| Previous changeset 10:02ea80c89fd1 (2025-02-21) Next changeset 12:7021ed347f7e (2025-06-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 9fe39fd1ad0c1a5af9e8d2d633fd3e7404adbac7 |
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modified:
artic_minion.xml test-data/clair3_models.loc tool-data/models.loc.sample |
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| 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 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="artic_minion" name="ARTIC minion" version="@TOOL_VERSION@+galaxy0" profile="20.09">\n+<tool id="artic_minion" name="ARTIC minion" version="@TOOL_VERSION@+galaxy1" profile="23.2">\n <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>\n <macros>\n <import>macros.xml</import>\n@@ -23,25 +23,35 @@\n mv \\$OUTNAME clair3_model &&\n #end if\n \n- #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table":\n- ln -s \'${primer_scheme_source.bed.fields.path}\' \'primer.bed\' &&\n- #else:\n- ln -s \'${primer_scheme_source.bed}\' \'primer.bed\' &&\n- #end if\n+ #if str( $fetch_primer_scheme.fetch ) == "no":\n+ #if str( $fetch_primer_scheme.primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table":\n+ ln -s \'${fetch_primer_scheme.primer_scheme_source.bed.fields.path}\' primer.bed &&\n+ #else:\n+ ln -s \'${fetch_primer_scheme.primer_scheme_source.bed}\' primer.bed &&\n+ #end if\n \n- #if str( $reference_source.reference_source_selector ) == "history":\n- ln -s \'${reference_source.reference}\' \'reference.fasta\' &&\n- samtools faidx \'reference.fasta\' &&\n- #else:\n- ln -s \'${reference_source.reference.fields.path}\' \'reference.fasta\' &&\n- samtools faidx \'reference.fasta\' &&\n+ #if str( $fetch_primer_scheme.reference_source.reference_source_selector ) == "history":\n+ ln -s \'${fetch_primer_scheme.reference_source.reference}\' reference.fasta &&\n+ samtools faidx reference.fasta &&\n+ #else:\n+ ln -s \'${fetch_primer_scheme.reference_source.reference.fields.path}\' reference.fasta &&\n+ samtools faidx reference.fasta &&\n+ #end if\n #end if\n \n artic minion\n --read-file \'${read_file}\'\n --threads \\${GALAXY_SLOTS:-1}\n+ #if str( $fetch_primer_scheme.fetch ) == "yes":\n+ --scheme-name \'${fetch_primer_scheme.scheme_name}\'\n+ --scheme-version \'${fetch_primer_scheme.scheme_version}\'\n+ #if $fetch_primer_scheme.scheme_length > 0:\n+ --scheme-length ${fetch_primer_scheme.scheme_length}\n+ #end if\n+ #else\n --bed primer.bed\n --ref reference.fasta\n+ #end if\n --model-dir .\n --model clair3_model\n \n@@ -71,9 +81,9 @@\n label="Minimum mapping score"\n help="Minimum mapping quality to consider (default: 20)"/>\n \n- <param argument="--normalise" type="integer" min="0" value="400"\n+ <param argument="--normalise" type="integer" min="0" value="100"\n label="Coverage normalisation depth"\n- help="Sample at most this number of reads per amplicon and strand. Set to 0 to use all available data" />\n+ help="Sample at most this number of reads per amplicon and strand. Set to 0 to use all available data (default: 100)" />\n \n <param argument="--primer-match-threshold" type="integer" value="35"\n label="Primer Match Threshold"\n@@ -87,45 +97,64 @@\n label="Align Consensus to reference"\n help="Run a MAFFT to align consensus to reference" />\n \n- <!-- Primer selection -->\n- <conditional name="primer_scheme_source">\n- <param name="primer_scheme_source_selector" type="select"\n- label="Select primer file"\n- help="See Help section below for how to find primer scheme data files.">\n- <option value="tool_data_table">From tool data table</option>\n- <option value="history">From history</option>\n+ <!-- Primer and Reference fetching -->\n+ \n+ <conditional name="fetch_primer_scheme">\n+ <param name="fetch" type="select" label="Fetch primer BED and reference"\n+ help="Fetch primer BED '..b' type="data" format="fasta" label="Use the following dataset as the reference sequence"\n+ help="You can upload a FASTA sequence to the history and use it as reference" />\n+ </when>\n+ </conditional>\n </when>\n </conditional>\n \n@@ -178,10 +207,17 @@\n <!-- Test: built in model selection, primer/reference selection from history -->\n <test>\n <param name="read_file" value="test.fastq.gz" />\n- <param name="reference_source_selector" value="history" />\n- <param name="reference" value="reference.fasta" />\n- <param name="primer_scheme_source_selector" value="history" />\n- <param name="bed" value="primers.bed" />\n+ <conditional name="fetch_primer_scheme">\n+ <param name="fetch" value="no" />\n+ <conditional name="primer_scheme_source">\n+ <param name="primer_scheme_source_selector" value="history" />\n+ <param name="bed" value="primers.bed" />\n+ </conditional>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="history" />\n+ <param name="reference" value="reference.fasta" />\n+ </conditional>\n+ </conditional>\n <conditional name="model_source">\n <param name="source" value="built-in" />\n <param name="select_built_in" value="r941_prom_hac_g360+g422" />\n@@ -204,11 +240,18 @@\n </test>\n <!-- Test: primer/reference selection from data table -->\n <test>\n+ <conditional name="fetch_primer_scheme">\n+ <param name="fetch" value="no" />\n+ <conditional name="primer_scheme_source">\n+ <param name="primer_scheme_source_selector" value="tool_data_table" />\n+ <param name="bed" value="test_bed" />\n+ </conditional>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="tool_data_table" />\n+ <param name="reference" value="test_fasta" />\n+ </conditional>\n+ </conditional>\n <param name="read_file" value="test.fastq.gz" />\n- <param name="reference_source_selector" value="tool_data_table" />\n- <param name="reference" value="test_fasta" />\n- <param name="primer_scheme_source_selector" value="tool_data_table" />\n- <param name="bed" value="test_bed" />\n <conditional name="model_source">\n <param name="source" value="built-in"/>\n <param name="select_built_in" value="r941_prom_hac_g360+g422"/>\n@@ -232,10 +275,17 @@\n <!-- Test: advanced input params -->\n <test>\n <param name="read_file" value="test.fastq.gz" />\n- <param name="reference_source_selector" value="history" />\n- <param name="reference" value="reference.fasta" />\n- <param name="primer_scheme_source_selector" value="history" />\n- <param name="bed" value="primers.bed" />\n+ <conditional name="fetch_primer_scheme">\n+ <param name="fetch" value="no" />\n+ <conditional name="primer_scheme_source">\n+ <param name="primer_scheme_source_selector" value="history" />\n+ <param name="bed" value="primers.bed" />\n+ </conditional>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="history" />\n+ <param name="reference" value="reference.fasta" />\n+ </conditional>\n+ </conditional>\n <param name="min_mapq" value="20" />\n <param name="min_depth" value="10" />\n <param name="align_consensus" value="True" />\n' |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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): -# -#<id> <name> <platform> <path> -# -#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): |