Mercurial > repos > rnateam > graphclust_align_cluster

diff align_cluster.xml @ 1:953353eacec2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 5fe196bd60c65c884ae1685d4b7fb33119564fa7
author rnateam
date Sun, 28 Oct 2018 18:52:14 -0400
parents c05c83b3ef0f
children 40371e8b6ee2
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line diff
--- a/align_cluster.xml	Sat Oct 27 13:21:39 2018 -0400
+++ b/align_cluster.xml	Sun Oct 28 18:52:14 2018 -0400
@@ -38,8 +38,8 @@
             #end if
         #end if
       "
-      && 
-      R-scape --outdir ./RESULTS/ result.aln.sth &&
+      &&
+      '$__tool_directory__/call_rscape.sh' ./RESULTS/ result.aln.sth &&
       RNAz --locarnate '$alignment_clustal' > alignment.rnaz.out &&
       #if  str($genomic_cons_opts.genomic_cons_opts_selector) != "no":
           clustal_to_alma.py '$alignment_clustal' $cluster_all &&
@@ -162,13 +162,29 @@
       <data name="evofold_out" format="txt" from_work_dir="alignment.evofold.out" label="evofold.out"  />
       <data name="cons_tsv" format="tabular" from_work_dir="conservation_metrics.tsv" label="conservation_metrics.tsv"  />    
   </outputs>
+ 
   <tests>
         <test>
+            <param name="cluster_all_fa" value="cluster3.all.fa"/>
+            <param name="cluster_all" value="cluster3.all"/>
+            <output name="cons_tsv" file="alignment3.cons.tsv"   compare="sim_size" delta="0"/>
+            <output name="rscape_out" file="rscape3.out" compare="sim_size"  delta="10"/>
+            <output name="structure_png" file="structure3.png" compare="sim_size" /> 
+            <output name="Rscape_R2R" file="alignment3_R2R.sto.pdf" compare="sim_size" />
+            <output name="alignment_sth" file="alignment3.sth"  compare="sim_size" delta="100" />
+            <conditional name="genomic_cons_opts">
+                <param name="genomic_cons_opts_selector" value="no"/>
+            </conditional>
+            <param name="results_top_num" value="5"/>
+        </test>
+  
+        <test>
             <param name="cluster_all_fa" value="cluster1.all.fa"/>
             <param name="cluster_all" value="cluster1.all"/>
             <output name="alignment_ps" file="alignment1.ps" compare="sim_size" />
             <output name="alignment_png" file="alignment1.png" compare="sim_size" />
             <output name="structure_ps" file="structure1.ps" compare="sim_size" />
+            <output name="rscape_out" file="rscape1.out" compare="sim_size"  delta="10"/>
             <output name="structure_png" file="structure1.png" compare="sim_size" /> 
             <output name="alignment_sth" file="alignment1.sth"  compare="sim_size" delta="100" />
             <output name="alignment_clustal_out" file="alignment1.clustal" />
@@ -210,7 +226,7 @@
                 <param name="transcript_loci_fasta" value="alignment2b-transcript.fa"/>
                 <param name="transcript_loci_bed" value="chr7 27162434 27166719 Hoxa9-Xtend5UTR 2 -"/>
             </conditional>
-        </test>
+        </test> 
     </tests>
     <help>
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