| Previous changeset 33:d999e774072a (2023-11-19) Next changeset 35:cbf3f518b668 (2024-02-22) |
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Commit message:
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 028e3e806ba6df913403a2a083a354dfa713755f |
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modified:
test-data/three_human_mRNA.fasta.gz test-data/tool_data_table_conf.xml.test tool-data/tool_data_table_conf.xml.sample tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml |
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| diff -r d999e774072a -r b6893f57f8d8 test-data/three_human_mRNA.fasta.gz |
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| Binary file test-data/three_human_mRNA.fasta.gz has changed |
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| diff -r d999e774072a -r b6893f57f8d8 test-data/tool_data_table_conf.xml.test --- a/test-data/tool_data_table_conf.xml.test Sun Nov 19 22:57:39 2023 +0000 +++ b/test-data/tool_data_table_conf.xml.test Thu Feb 22 14:47:01 2024 +0000 |
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| @@ -12,4 +12,8 @@ <columns>value, name, path</columns> <file path="${__HERE__}/blastdb_d.loc" /> </table> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/all_fasta.loc" /> + </table> </tables> |
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| diff -r d999e774072a -r b6893f57f8d8 tool-data/tool_data_table_conf.xml.sample --- a/tool-data/tool_data_table_conf.xml.sample Sun Nov 19 22:57:39 2023 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Thu Feb 22 14:47:01 2024 +0000 |
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| @@ -11,4 +11,8 @@ <columns>value, name, path</columns> <file path="tool-data/blastdb_d.loc" /> </table> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc.sample" /> + </table> </tables> |
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| diff -r d999e774072a -r b6893f57f8d8 tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Sun Nov 19 22:57:39 2023 +0000 +++ b/tools/ncbi_blast_plus/README.rst Thu Feb 22 14:47:01 2024 +0000 |
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| @@ -136,6 +136,10 @@ ============== =============================================================== Version Changes -------------- --------------------------------------------------------------- +2.14.1+galaxy2 - Add usage of genome FASTA files on the Galaxy server with + ``makeblastdb`` (contribution from Wolfgang Maier and + Elischa Berger) +2.14.1+galaxy1 - Fix for get_species_taxids 2.14.1+galaxy0 - Updated for NCBI BLAST+ 2.14.1 release. 2.10.1+galaxy3 - Silenced ``deltablast`` warning about using ``-num_threads`` with ``--subject`` (i.e. FASTA file from your history). |
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| diff -r d999e774072a -r b6893f57f8d8 tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Sun Nov 19 22:57:39 2023 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Thu Feb 22 14:47:01 2024 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.14.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">16.10</token> <xml name="parallelism"> <!-- If job splitting is enabled, break up the query file into parts --> |
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| diff -r d999e774072a -r b6893f57f8d8 tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Sun Nov 19 22:57:39 2023 +0000 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Feb 22 14:47:01 2024 +0000 |
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| b'@@ -8,21 +8,36 @@\n <requirement type="package" version="3.9">python</requirement>\n </expand>\n <command detect_errors="aggressive" strict="true"><![CDATA[\n+#set $inputs = []\n+#set $input_compression = []\n+#for r in $input.selection:\n+ #if $input.type == "protein":\n+ #silent $inputs.append($r.input_file)\n+ #silent $input_compression.append($r.input_file.is_of_type(\'fasta.gz\'))\n+ #elif $r.nuc_choice.source == "history":\n+ #silent $inputs.append($r.nuc_choice.input_file)\n+ #silent $input_compression.append($r.nuc_choice.input_file.is_of_type(\'fasta.gz\'))\n+ #else:\n+ #silent $inputs.append($r.nuc_choice.input_file.fields.path)\n+ #silent $input_compression.append(False)\n+ #end if\n+#end for\n+\n python $__tool_directory__/check_no_duplicates.py\n ##First check for duplicates (since BLAST+ 2.2.28 fails to do so)\n ##and abort (via the ampersand ampersand trick) if any are found.