# HG changeset patch
# User rnateam
# Date 1571872042 14400
# Node ID f880686a9194f0c6f421af4c2a6e3404d119db13
# Parent  4dbe81be8b8149d4094b5967a079b07830c6177b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"

diff -r 4dbe81be8b81 -r f880686a9194 paralyzer.xml
--- a/paralyzer.xml	Tue Dec 06 03:28:59 2016 -0500
+++ b/paralyzer.xml	Wed Oct 23 19:07:22 2019 -0400
@@ -1,16 +1,13 @@
 <tool id="paralyzer" name="PARalyzer" version="1.5">
-
     <description>A method to map interaction sites between RNA-binding proteins
       and their targets</description>
-
     <requirements>
         <!-- conda dependency -->
         <requirement type="package" version="1.5">paralyzer</requirement>
         <requirement type="package" version="324">ucsc-fatotwobit</requirement>
     </requirements>
+    <command detect_errors="aggressive"><![CDATA[
 
-    <command>
-<![CDATA[
     #if $refGenomeSource.genomeSource == "history":
         faToTwoBit '$refGenomeSource.ownFile' ownFile.2bit
         &&
@@ -24,6 +21,46 @@
 
 ]]>
     </command>
+    <configfiles>
+      <configfile name="input_ini">
+## genome source
+#if $refGenomeSource.genomeSource == "history":
+GENOME_2BIT_FILE=ownFile.2bit
+#else
+GENOME_2BIT_FILE=$refGenomeSource.builtin.fields.path
+#end if
+
+SAM_FILE=$input_sam$collapse
+
+#if $methods.choice == "ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL":
+ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL=$methods.max_num
+#else:
+$methods.choice
+#end if
+
+#if $conversion.selection == "custom":
+CONVERSION=$conversion.character_from>$conversion.character_to
+#end if
+
+## required parameters
+#if $params.settingsType == "custom":
+BANDWIDTH=$params.BANDWIDTH
+MINIMUM_READ_COUNT_PER_GROUP=$params.min_read_group
+MINIMUM_READ_COUNT_PER_CLUSTER=$params.min_read_cluster
+MINIMUM_READ_COUNT_FOR_KDE=$params.min_read_kde
+MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=$params.min_read_cluster_inc
+MINIMUM_CLUSTER_SIZE=$params.min_cluster_size
+MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=$params.min_conv_loc_cluster
+MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=$params.min_conv_cluster
+MINIMUM_READ_LENGTH=$params.min_read_len
+MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=$params.max_num_conv_mis
+#end if
+
+OUTPUT_DISTRIBUTIONS_FILE=out.distribution
+OUTPUT_GROUPS_FILE=out.groups
+OUTPUT_CLUSTERS_FILE=out.clusters
+      </configfile>
+    </configfiles>
     <inputs>
         <param name="input_sam" type="data"
             format="sam" label="Alignment"
@@ -207,46 +244,6 @@
             </when>  <!-- full -->
         </conditional>
     </inputs>
-    <configfiles>
-      <configfile name="input_ini">
-## genome source
-#if $refGenomeSource.genomeSource == "history":
-GENOME_2BIT_FILE=ownFile.2bit
-#else
-GENOME_2BIT_FILE=$refGenomeSource.builtin.fields.path
-#end if
-
-SAM_FILE=$input_sam$collapse
-
-#if $methods.choice == "ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL":
-ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL=$methods.max_num
-#else:
-$methods.choice
-#end if
-
-#if $conversion.selection == "custom":
-CONVERSION=$conversion.character_from>$conversion.character_to
-#end if
-
-## required parameters
-#if $params.settingsType == "custom":
-BANDWIDTH=$params.BANDWIDTH
-MINIMUM_READ_COUNT_PER_GROUP=$params.min_read_group
-MINIMUM_READ_COUNT_PER_CLUSTER=$params.min_read_cluster
-MINIMUM_READ_COUNT_FOR_KDE=$params.min_read_kde
-MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=$params.min_read_cluster_inc
-MINIMUM_CLUSTER_SIZE=$params.min_cluster_size
-MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=$params.min_conv_loc_cluster
-MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=$params.min_conv_cluster
-MINIMUM_READ_LENGTH=$params.min_read_len
-MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=$params.max_num_conv_mis
-#end if
-
-OUTPUT_DISTRIBUTIONS_FILE=out.distribution
-OUTPUT_GROUPS_FILE=out.groups
-OUTPUT_CLUSTERS_FILE=out.clusters
-      </configfile>
-    </configfiles>
     <outputs>
         <data name="distribution" format="txt"
         from_work_dir="out.distribution"