diff tophat_fusion_post.xml @ 2:3279e193b966 draft default tip

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

--- a/tophat_fusion_post.xml	Mon Jan 27 13:11:25 2014 -0500
+++ b/tophat_fusion_post.xml	Tue Oct 13 12:33:55 2015 -0400
@@ -2,14 +2,16 @@
     <description>post-processing to identify fusion genes</description>
     <version_command>tophat-fusion-post --version</version_command>
     <requirements>
-        <requirement type="package">tophat2</requirement>
+        <requirement type="package" version="2.2.28">blast+</requirement>
+        <requirement type="package" version="0.12.7">bowtie</requirement>
+        <requirement type="package" version="2.0.9">tophat2</requirement>
     </requirements>
     <command>
         ## Set up tophat_out structure.
         mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out;
 
         ## Set up blast directory structure.
-        #set blast_db_path = ${__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
+        #set blast_db_path = $__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')
         ln -s ${blast_db_path}/ blast;
 
         ## Set up additional files:
@@ -18,14 +20,14 @@
         ln -s ${blast_db_path}/mcl .;
 
         ## Run tophat-fusion-post
-        tophat-fusion-post -p 22
+        tophat-fusion-post -p \${GALAXY_SLOTS:-4}
         --num-fusion-reads $num_fusion_reads --num-fusion-pairs $num_fusion_pairs --num-fusion-both $num_fusion_both --fusion-read-mismatches $fusion_read_mismatches --fusion-multireads $fusion_multireads
         #if str($is_human) == 'No':
               --non-human
         #end if
 
-	## Bowtie2 indices.
-	${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
+	    ## Bowtie indices.
+	    ${__get_data_table_entry__('bowtie_indexes', 'value', $accepted_hits.dbkey, 'path')}
     </command>
 
     <inputs>
@@ -47,7 +49,8 @@
     </stdio>
 
     <outputs>
-        <data format="txt" name="results_txt" label="${tool.name} on ${on_string}: text results" from_work_dir="tophatfusion_out/result.txt"/>
+        <data format="tabular" name="results_txt" label="${tool.name} on ${on_string}: text results" from_work_dir="tophatfusion_out/result.txt"/>
         <data format="html" name="results_html" label="${tool.name} on ${on_string}: html results" from_work_dir="tophatfusion_out/result.html"/>
     </outputs>
+    
 </tool>