| Previous changeset 61:e7470d424809 (2024-12-19) Next changeset 63:b87f07ac9edc (2024-12-19) |
|
Commit message:
"planemo upload" |
|
modified:
csp2_snp.xml |
| csp2_snp.xml |
| diff -r e7470d424809 -r 0552b9528fc4 csp2_snp.xml |
| csp2_snp.xml |
| --- a/csp2_snp.xml Thu Dec 19 13:02:58 2024 -0500 +++ b/csp2_snp.xml Thu Dec 19 13:20:18 2024 -0500 @@ -20,6 +20,12 @@ export REF_FASTA_SELECT="$ref_fasta.ref_fasta_select" export REF_READS_SELECT="$ref_reads.ref_reads_select" +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" == 'collection' ]]; then #set query_fasta_input=$query_fasta.coll.elements elif [[ "\$QUERY_FASTA_SELECT" == 'history' ]]; then @@ -42,17 +48,11 @@ if [[ "\$REF_READS_SELECT" == 'collection' ]]; then #set ref_reads_forward=$ref_reads.coll.forward #set ref_reads_reverse=$ref_reads.coll.reverse -elif [[ "\$REF_READS_SELECT" =='history' ]]; then +elif [[ "\$REF_READS_SELECT" == 'history' ]]; then #set ref_reads_forward=$ref_reads.list fi; -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 +if [[ "\$QUERY_FASTA_SELECT" == 'none' ]]; then export QUERY_FASTA_ARG=""; else #for query in $query_fasta_input: @@ -61,8 +61,7 @@ export QUERY_FASTA_ARG="--fasta ./queries"; fi; - -if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then +if [[ "\$REF_FASTA_SELECT" == "none" ]]; then export REF_FASTA_ARG=""; else #for ref in $ref_fasta_input: @@ -71,7 +70,7 @@ export REF_FASTA_ARG="--fasta ./references"; fi; -if [[ "$query_reads.query_reads_select" == "none" ]]; then +if [[ "\$QUERY_READS_SELECT" == "none" ]]; then export QUERY_READS_ARG=""; else #for query in $query_reads_forward $query_reads_reverse: @@ -80,7 +79,7 @@ export QUERY_READS_ARG="--reads ./queries"; fi; -if [[ "$ref_reads.ref_reads_select" == "none" ]]; then +if [[ "\$REF_READS_SELECT" == "none" ]]; then export QUERY_READS_ARG=""; else #for ref in $ref_reads_forward $ref_reads_reverse: |