| Previous changeset 64:6f3b67127e44 (2024-12-19) Next changeset 66:90e29c1ddeca (2024-12-19) |
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Commit message:
"planemo upload" |
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modified:
csp2_snp.xml |
| csp2_snp.xml |
| diff -r 6f3b67127e44 -r c2a886313008 csp2_snp.xml |
| csp2_snp.xml |
| --- a/csp2_snp.xml Thu Dec 19 14:35:57 2024 -0500 +++ b/csp2_snp.xml Thu Dec 19 14:51:58 2024 -0500 @@ -28,8 +28,8 @@ #for _, $ref_assembly in enumerate($ref_fasta.coll): ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier}; #end for - export REF_FASTA_ARG="--fasta ./queries"; -else + export REF_FASTA_ARG="--fasta ./references"; +#else #for _, $ref_assembly in enumerate($ref_fasta.list): ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier}; #end for @@ -40,11 +40,11 @@ export QUERY_READS_ARG=""; #elif (str($query_reads.query_reads_select) == "collection"): #for _, $pair in enumerate($query_reads.coll): - ln -sf '$pair.forward' ./queries/${pair.forward.element_identifier}; - ln -sf '$pair.reverse' ./queries/${pair.reverse.element_identifier}; + ln -sf ${pair.forward} ./queries/${pair.forward.element_identifier}; + ln -sf ${pair.reverse} ./queries/${pair.reverse.element_identifier}; #end for export QUERY_READS_ARG="--reads ./queries"; -else +#else #for _, $read_file in enumerate($query_reads.list): ln -sf ${read_file} ./queries/${read_file.element_identifier}; #end for @@ -55,11 +55,11 @@ export REF_READS_ARG=""; #elif (str($ref_reads.ref_reads_select) == "collection"): #for _, $pair in enumerate($ref_reads.coll): - ln -sf '$pair.forward' ./references/${pair.forward.element_identifier}; - ln -sf '$pair.reverse' ./references/${pair.reverse.element_identifier}; + ln -sf ${pair.forward} ./references/${pair.forward.element_identifier}; + ln -sf ${pair.reverse} ./references/${pair.reverse.element_identifier}; #end for export REF_READS_ARG="--ref_reads ./references"; -else +#else #for _, $read_file in enumerate($ref_reads.list): ln -sf ${read_file} ./references/${read_file.element_identifier}; #end for |