Mercurial > repos > rliterman > csp2
changeset 61:e7470d424809
"planemo upload"
| author | rliterman |
|---|---|
| date | Thu, 19 Dec 2024 13:02:58 -0500 |
| parents | 5378cd1e3a39 |
| children | 0552b9528fc4 |
| files | csp2_snp.xml |
| diffstat | 1 files changed, 24 insertions(+), 13 deletions(-) [+] |
line wrap: on
line diff
--- a/csp2_snp.xml Thu Dec 19 12:31:39 2024 -0500 +++ b/csp2_snp.xml Thu Dec 19 13:02:58 2024 -0500 @@ -15,33 +15,44 @@ #set ref_reads_forward="" #set ref_reads_reverse="" -#if "$query_fasta.query_fasta_select" == 'collection' +export QUERY_FASTA_SELECT="$query_fasta.query_fasta_select" +export QUERY_READS_SELECT="$query_reads.query_reads_select" +export REF_FASTA_SELECT="$ref_fasta.ref_fasta_select" +export REF_READS_SELECT="$ref_reads.ref_reads_select" + +if [[ "\$QUERY_FASTA_SELECT" == 'collection' ]]; then #set query_fasta_input=$query_fasta.coll.elements -#elseif "$query_fasta.query_fasta_select" == 'history' +elif [[ "\$QUERY_FASTA_SELECT" == 'history' ]]; then #set query_fasta_input=$query_fasta.list -#end if +fi; -#if "$ref_fasta.ref_fasta_select" == 'collection' +if [[ "\$REF_FASTA_SELECT" == 'collection' ]]; then #set ref_fasta_input=$ref_fasta.coll.elements -#elseif "$ref_fasta.ref_fasta_select" == 'history' +elif [[ "\$REF_FASTA_SELECT" == 'history' ]]; then #set ref_fasta_input=$ref_fasta.list -#end if +fi; -#if "$query_reads.query_reads_select" == 'collection' +if [[ "\$QUERY_READS_SELECT" == 'collection' ]]; then #set query_reads_forward=$query_reads.coll.forward #set query_reads_reverse=$query_reads.coll.reverse -#elseif "$query_reads.query_reads_select" == 'history' +elif [[ "\$QUERY_READS_SELECT" == 'history' ]]; then #set query_reads_forward=$query_reads.list -#end if +fi; -#if "$ref_reads.ref_reads_select" == 'collection' +if [[ "\$REF_READS_SELECT" == 'collection' ]]; then #set ref_reads_forward=$ref_reads.coll.forward #set ref_reads_reverse=$ref_reads.coll.reverse -#elseif "$ref_reads.ref_reads_select" == 'history' +elif [[ "\$REF_READS_SELECT" =='history' ]]; then #set ref_reads_forward=$ref_reads.list -#end if +fi; -if [[ "$query_fasta.query_fasta_select" == "none" ]]; then +echo "Query Fasta: \$QUERY_FASTA_SELECT"; +echo "Ref Fasta: \$REF_FASTA_SELECT"; + +echo "Query Reads: \$QUERY_READS_SELECT"; +echo "Ref Reads: \$REF_READS_SELECT"; + +if [[ "\$QUERY_FASTA_SELECT" == 'none']]; then export QUERY_FASTA_ARG=""; else #for query in $query_fasta_input: