Mercurial > repos > rnateam > graphclust_postprocessing

diff glob_report.xml @ 4:dbcea781900e draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit f971832d2b34a182314e5201ea6895dd207c5923
author rnateam
date Mon, 13 Mar 2017 17:54:32 -0400
parents a8fde40f00fc
children fc701681ca6e
line wrap: on
line diff
--- a/glob_report.xml	Sat Jan 21 17:25:15 2017 -0500
+++ b/glob_report.xml	Mon Mar 13 17:54:32 2017 -0400
@@ -1,6 +1,6 @@
-<tool id="glob_report" name="Report_Results" version="0.1">
+<tool id="glob_report" name="cluster_collection_report" version="0.1">
   <requirements>
-    <requirement type="package" version="0.1.7">graphclust-wrappers</requirement>
+    <requirement type="package" version="0.1.10">graphclust-wrappers</requirement>
     <requirement type="package" version='0.5'>perl-array-utils</requirement>
     <requirement type="package" version='0.18.1'>scikit-learn</requirement>
     <requirement type="package" version='1.8.10'>locarna</requirement>
@@ -8,6 +8,8 @@
     <requirement type="package" version="1.1">infernal</requirement>
     <requirement type="package" version='2.2.10'>viennarna</requirement>
     <requirement type="package" version='1.3.23'>graphicsmagick</requirement>
+    <requirement type="package" version='0.3.1'>rscape</requirement>
+
   </requirements>
   <stdio>
     <exit_code range="1:" />
@@ -153,13 +155,16 @@
     <collection name="topDot" type="list" label="Top $results_top_num aln.ps">
       <discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.aln.png$)"  />
     </collection>
+    <collection name="rscapePlot" type="list" label="R-scape Plot">
+      <discover_datasets format="pdf" pattern="(?P&lt;name&gt;^.*\.pdf$)"  />
+    </collection>
     <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip"  />
   </outputs>
   <tests>
     <test>
       <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
-      <param name="cmsearch_results" value="1.tabular,2.tabular"/>
-      <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
+      <param name="cmsearch_results" value="1.tabular,2.tabular,3.tabular,4.tabular,5.tabular"/>
+      <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa,1.3.model.tree.fa,1.4.model.tree.fa,1.5.model.tree.fa"/>
       <param name="partition_type" value="0"/>
       <param name="cut_type" value="0"/>
       <conditional name="iteration_num">
@@ -175,19 +180,23 @@
       <output_collection name="clusters" type="list">
         <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
         <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
+        <element name="3.cluster.all" file="RESULTS/3.cluster.all" compare="contains"/>
+        <element name="4.cluster.all" file="RESULTS/4.cluster.all" compare="contains"/>
       </output_collection>
       <output_collection name="partitions">
         <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
           <assert_contents>
-            <has_text text="1.1  1.1" />
-            <has_text text="1.2  1.2" />
+            <has_text text="1.1  1.1  1.2" />
+            <has_text text="1.3  1.3" />
+            <has_text text="1.4  1.4" />
+            <has_text text="1.5  1.5 " />
           </assert_contents>
         </element>
         <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">
           <assert_contents>
-            <has_text text="MODEL CLASS 0 0" />
-            <has_text text="1.2" />
-            <has_text text="1.1" />
+            <has_text text="MODEL CLASS 0 0 0 0 0" />
+            <!--has_text text="1.2" />
+            <has_text text="1.1" /-->
           </assert_contents>
         </element>
         <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
@@ -199,12 +208,24 @@
       <output_collection name="topSecondaryStruct" type="list">
         <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
         <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
+        <element name="3.cluster.top5.alirna.png" file="3.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
+        <element name="4.cluster.top5.alirna.png" file="4.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
       </output_collection>
       <output_collection name="topDot" type="list">
         <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png"  ftype="png" compare="sim_size" />
         <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png"  ftype="png" compare="sim_size" />
+        <element name="3.cluster.top5.aln.png" file="3.cluster.top5.aln.png"  ftype="png" compare="sim_size" />
+        <element name="4.cluster.top5.aln.png" file="4.cluster.top5.aln.png"  ftype="png" compare="sim_size" />
       </output_collection>
-      <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" />
+
+      <output_collection name="rscapePlot" type="list">
+        <element name="1.cluster.top5.result.aln_1.R2R.sto.pdf" file="1.cluster.top5.result.aln_1.R2R.sto.pdf"  ftype="pdf" compare="sim_size" />
+        <element name="2.cluster.top5.result.aln_1.R2R.sto.pdf" file="2.cluster.top5.result.aln_1.R2R.sto.pdf"  ftype="pdf" compare="sim_size" />
+        <element name="3.cluster.top5.result.aln_1.R2R.sto.pdf" file="3.cluster.top5.result.aln_1.R2R.sto.pdf"  ftype="pdf" compare="sim_size" />
+        <element name="4.cluster.top5.result.aln_1.R2R.sto.pdf" file="4.cluster.top5.result.aln_1.R2R.sto.pdf"  ftype="pdf" compare="sim_size" />
+      </output_collection>
+
+      <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" delta="20000"/>
 
     </test>
   </tests>