--- a/crossmap_vcf.xml	Thu Jan 20 04:32:23 2022 +0000
+++ b/crossmap_vcf.xml	Mon Sep 02 12:01:12 2024 +0000
@@ -6,13 +6,12 @@
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>
-
     <command detect_errors="aggressive"><![CDATA[
 #set $input_file = str($seq_source.input)
 
 ln -s '${seq_source.input_fasta}' 'genome.fasta' &&
 
-CrossMap.py vcf
+CrossMap vcf
 
 #if $seq_source.index_source_s == "cached"
     ## This is the 2nd dbkey, and the corresponding value has to be looked up
@@ -26,7 +25,6 @@
 $no_comp_alleles
 output
     ]]></command>
-
     <inputs>
         <conditional name="seq_source">
             <param name="index_source_s" type="select" label="Source for Input Data">
@@ -45,25 +43,20 @@
                 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
                     <options from_data_table="all_fasta"/>
                 </param>
-
-                <expand macro="chain" />
+                <expand macro="chain"/>
             </when>
-
             <when value="history">
                 <param name="input" type="data" format="vcf" label="VCF file"/>
                 <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/>
-
-                <expand macro="chain" />
+                <expand macro="chain"/>
             </when>
         </conditional>
         <param argument="--no-comp-alleles" type="boolean" truevalue="" falsevalue="--no-comp-alleles" checked="true" label="Check if the reference allele is different from the alternate allele"/>
     </inputs>
-
     <outputs>
-        <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output" />
-        <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap" />
+        <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output"/>
+        <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap"/>
     </outputs>
-
     <tests>
         <test>
             <param name="index_source_s" value="history"/>
@@ -71,11 +64,10 @@
             <param name="index_source" value="history"/>
             <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
             <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>
-
             <output name="output">
                 <assert_contents>
                     <has_text text="##fileformat=VCFv4.2"/>
-                    <has_text_matching expression="##liftOverProgram=&lt;CrossMap,version=[0-9.]+,website=https://sourceforge.net/projects/crossmap&gt;"/>
+                    <has_text_matching expression="##liftOverProgram=CrossMap,version=[0-9.]+,website=https://crossmap.readthedocs.io/en/latest"/>
                     <has_text text="##targetRefGenome="/>
                     <has_text text="#CHROM"/>
                     <has_text_matching expression="2.*?rs11449.*?PASS"/>
@@ -108,7 +100,6 @@
 - In the output VCF file, whether the chromosome IDs contain “chr” or not
   depends on the format of the input VCF file.
     ]]></help>
-
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>
     </citations>