diff metaquantome_viz.xml @ 1:8c30496a665a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"

--- a/metaquantome_viz.xml	Thu Apr 25 13:48:59 2019 -0400
+++ b/metaquantome_viz.xml	Wed Sep 23 17:01:47 2020 +0000
@@ -31,6 +31,9 @@
           <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe">
                   <validator type="empty_field"/>
           </param>
+          <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value 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"
@@ -44,11 +47,16 @@
               <param argument="--alpha" type="float"
               value="0.05" min="0.0" max="1.0"
               label="The q-value significance level"/>
+              <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
+                <validator type="empty_field"/>
+              </param>
             </when>
             <when value="false">
               <!-- do nothing -->
             </when>
           </conditional>
+          <param argument="--feature_cluster_size" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree. Default = 2"/>
+          <param argument="--sample_cluster_size" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree. Default = 2"/>
         </xml>
         <xml name="pca_calcsep">
           <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false"
@@ -69,13 +77,15 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
+        cp '$infile' '$infile.name'
+        &&
         metaquantome viz
         --samps '$samps'
         --mode '$mode_args.mode'
         #if str($mode_args.mode) == 'f'
             --ontology='$mode_args.ontology'
         #end if
-        --infile='$infile'
+        --infile='$infile.name'
         --plottype='$mode_args.plot.plottype'
         #if $mode_args.plot.plottype == 'bar':
             #if str($mode_args.mode) == 't':
@@ -93,6 +103,7 @@
             --barcol=$mode_args.plot.barcol
         #elif $mode_args.plot.plottype == 'volcano':
             --fc_name='$mode_args.plot.fc_name'
+            --fc_corr_p='$mode_args.plot.fc_corr_p'
             #if $mode_args.plot.textannot:
                 --textannot='$mode_args.plot.textannot'
             #end if
@@ -104,6 +115,13 @@
             #if $mode_args.plot.heatmap.filter_to_sig:
               --filter_to_sig
               --alpha=$mode_args.plot.heatmap.alpha
+              --fc_corr_p='mode_args.plot.fc_corr_p'
+            #end if
+            #if feature_cluster_size:
+                --feature_cluster_size='$mode_args.plot.feature_cluster_size'
+            #end if
+            #if sample_cluster_size:
+                --sample_cluster_size='$mode_args.plot.sample_cluster_size'
             #end if
         #elif $mode_args.plot.plottype == 'pca':
             $mode_args.plot.calculate_sep
@@ -315,6 +333,24 @@
         from_work_dir="plotdata.tab">
         <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
       </data>
+      
+      <data format="tabular" name="heatmap_feature_cluster"
+        label="${mode_args.plot.plottype}: feature cluster data"
+        from_work_dir="feature_cluster_${infile.name.rsplit('.',1)[0]}.txt">
+        <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
+      </data>
+      <data format="tabular" name="heatmap_sample_cluster"
+        label="${mode_args.plot.plottype}: sample cluster data"
+        from_work_dir="sample_cluster_${infile.name.rsplit('.',1)[0]}.txt">
+        <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
+      </data>
+      
+      <data format="tabular" name="heatmap_sample_cluster"
+        label="${mode_args.plot.plottype}: sample cluster data"
+        from_work_dir="PC_Data_${infile.name.rsplit('.',1)[0]}.txt">
+        <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
+      </data>
+      
     </outputs>
     <tests>
         <test>
@@ -337,6 +373,7 @@
              <param name="plottype" value="volcano" />
              <param name="target_rank" value="genus" />
              <param name="fc_name" value="log2fc_NS_over_WS" />
+             <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
              <param name="textannot" value="taxon_name" />
              <output name="wrapped_outfile">
                 <assert_contents>
@@ -387,6 +424,7 @@
              <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
              <param name="plottype" value="volcano" />
              <param name="fc_name" value="log2fc_NS_over_WS" />
+             <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
              <output name="wrapped_outfile">
                 <assert_contents>
                     <has_text text="To download the image" />