Interval2Maf_pairwise1 fails at http://usegalaxy.org, needs same fix as for GeneBed_Maf_Fasta2

[jennaj]

Fix tool for legacy environment the same as for GeneBed_Maf_Fasta2 #3931

I checked and this tool was not listed here: 33d6628

Maybe we should double check that all tools that are in this tool suite get added? If you want me to check and add them here by tool name, I could, lmk.

ping @jmchilton

[jmchilton]

I reviewed all the Python wrappers and added the matching tools to the list - but it turns out these problematic cases had multiple tools for the same wrapper. I'll review the actual tools now.

[jmchilton]

    <tool file="maf/maf_to_bed.xml" /> <!-- doesn't use galaxy -->
    <tool file="maf/maf_to_interval.xml" /> <!-- already added -->
    <tool file="maf/maf_to_fasta.xml" /> <!-- doesn't use galaxy -->
    <tool file="maf/interval2maf_pairwise.xml" /> <!-- fixing in PR for this issue -->
    <tool file="maf/interval2maf.xml" /> <!-- already added -->
    <tool file="maf/maf_split_by_species.xml" /><!-- already added -->
    <tool file="maf/interval_maf_to_merged_fasta.xml" /> <!-- already added ->
    <tool file="maf/genebed_maf_to_fasta.xml" /><!-- just fixed -->
    <tool file="maf/maf_stats.xml" /> <!-- already added -->
    <tool file="maf/maf_thread_for_species.xml" /> <!-- doesn't use galaxy -->
    <tool file="maf/maf_limit_to_species.xml" /><!-- was missing - probably got confused with next tool - will fix -->
    <tool file="maf/maf_limit_size.xml" /> <!-- was falsely flagged as requiring - will be fixed -->
    <tool file="maf/maf_by_block_number.xml" /> <!-- already listed -->
    <tool file="maf/maf_reverse_complement.xml" /> <!-- already listed -->
    <tool file="maf/maf_filter.xml" /> <!-- already listed -->
    <tool file="maf/vcf_to_maf_customtrack.xml" /> <!-- doesn't use galaxy - just sequence_utils -->

[jennaj]

wow - thank you, John, for sorting this all out!