# HG changeset patch
# User jjohnson
# Date 1578341900 18000
# Node ID 7e2debc267eb034cade22db0c3b92476774048da
# Parent  b59ae99e47d4ed87df16c60c6e1804b53264360a
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit 3898da7c3685e3deca68c998abd7c7104740f5f3"

diff -r b59ae99e47d4 -r 7e2debc267eb drep_compare.xml
--- a/drep_compare.xml	Mon Jan 06 11:11:06 2020 -0500
+++ b/drep_compare.xml	Mon Jan 06 15:18:20 2020 -0500
@@ -19,19 +19,10 @@
         <expand macro="clustering_options"/>
         <expand macro="taxonomy_options"/>
         <expand macro="warning_options"/>
+        <expand macro="select_outputs"/>
     </inputs>
     <outputs>
         <expand macro="common_outputs" />
-<!--
-outdir/data_tables/Cdb.csv
-outdir/data_tables/Mdb.csv
-outdir/data_tables/Ndb.csv
-outdir/data_tables/Bdb.csv
-
-        <data name="foldChange" format="tabular" label="${tool.name} on ${on_string}: BayesianFoldChangeAnalysis.tsv" from_work_dir="out/BayesianFoldChangeAnalysis.tsv">
-            <filter>'bayesian' in experiment and 'ctr' in experiment['bayesian']</filter>
-        </data>
--->
     </outputs>
     <help><![CDATA[
         TODO: Fill in help.
diff -r b59ae99e47d4 -r 7e2debc267eb drep_dereplicate.xml
--- a/drep_dereplicate.xml	Mon Jan 06 11:11:06 2020 -0500
+++ b/drep_dereplicate.xml	Mon Jan 06 15:18:20 2020 -0500
@@ -23,12 +23,13 @@
         <expand macro="scoring_options"/>
         <expand macro="taxonomy_options"/>
         <expand macro="warning_options"/>
+        <expand macro="select_drep_outputs"/>
     </inputs>
     <outputs>
-        <expand macro="common_outputs" />
         <collection name="dereplicated_genomes" type="list" label="dereplicated_genomes">
-             <discover_datasets pattern="__designation__" directory="out_drep/dereplicated_genomes" ext='fasta'/>
+             <discover_datasets pattern="__designation__" directory="outdir/dereplicated_genomes" ext='fasta'/>
         </collection>
+        <expand macro="drep_outputs" />
     </outputs>
     <help><![CDATA[
         TODO: Fill in help.
diff -r b59ae99e47d4 -r 7e2debc267eb macros.xml
--- a/macros.xml	Mon Jan 06 11:11:06 2020 -0500
+++ b/macros.xml	Mon Jan 06 15:18:20 2020 -0500
@@ -255,18 +255,62 @@
         #end if
 ]]></token>
 
-   <xml name="select_outputs">
-   </xml>
+    <xml name="select_outputs">
+        <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
+            <option value="log" selected="true">log</option>
+            <option value="warnings" selected="true">Warnings</option>
+            <option value="Primary_clustering_dendrogram" selected="true">Primary_clustering_dendrogram.pdf</option>
+            <option value="Secondary_clustering_dendrograms">Secondary_clustering_dendrograms.pdf</option>
+            <option value="Secondary_clustering_MDS">Secondary_clustering_MDS.pdf</option>
+            <option value="Clustering_scatterplots" selected="true">Clustering_scatterplots.pdf</option>
+            <yield/>
+        </param>
+    </xml>
+    <xml name="select_drep_outputs">
+        <expand macro="select_outputs">
+            <option value="Cluster_scoring">Cluster_scoring.pdf</option>
+            <option value="Winning_genomes">Winning_genomes.pdf</option>
+            <option value="Widb">Widb.csv</option>
+            <option value="Chdb">Chdb.tsv</option>
+        </expand>
+    </xml>
 
    <xml name="common_outputs">
-       <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log"/>
-       <data name="warnings" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/warnings.txt"/>
-       <data name="Primary_clustering_dendrogram" format="pdf" label="${tool.name} on ${on_string}: Primary_clustering_dendrogram.pdf" from_work_dir="outdir/figures/Primary_clustering_dendrogram.pdf"/>
-       <data name="Secondary_clustering_dendrograms" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_dendrograms.pdf" from_work_dir="outdir/figures/Secondary_clustering_dendrograms.pdf"/>
-       <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf"/>
-       <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf"/>
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log">
+            <filter>'log' in select_outputs or not select_outputs</filter>
+        </data>
+        <data name="warnings" format="txt" label="${tool.name} on ${on_string}: Warnings" from_work_dir="outdir/log/warnings.txt">
+            <filter>'warnings' in select_outputs</filter>
+        </data>
+        <data name="Primary_clustering_dendrogram" format="pdf" label="${tool.name} on ${on_string}: Primary_clustering_dendrogram.pdf" from_work_dir="outdir/figures/Primary_clustering_dendrogram.pdf">
+            <filter>'Primary_clustering_dendrogram' in select_outputs</filter>
+        </data>
+        <data name="Secondary_clustering_dendrograms" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_dendrograms.pdf" from_work_dir="outdir/figures/Secondary_clustering_dendrograms.pdf">
+            <filter>'Secondary_clustering_dendrograms' in select_outputs</filter>
+        </data>
+        <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf">
+            <filter>'Secondary_clustering_MDS' in select_outputs</filter>
+        </data>
+        <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf">
+            <filter>'Clustering_scatterplots' in select_outputs</filter>
+        </data>
     </xml>
-   <xml name="common_outputs2">
+
+
+    <xml name="drep_outputs">
+        <expand macro="common_outputs"/>
+        <data name="Cluster_scoring" format="pdf" label="${tool.name} on ${on_string}: Cluster_scoring.pdf" from_work_dir="outdir/figures/Cluster_scoring.pdf">
+            <filter>'Cluster_scoring' in select_outputs</filter>
+        </data>
+        <data name="Winning_genomes" format="pdf" label="${tool.name} on ${on_string}: Winning_genomes.pdf" from_work_dir="outdir/figures/Winning_genomes.pdf">
+            <filter>'Winning_genomes' in select_outputs</filter>
+        </data>
+        <data name="Widb" format="csv" label="${tool.name} on ${on_string}: Widb.csv" from_work_dir="outdir/data_tables/Widb.csv">
+            <filter>'Widb' in select_outputs</filter>
+        </data>
+        <data name="Chdb" format="tabular" label="${tool.name} on ${on_string}: Chdb.tsv" from_work_dir="outdir/data/checkM/checkM_outdir/Chdb.tsv">
+            <filter>'Chdb' in select_outputs</filter>
+        </data>
     </xml>
 
     <token name="@GENOMES_HELP@"><![CDATA[