Fixed the unexpected behaviour due to --assembly parameter of `pair…

…tools parse` (galaxyproject#5953)

* Fixed Label Swapping issue

* Debugging of --assembly name parameter

* Eliminated conditional for assembly

* Added a test for assembly name

* Version bump for parse

tools/pairtools/parse.xml

@@ -1,4 +1,4 @@
-<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
+<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy1" profile="23.2" license="MIT">
     <description>Find ligation pairs in alignments and create pairs.</description>
     <macros>
         <import>macros.xml</import>
@@ -8,7 +8,9 @@
         pairtools parse
             '$sam_path'
             -c '$chroms_path'
-            $assembly
+            #if str($assembly_name).strip(): 
+                --assembly '$assembly_name'
+            #end if
             -o '$output_parsed_pairs'
             --min-mapq '$min_mapq'
             --max-molecule-size '$max_molecule_size'
@@ -27,7 +29,7 @@
     <inputs>
         <param name="sam_path" type="data" format="sam,bam" label="Input SAM/BAM file" help="Input SAM or BAM file with paired-end sequence alignments of Hi-C molecules."/>    
         <param name="chroms_path" argument="-c" type="data" format="tabular" label="Input a chromosome order file" help="Chromosome order used to flip interchromosomal mates. Any scaffolds not listed will be ordered lexicographically."/>
-        <param name="assembly" type="text" value="" label="Input a name of a genome assembly" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>
+        <param name="assembly_name" type="text" value="" label="Input a name of genome assembly" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>
         <param argument="--min-mapq" type="integer" value="40" min="0" label="Minimal MAPQ" help="Minimal MAPQ score to consider a read as uniquely mapped."/>
         <param argument="--max-molecule-size" type="integer" min="0" value="750" label="Input the maximal size of a Hi-C molecule" help="The maximal size of a Hi-C molecule; used to rescue single ligations(from molecules with three alignments) and to rescue complex ligations."></param>
         <param argument="--drop-readid" type="boolean" truevalue="--drop-readid" falsevalue="" checked="False" label="Do not add read ids to the output"></param>
@@ -112,6 +114,16 @@
             <param name="output_stats" value="true"></param>
             <output name="parsed_pairs_stats" file="output_parsed_pairs.stats" lines_diff="10"/>
         </test>
+        <!--Test 08 with SAM file as input and default parameters and assembly name -->
+        <test expect_num_outputs="1">
+            <param name="sam_path" value="test.sam"/>
+            <param name="chroms_path" value="test.genome"/>
+            <param name="assembly_name" value="test_assembly"/>
+            <param name="min_mapq" value="1"/>
+            <param name="walks_policy" value="mask"/>
+            <param name="max_inter_algn_gap" value="20"/>
+            <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam_assemblyname.pairs" lines_diff="10"/>
+        </test>
 
     </tests>
     <help><![CDATA[