--- a/takeabreak.xml	Mon Aug 17 10:40:40 2020 -0400
+++ b/takeabreak.xml	Thu May 06 12:46:24 2021 +0000
@@ -1,5 +1,4 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool profile="16.04" id="takeabreak" name="TakeABreak" version="1.1.2">
+<tool id="takeabreak" name="TakeABreak" version="1.1.2+galaxy0" profile="@PROFILE@">
     <description>is a tool that can detect inversion breakpoints directly from raw NGS reads</description>
     <macros>
         <import>macros.xml</import>
@@ -7,31 +6,22 @@
     <requirements>
         <requirement type="package" version="1.1.2">takeabreak</requirement>
     </requirements>
-    <command><![CDATA[
-
-        ## if single reads
-        #if str( $input_type_option.input_type ) == "simple"
+    <command detect_errors="exit_code"><![CDATA[
+        #if str($input_type_option.input_type) == "simple"
             #for $input in $input_type_option.reads
-                #if $input
-                    #set $filename = os.path.basename(str($input)) + "." + $input.ext
-                    ln -sf '${input}' '${filename}' &&
-                    echo "${filename}" >> input.fof &&
-                #end if
+                @single_reads@
+                echo "${filename}" >> input.fof &&
             #end for
         #else
-            ## if paired reads in a list
-            #for $i, $list in enumerate( $input_type_option.reads_lists )
-                #for $read in $list.list_reads
-                    #set $filename = os.path.basename(str($read)) + "." + $read.ext
-                    ln -sf '${read}' '${filename}' &&
+            #for $i, $list in enumerate($input_type_option.reads_lists)
+                #for $input in $list.list_reads
+                    @single_reads@
                     echo "${filename}" >> "indiv_${i}.fof" &&
                 #end for
                 echo "indiv_${i}.fof" >> input.fof &&
             #end for
         #end if
-
         TakeABreak
-
         -in input.fof
         -kmer-size ${kmer_size}
         -abundance-min '${abundance_min}'
@@ -40,40 +30,34 @@
         -lct ${lct}
         -max-sim ${max_sim}
         -repeat ${repeat}
-
     ]]></command>
-
     <inputs>
-        <!-- Input data files -->
         <conditional name="input_type_option">
             <param name="input_type" type="select" label="Input option">
                 <option value="simple">one individual = one read </option>
                 <option value="list">one individual = several reads</option>
             </param>
             <when value="simple">
-                <param name='reads' argument="-in" format="fasta,fastq" type="data" multiple="true" label="Single read files" optional="True" />
+                <param name='reads' argument="-in" format="fasta,fasta.gz,fastq,fastq.gz" type="data" multiple="true" label="Single read files" optional="True" />
             </when>
             <when value="list">
                 <repeat name="reads_lists" title="Individual" min="1">
-                    <param name='list_reads' argument="-in" format="fasta,fastq" type="data_collection" collection_type="list" multiple="true" label="Individual read files list"/>
+                    <param name='list_reads' argument="-in" format="fasta,fasta.gz,fastqfastq.gz" type="data_collection" collection_type="list" multiple="true" label="Individual read files list"/>
                 </repeat>
             </when>
         </conditional>
         <param name="kmer_size" argument="-kmer-size" type="integer" label="Length of the k-mers" value="31" help="Set the length of used kmers" />
         <param name="abundance_min" argument="-abundance-min" type="text" label="Minimal abundance threshold" value="auto" />
         <param name="abundance_max" argument="-abundance-max" type="integer" label="Maximal abundance threshold" value="2147483647" />
-
         <param name="solidity_kind" argument="-solidity-kind" type="select" label="Way to consider a solid kmer with several input datasets" >
             <option value="one">One</option>
             <option value="sum">Sum</option>
             <option value="all">All</option>
         </param>
-
         <param argument="-lct" type="integer" label="local complexity threshold" value="100" help="Local complexity threshold" />
         <param name="max_sim" argument="-max-sim" type="integer" label="max similarity percentage" value="80" help="Inversions with a and b' (or u and v') whose longest common subsequence size is bigger than k*(this value)/100 are discarded" />
         <param argument="-repeat" type="integer" label="maximal repeat size" value="8" help="Maximal repeat size at the breakpoint. Longest common suffix between a and b" />
     </inputs>
-
     <outputs>
         <data format="fasta" name="inversion" from_work_dir="TakeABreak_*.fasta" label="Inversions with ${tool.name} on ${on_string}"/>
     </outputs>
@@ -84,8 +68,8 @@
                 <repeat name="reads_lists">
                     <param name="list_reads">
                         <collection type="list">
-                            <element name="example_reads" value="takeabreak/toy_example_reads.fasta" ftype="fasta"/>
-                            <element name="example_reads_with_inv" value="takeabreak/toy_example_with_inv_reads.fasta" ftype="fasta"/>
+                            <element name="example_reads" value="takeabreak/toy_example_reads.fasta.gz" ftype="fasta.gz"/>
+                            <element name="example_reads_with_inv" value="takeabreak/toy_example_with_inv_reads.fasta.gz" ftype="fasta.gz"/>
                         </collection>
                     </param>
                 </repeat>
@@ -95,7 +79,7 @@
         <test>
             <conditional name="input_type_option">
                 <param name="input_type" value="simple" />
-                <param name="reads" value="takeabreak/toy_example_reads.fasta,takeabreak/toy_example_with_inv_reads.fasta" />
+                <param name="reads" value="takeabreak/toy_example_reads.fasta.gz,takeabreak/toy_example_with_inv_reads.fasta.gz" />
             </conditional>
             <output name="inversion" file="takeabreak/inversion.fasta"/>
         </test>