# HG changeset patch
# User bgruening
# Date 1510243988 18000
# Node ID c3cff36fcd33adea8088c7727ca75042491b6c34
# Parent  548c44b47dfb305cf52ebd697a0cb7f4c7528e1f
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit e6a9507eb198c6bf2c63ddae387c262bfc8dbd16

diff -r 548c44b47dfb -r c3cff36fcd33 hicup_filter.xml
--- a/hicup_filter.xml	Tue Nov 07 02:45:59 2017 -0500
+++ b/hicup_filter.xml	Thu Nov 09 11:13:08 2017 -0500
@@ -1,12 +1,10 @@
 <tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0">
-        <description>classifies read pairs, identifying valid Hi-C di-tags.</description>
-
+    <description>classifies read pairs, identifying valid Hi-C di-tags.</description>
     <macros>
         <import>hicup_macros.xml</import>
     </macros>
     <expand macro="requirements_hicup" />
     <expand macro="stdio" />
-
     <command><![CDATA[    
         hicup_filter --digest '$digest'
         #if $advanced_options.longest:
diff -r 548c44b47dfb -r c3cff36fcd33 hicup_macros.xml
--- a/hicup_macros.xml	Tue Nov 07 02:45:59 2017 -0500
+++ b/hicup_macros.xml	Thu Nov 09 11:13:08 2017 -0500
@@ -14,9 +14,9 @@
         </stdio>
     </xml>
     <xml name="citation_hicup">
-       <citations>
-	        <citation type="doi">10.12688/f1000research.7334.1</citation>
-	    </citations>  
+	<citations>
+        <citation type="doi">10.12688/f1000research.7334.1</citation>
+	</citations>  
     </xml>
     <xml name="reference_genome_macro">
         <conditional name="reference_genome">
@@ -26,7 +26,7 @@
             </param>
             <when value="indexed">
                 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-                <options from_data_table="bowtie2_indices">
+                <options from_data_table="bowtie2_indexes">
                     <filter type="sort_by" column="2"/>
                     <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                 </options>
@@ -62,7 +62,6 @@
         <data name="dataset2_trunc" format="fastq" label="Hicup Dataset2 Truncation" from_work_dir="dataset2.trunc.fastq" />
         <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1.truncation_barchart.svg" />
         <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2.truncation_barchart.svg" />
-        
     </xml>
     <xml name="input_files">
         <param name="input_first_sequence" type="data" format="fastq" label="First input sequence" help="The first sequence:"/>