diff parse.xml @ 9:d3a7b17714c1 draft default tip

planemo upload for repository https://github.com/open2c/pairtools commit 13aa776596c927adff29d936740ac80f0e37375d

--- a/parse.xml	Tue Apr 30 12:03:00 2024 +0000
+++ b/parse.xml	Tue May 21 16:05:04 2024 +0000
@@ -27,7 +27,7 @@
             --nproc-out \${GALAXY_SLOTS:-4}
     ]]></command>
     <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="sam_path" type="data" format="sam,qname_input_sorted.bam,qname_sorted.bam" label="Input SAM/BAM file" help="Input SAM or BAM (unsorted/name-sorted) 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_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."/>
@@ -131,7 +131,7 @@
 
         Detects ligation events in the aligned sequences of DNA molecules formed in Hi-C experiments and reports them in the .pairs/.pairsam format.
         
-        sam_path : an input .sam/.bam file with paired-end sequence alignments of Hi-C molecules. 
+        sam_path : an input .sam/.bam (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules. 
               
     ]]></help>
     <expand macro="citations"/>