# HG changeset patch # User iuc # Date 1740405280 0 # Node ID 93cfe7df7f8abf45162805ab31de95496c44a62d # Parent 02ea80c89fd186a7f5624dfa3b7b5d8b21ff5304 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 9fe39fd1ad0c1a5af9e8d2d633fd3e7404adbac7 diff -r 02ea80c89fd1 -r 93cfe7df7f8a artic_minion.xml --- a/artic_minion.xml Fri Feb 21 22:12:51 2025 +0000 +++ b/artic_minion.xml Mon Feb 24 13:54:40 2025 +0000 @@ -1,4 +1,4 @@ - + Build consensus sequence and call variants from amplicon-based nanopore sequence data macros.xml @@ -23,25 +23,35 @@ mv \$OUTNAME clair3_model && #end if - #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table": - ln -s '${primer_scheme_source.bed.fields.path}' 'primer.bed' && - #else: - ln -s '${primer_scheme_source.bed}' 'primer.bed' && - #end if + #if str( $fetch_primer_scheme.fetch ) == "no": + #if str( $fetch_primer_scheme.primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table": + ln -s '${fetch_primer_scheme.primer_scheme_source.bed.fields.path}' primer.bed && + #else: + ln -s '${fetch_primer_scheme.primer_scheme_source.bed}' primer.bed && + #end if - #if str( $reference_source.reference_source_selector ) == "history": - ln -s '${reference_source.reference}' 'reference.fasta' && - samtools faidx 'reference.fasta' && - #else: - ln -s '${reference_source.reference.fields.path}' 'reference.fasta' && - samtools faidx 'reference.fasta' && + #if str( $fetch_primer_scheme.reference_source.reference_source_selector ) == "history": + ln -s '${fetch_primer_scheme.reference_source.reference}' reference.fasta && + samtools faidx reference.fasta && + #else: + ln -s '${fetch_primer_scheme.reference_source.reference.fields.path}' reference.fasta && + samtools faidx reference.fasta && + #end if #end if artic minion --read-file '${read_file}' --threads \${GALAXY_SLOTS:-1} + #if str( $fetch_primer_scheme.fetch ) == "yes": + --scheme-name '${fetch_primer_scheme.scheme_name}' + --scheme-version '${fetch_primer_scheme.scheme_version}' + #if $fetch_primer_scheme.scheme_length > 0: + --scheme-length ${fetch_primer_scheme.scheme_length} + #end if + #else --bed primer.bed --ref reference.fasta + #end if --model-dir . --model clair3_model @@ -71,9 +81,9 @@ label="Minimum mapping score" help="Minimum mapping quality to consider (default: 20)"/> - + help="Sample at most this number of reads per amplicon and strand. Set to 0 to use all available data (default: 100)" /> - - - - - + + + + + + - - - - - - - - - + + + + - + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + @@ -178,10 +207,17 @@ - - - - + + + + + + + + + + + @@ -204,11 +240,18 @@ + + + + + + + + + + + - - - - @@ -232,10 +275,17 @@ - - - - + + + + + + + + + + + diff -r 02ea80c89fd1 -r 93cfe7df7f8a test-data/clair3_models.loc --- a/test-data/clair3_models.loc Fri Feb 21 22:12:51 2025 +0000 +++ b/test-data/clair3_models.loc Mon Feb 24 13:54:40 2025 +0000 @@ -7,4 +7,4 @@ # #So, clair3_models.loc could look something like this: test_model ont $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422 clair3 -r1041_e82_400bps_sup_v500 r1041_e82_400bps_sup_v500 ont 01c05768661bdd7de611e6bae1043c43b7523a54b223e029c683bfac0db7a678 /no/such/model rerio +r1041_e82_400bps_sup_v500 ont 01c05768661bdd7de611e6bae1043c43b7523a54b223e029c683bfac0db7a678 /no/such/model rerio diff -r 02ea80c89fd1 -r 93cfe7df7f8a tool-data/models.loc.sample --- a/tool-data/models.loc.sample Fri Feb 21 22:12:51 2025 +0000 +++ b/tool-data/models.loc.sample Mon Feb 24 13:54:40 2025 +0000 @@ -1,13 +1,4 @@ -#Enter the model names in the second column, the platform name in the second and the path in the third. -#This file lists the locations and dbkeys of all the model files -#under the "models" directory (a directory that contains a directory -#for each build). This file has the format (white space characters are -#TAB characters): -# -# -# -#So, all_model.loc could look something like this: -test_model "the_model_name" r941_prom_hac_g360+g422 $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422#This file lists the names and locations of all the clair3 model files +#This file lists the names and locations of all the clair3 model files #under the "clair3_models" directory (a directory that contains a directory #for each build). This file has the format (white space characters are #TAB characters):