    <option value="bp">Biological Process</option>
+                    <option value="mf">Molecular Function</option>
+                    <option value="cc">Cellular Component</option>
+                </param>
+                <expand macro="img_size"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="png" name="outfile" label="${tool.name} on ${on_string} ${plot.plottype}" from_work_dir="outfile.png"/>
+    </outputs>
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+    <expand macro="citations" />
+</tool>