--- a/hicBuildMatrix.xml	Wed Oct 18 10:48:01 2023 +0000
+++ b/hicBuildMatrix.xml	Mon Jul 01 19:52:43 2024 +0000
@@ -5,7 +5,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.9">samtools</requirement>
+        <requirement type="package" version="1.19">samtools</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -18,7 +18,7 @@
             #end for
 
             --restrictionCutFile '$restrictionCutFile'
-            
+
             #if $restrictionSequence:
                 --restrictionSequence '$restrictionSequence'
             #end if
@@ -31,7 +31,7 @@
             #if $maxLibraryInsertSize:
                 --maxLibraryInsertSize $maxLibraryInsertSize
             #end if
-           
+
             #if $binSizes:
                 --binSize
                 #for $repeat in $binSizes
@@ -39,13 +39,20 @@
                 #end for
             #end if
 
-            --genomeAssembly $samFiles[0].samFile.metadata.dbkey
+            #if $chromosomeSizes:
+                --chromosomeSizes '$chromosomeSizes'
+            #end if
+            #if $dbKey:
+                --genomeAssembly '$dbKey'
+            #else
+                --genomeAssembly '$samFiles[0].samFile.metadata.dbkey'
+            #end if
 
             #if $region:
                 --region '$region'
             #end if
 
-            --outFileName matrix.$outputFormat
+            --outFileName 'matrix.$outputFormat'
 
             #if $outBam:
                 $outBam ./unsorted.bam
@@ -59,10 +66,6 @@
                 --minMappingQuality $minMappingQuality
             #end if
 
-            #if $chromosomeSizes:
-                --chromosomeSizes '$chromosomeSizes'
-            #end if
-
             --threads @THREADS@
 
             --QCfolder ./QCfolder
@@ -81,7 +84,6 @@
         <!-- can we use multiple=True here with min="2" and max="2" ? -->
         <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
             <param name="samFile" type="data" format="sam,qname_input_sorted.bam">
-                <validator type="unspecified_build" />
             </param>
         </repeat>
 
@@ -107,11 +109,13 @@
         <expand macro="minMappingQuality" />
         <param argument="--skipDuplicationCheck" type="boolean" truevalue="--skipDuplicationCheck" falsevalue="" label="Skip duplication check" help="Identification of duplicated read pairs is memory consuming. Thus, in case of memory errors this check can be skipped." />
         <param argument="--chromosomeSizes" type="data" format="tabular" optional="true" label="Chromosome sizes for your genome" help="File with the chromosome sizes for your genome. A tab-delimited two column layout 'chr_name size' is expected
-                    Usually the sizes can be determined from the SAM/BAM input files, however, 
-                    for cHi-C or scHi-C it can be that at the start or end no data is present. 
+                    Usually the sizes can be determined from the SAM/BAM input files, however,
+                    for cHi-C or scHi-C it can be that at the start or end no data is present.
                     Please consider that this option causes that only reads are considered which are on the listed chromosomes.
-                    Use this option to guarantee fixed sizes. An example file is available via UCSC: 
+                    Use this option to guarantee fixed sizes. An example file is available via UCSC:
                     http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes" />
+        <param name="dbKey" type="text" optional="true" label="Use this dbkey for your history genome"
+        help="You can set the reference genome in your history as metadata. In case you have not you can specify it here." />
 
         <param argument="--outBam" type="boolean" truevalue="--outBam" falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file" help="A bam
                     file containing all valid Hi-C reads can be created
@@ -154,7 +158,7 @@
             <param name="restrictionSequence" value="GATC" />
             <param name="danglingSequence" value="GATC" />
             <param name="outBam" value="True" />
-            <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" />
+            <output name="outfileBam" file="small_test_matrix_result_sorted.bam" compare="diff" lines_diff="2" ftype="bam" />
             <output name="outFileName" ftype="h5">
                 <assert_contents>
                     <has_h5_keys keys="intervals,matrix" />
@@ -177,7 +181,7 @@
             <param name="danglingSequence" value="GATC" />
             <param name="outputFormat" value="cool" />
             <param name="outBam" value="True" />
-            <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" />
+            <output name="outfileBam" file="small_test_matrix_result_sorted.bam" compare="diff" lines_diff="2" ftype="bam" />
             <output name="outFileName" ftype="cool">
                 <assert_contents>
                     <has_h5_keys keys="bins,chroms,indexes,pixels" />