Unused tool parameters

[bernt-matthias]

Describe the bug

With galaxyproject/galaxy#12724 planemo lint may error on input parameters that are not used:

• tools/gatk4/Mutect2.xml has some .. tool should be deprecated (is in IUC)
• tools/justgzip/gzip.xml
  • datatype
• tools/manta/manta.xml
  • additional_param
• tools/pathifier/pathifier.xml
  • rdata
• tools/small_rna_clusters/small_rna_clusters.xml
  • first_plot

[drosofff]

@bernt-matthias wrote:

tools/justgzip/gzip.xml
datatype

the datatype parameter is used in the <change_format> tag:

   <change_format>
       <when input="datatype" value="sanger" format="fastqsanger.gz" />
       <when input="datatype" value="illumina" format="fastqillumina.gz" />
   </change_format>

[bernt-matthias]

the datatype parameter is used in the <change_format> tag:

True, still this #580 might be better?