\n-#for i in $input_file#\'${i}\' #end for#\n+#for i in $inputs#\'$i\' #end for#\n &&\n ##makeblastdb does not like input redirects of the sort\n ##makeblastdb -in <(gunzip -c gzipped_fasta_file)\n ##therefore we\'re cramming everything\n ##into a single cat command below\n cat\n-#for i in $input_file:\n- #if $i.is_of_type(\'fasta.gz\') and $i.ext != "fasta":\n- <(gunzip -c ${i})\n+#for i, is_gzipped in zip($inputs, $input_compression):\n+ #if $is_gzipped:\n+ <(gunzip -c \'$i\')\n #else:\n- ${i}\n+ \'$i\'\n #end if\n #end for\n | makeblastdb -out \'${os.path.join($outfile.files_path, "blastdb")}\'\n@@ -36,7 +51,12 @@\n ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful\n -title \'BLAST Database\'\n #end if\n--dbtype $dbtype\n+-dbtype\n+#if $input.type == "protein":\n+ prot\n+#else:\n+ nucl\n+#end if\n ## --------------------------------------------------------------------\n ## Masking\n ## --------------------------------------------------------------------\n@@ -60,15 +80,39 @@\n > \'$outfile\'\n ]]></command>\n <inputs>\n- <param argument="-dbtype" type="select" display="radio" label="Molecule type of input">\n- <option value="prot">protein</option>\n- <option value="nucl">nucleotide</option>\n- </param>\n- <!-- TODO Allow merging of existing BLAST databases (conditional on the database type)?\n- NOTE Double check the new database would be self contained first\n- -->\n- <!-- Note this is a mandatory parameter - default should be most recent FASTA file -->\n- <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="fasta,fasta.gz" label="Input FASTA files(s)" help="One or more FASTA files" />\n+ <conditional name="input">\n+ <param argument="-dbtype" name="type" type="select" label="Molecule type of input">\n+ <option value="protein">protein</option>\n+ <option value="nucleotide">nucleotide</option>\n+ </param>\n+ <!-- TODO Allow merging of existing BLAST databases (conditional on the database type)?\n+ NOTE Double check the new database would be self contained first\n+ -->\n+ <when value="protein">\n+ <repeat name="selection" title="Select input" min="1" default="1">\n+ <!-- Note this is a mandatory parameter - default should be most recent FASTA file -->\n+ <param name="input_file" argument="-in" type="data" format="fasta,fasta.gz" label="FASTA input" help="FASTA file with one or more sequences to add to the database" />\n+ </repeat>\n+ </when>\n+ <when value="nucleotide">\n+ <repeat name="selection" title="Select input" min="1" default="1">\n+ <conditional name="nuc_choice">\n+ <param name="source" type="select" label="Input is a">\n+ <option value="history">Dataset in history</option>\n+ '..b'"parse_seqids" value="" />\n <param name="hash_index" value="true" />\n@@ -132,8 +181,12 @@\n </output>\n </test>\n <test>\n- <param name="dbtype" value="prot" />\n- <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />\n+ <conditional name="input">\n+ <param name="type" value="protein"/>\n+ <repeat name="selection">\n+ <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />\n+ </repeat>\n+ </conditional> \n <param name="title" value="Just 4 human proteins" />\n <param name="parse_seqids" value="" />\n <param name="hash_index" value="true" />\n@@ -151,8 +204,12 @@\n </output>\n </test>\n <test>\n- <param name="dbtype" value="prot" />\n- <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />\n+ <conditional name="input">\n+ <param name="type" value="protein"/>\n+ <repeat name="selection">\n+ <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" />\n+ </repeat>\n+ </conditional> \n <param name="title" value="Just 4 human proteins" />\n <param name="parse_seqids" value="" />\n <param name="hash_index" value="true" />\n@@ -169,8 +226,41 @@\n </output>\n </test>\n <test>\n- <param name="dbtype" value="nucl" />\n- <param name="input_file" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" />\n+ <conditional name="input">\n+ <param name="type" value="nucleotide"/>\n+ <repeat name="selection">\n+ <conditional name="nuc_choice">\n+ <param name="source" value="history"/>\n+ <param name="input_file" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" />\n+ </conditional> \n+ </repeat>\n+ </conditional> \n+ <param name="title" value="Just 3 human mRNA sequences" />\n+ <param name="parse_seqids" value="" />\n+ <param name="hash_index" value="true" />\n+ <param name="taxselect" value="id" />\n+ <param name="taxid" value="9606" />\n+ <output name="outfile" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn">\n+ <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" compare="sim_size" delta="8" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nsq" name="blastdb.nsq" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nog" name="blastdb.nog" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nhd" name="blastdb.nhd" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nhi" name="blastdb.nhi" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nsd" name="blastdb.nsd" />\n+ <extra_files type="file" value="three_human_mRNA.fasta.nsi" name="blastdb.nsi" />\n+ </output>\n+ </test>\n+ <test>\n+ <conditional name="input">\n+ <param name="type" value="nucleotide"/>\n+ <repeat name="selection">\n+ <conditional name="nuc_choice">\n+ <param name="source" value="cached"/>\n+ <param name="input_file" value="three_human_mRNA" />\n+ </conditional> \n+ </repeat>\n+ </conditional> \n <param name="title" value="Just 3 human mRNA sequences" />\n <param name="parse_seqids" value="" />\n <param name="hash_index" value="true" />\n' |