Mercurial > repos > rnateam > graphclust_postprocessing

diff glob_report.xml @ 12:b5f49453af8c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
author rnateam
date Wed, 31 May 2017 14:53:30 -0400
parents e080ebe95476
children 23dc3b4545d5
line wrap: on
line diff
--- a/glob_report.xml	Sat Mar 25 16:50:38 2017 -0400
+++ b/glob_report.xml	Wed May 31 14:53:30 2017 -0400
@@ -1,6 +1,6 @@
 <tool id="glob_report" name="cluster_collection_report" version="0.1">
   <requirements>
-    <requirement type="package" version="0.1.12">graphclust-wrappers</requirement>
+    <requirement type="package" version="0.2.0">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>
@@ -172,8 +172,9 @@
   <tests>
     <test>
       <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
-      <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="cmsearch_results" value="1.1.tree,1.2.tree"/>
+      <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
+      <param name="combined_cm_out" value="combined_cm_out"/>
       <param name="partition_type" value="0"/>
       <param name="cut_type" value="0"/>
       <conditional name="iteration_num">
@@ -184,26 +185,23 @@
       <param name="min_cluster_size" value="3"/>
       <param name="cm_min_bitscore" value="20"/>
       <param name="cm_max_eval" value="0.001"/>
-      <param name="cm_bitscore_sig" value="1"/>
+      <param name="cm_bitscore_sig" value="0"/>
       <output name="final_stats" file="RESULTS/cluster.final.stats" />
       <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  1.2" />
-            <has_text text="1.3  1.3" />
-            <has_text text="1.4  1.4" />
-            <has_text text="1.5  1.5 " />
+            <has_text text="1.1  1.1 " />
+            <has_text text="1.2  1.2" />
           </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 0 0 0" />
+            <has_text text="MODEL CLASS 0 0" />
             <!--has_text text="1.2" />
             <has_text text="1.1" /-->
           </assert_contents>
@@ -217,21 +215,15 @@
       <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_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"/>