Mercurial > repos > devteam > ncbi_blast_plus
changeset 36:fc35ffc8c548 draft default tip
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit eb397ba9bd3d2f3db13757f3bce094a89c4de9b3
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--- a/test-data/blastn_chimera_vs_three_human_max1.txt Thu Feb 22 15:07:36 2024 +0000 +++ b/test-data/blastn_chimera_vs_three_human_max1.txt Wed Mar 26 16:47:10 2025 +0000 @@ -1,4 +1,4 @@ -BLASTN 2.14.1+ +BLASTN 2.16.0+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
--- a/test-data/blastn_rhodopsin_vs_three_human.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human.xml Wed Mar 26 16:47:10 2025 +0000 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastn</BlastOutput_program> - <BlastOutput_version>BLASTN 2.14.1+</BlastOutput_version> + <BlastOutput_version>BLASTN 2.16.0+</BlastOutput_version> <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
--- a/test-data/blastp_four_human_vs_rhodopsin.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Wed Mar 26 16:47:10 2025 +0000 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastp</BlastOutput_program> - <BlastOutput_version>BLASTP 2.14.1+</BlastOutput_version> + <BlastOutput_version>BLASTP 2.16.0+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Q9BS26</BlastOutput_query-ID>
--- a/test-data/blastx_rhodopsin_vs_four_human.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Wed Mar 26 16:47:10 2025 +0000 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastx</BlastOutput_program> - <BlastOutput_version>BLASTX 2.14.1+</BlastOutput_version> + <BlastOutput_version>BLASTX 2.16.0+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Wed Mar 26 16:47:10 2025 +0000 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>tblastn</BlastOutput_program> - <BlastOutput_version>TBLASTN 2.14.1+</BlastOutput_version> + <BlastOutput_version>TBLASTN 2.16.0+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Wed Mar 26 16:47:10 2025 +0000 @@ -7,7 +7,7 @@ <requirement type="package" version="3.9">python</requirement> </requirements> <version_command>python $__tool_directory__/blastxml_to_tabular.py --version</version_command> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ python $__tool_directory__/blastxml_to_tabular.py -o '$tabular_file' #if $output.out_format == "cols": #set cols = (str($output.std_cols)+","+str($output.ext_cols)).replace("None", " ").replace(",,", ",").replace(",", " ") @@ -16,7 +16,7 @@ -c '$output.out_format' #end if #for i in $blastxml_file#'${i}' #end for# - </command> + ]]></command> <inputs> <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/> <conditional name="output"> @@ -66,73 +66,97 @@ <tests> <test> <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar --> <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> - <param name="out_format" value="ext" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar --> <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <!-- Note this has some white space differences from the actual blastp output --> <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <!-- Note this has some white space differences from the actual blastx output --> <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> - <param name="out_format" value="ext" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> <!-- Note this has some white space and XXXX masking differences from the actual blastx output --> <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <!-- Note this has some white space differences from the actual blastx output --> <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <!-- Note this has some white space differences from the actual blastp output --> <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> - <param name="out_format" value="ext" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> <!-- Note this has some white space differences from the actual blastp output --> <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <output name="tabular_file" file="blastn_arabidopsis.standard.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" /> - <param name="out_format" value="ext" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> <output name="tabular_file" file="blastn_arabidopsis.extended.tabular" ftype="tabular" /> </test> <!-- there are some harmless white space differences in our conversion to the BLAST+ output here: --> <test> <param name="blastxml_file" value="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> + <conditional name="output"> + <param name="out_format" value="std" /> + </conditional> <output name="tabular_file" file="blastn_rhodopsin_vs_three_human_converted.tabular" ftype="tabular" /> </test> <test> <param name="blastxml_file" value="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> - <param name="out_format" value="cols" /> - <param name="std_cols" value="qseqid,sseqid,pident" /> - <param name="ext_cols" value="qlen,slen" /> + <conditional name="output"> + <param name="out_format" value="cols" /> + <param name="std_cols" value="qseqid,sseqid,pident" /> + <param name="ext_cols" value="qlen,slen" /> + </conditional> <output name="tabular_file" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> </test> </tests>
--- a/tools/ncbi_blast_plus/get_species_taxids.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/get_species_taxids.xml Wed Mar 26 16:47:10 2025 +0000 @@ -3,7 +3,8 @@ <macros> <import>ncbi_macros.xml</import> </macros> - <expand macro="preamble"/> + <expand macro="requirements"/> + <version_command>echo "@TOOL_VERSION@"</version_command> <command detect_errors="aggressive"><![CDATA[ #if $type_cond.type_sel == 'names' #for name in $type_cond.names.split(',') @@ -93,14 +94,6 @@ Returns a list of species taxids for a taxon. It relies on the get_species_taxids.sh script of the BLAST+ package https://www.ncbi.nlm.nih.gov/books/NBK546209/ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations"/> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Mar 26 16:47:10 2025 +0000 @@ -5,11 +5,11 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ blastdbcmd @DBCMD_OPTS@ -info -out "$info" - </command> + ]]></command> <inputs> <expand macro="input_conditional_choose_db_type" /> </inputs> @@ -46,14 +46,6 @@ switch to give summary information about a BLAST database, such as the size (number of sequences and total length) and date. -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Mar 26 16:47:10 2025 +0000 @@ -5,7 +5,7 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive" strict="true"> + <command detect_errors="aggressive" strict="true"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastdbcmd @@ -41,11 +41,11 @@ #if str($outfmt)=="blastid": -out '$seq' #else if sys.platform == "darwin": -| sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq" +| sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq" #else: -| sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq" +| sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq" #end if - </command> + ]]></command> <inputs> <expand macro="input_conditional_choose_db_type" /> <conditional name="id_opts"> @@ -152,14 +152,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Mar 26 16:47:10 2025 +0000 @@ -4,10 +4,8 @@ <token name="@BINARY@">blastn</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="parallelism" /> <expand macro="preamble" /> - <command detect_errors="aggressive"> -<![CDATA[ + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastn @@ -36,8 +34,7 @@ @ADV_GAPEXTEND@ ## End of advanced options: #end if -]]> - </command> + ]]></command> <inputs> <expand macro="nucl_query" /> <expand macro="input_conditional_nucleotide_db" /> @@ -83,93 +80,147 @@ <tests> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-40" /> - <param name="out_format" value="5" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="5" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> </test> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-40" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-40" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-40" /> - <param name="out_format" value="cols" /> - <param name="std_cols" value="qseqid,sseqid,pident" /> - <param name="ext_cols" value="qlen,slen" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="cols" /> + <param name="std_cols" value="qseqid,sseqid,pident" /> + <param name="ext_cols" value="qlen,slen" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> </test> <test> <param name="query" value="chimera.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="db" /> - <param name="database" value="three_human_mRNA" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="max_hits" value="1" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="db" /> + <param name="database" value="three_human_mRNA" /> + </conditional> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <param name="max_hits" value="1" /> + </conditional> <output name="output1" file="blastn_chimera_vs_three_human_max1.tabular" ftype="tabular" /> </test> <test> <param name="query" value="chimera.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="db" /> - <param name="database" value="three_human_mRNA" /> - <param name="out_format" value="0" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="max_hits" value="1" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="db" /> + <param name="database" value="three_human_mRNA" /> + </conditional> + <conditional name="output"> + <param name="out_format" value="0" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <param name="max_hits" value="1" /> + </conditional> <output name="output1" file="blastn_chimera_vs_three_human_max1.txt" ftype="txt" /> </test> <test> <param name="query" value="chimera.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="db" /> - <param name="database" value="three_human_mRNA" /> - <param name="out_format" value="6" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="db" /> + <param name="database" value="three_human_mRNA" /> + </conditional> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> <output name="output1" file="blastn_chimera_vs_three_human_db.tabular" ftype="tabular" /> </test> <test> <param name="query" value="chimera.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="db" /> - <param name="database" value="rhodopsin_nucs" /> - <param name="out_format" value="6" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="db" /> + <param name="database" value="rhodopsin_nucs" /> + </conditional> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> <output name="output1" file="blastn_chimera_vs_rhodopsin_db.tabular" ftype="tabular" /> </test> <test> <param name="query" value="chimera.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="db" /> - <param name="database" value="rhodopsin_nucs" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="max_hsps" value="1" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="db" /> + <param name="database" value="rhodopsin_nucs" /> + </conditional> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <param name="max_hsps" value="1" /> + </conditional> <output name="output1" file="blastn_chimera_vs_rhodopsin_db_max_hsps1.tabular" ftype="tabular" /> </test> <!-- next test is passing in two blast databases --> <test> <param name="query" value="chimera.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="db" /> - <param name="database" value="three_human_mRNA,rhodopsin_nucs" /> - <param name="out_format" value="6" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="db" /> + <param name="database" value="three_human_mRNA,rhodopsin_nucs" /> + </conditional> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> <output name="output1" file="blastn_chimera_vs_three_human_and_rhodopsin_db.tabular" ftype="tabular" /> </test> </tests> @@ -193,14 +244,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Mar 26 16:47:10 2025 +0000 @@ -4,9 +4,8 @@ <token name="@BINARY@">blastp</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="parallelism" /> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastp @@ -31,7 +30,7 @@ @ADV_COMP_BASED_STATS@ ## End of advanced options: #end if - </command> + ]]></command> <inputs> <expand macro="prot_query" /> @@ -75,92 +74,136 @@ <tests> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-8" /> <param name="blast_type" value="blastp" /> - <param name="out_format" value="5" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM62" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="" /> - <param name="window_size" value="40" /> - <param name="parse_deflines" value="true" /> - <param name="qcov_hsp_perc" value="25" /> + <conditional name="output"> + <param name="out_format" value="5" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <conditional name="matrix_gapcosts"> + <param name="matrix" value="BLOSUM62" /> + </conditional> + <param name="max_hits" value="0" /> + <!-- <param name="word_size" value="" /> --> + <param name="window_size" value="40" /> + <param name="parse_deflines" value="true" /> + <param name="qcov_hsp_perc" value="25" /> + </conditional> <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> </test> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-8" /> <param name="blast_type" value="blastp" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM62" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="" /> - <param name="window_size" value="40" /> - <param name="parse_deflines" value="true" /> - <param name="qcov_hsp_perc" value="25" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <conditional name="matrix_gapcosts"> + <param name="matrix" value="BLOSUM62" /> + </conditional> + <param name="max_hits" value="0" /> + <!-- <param name="word_size" value="" /> --> + <param name="window_size" value="40" /> + <param name="parse_deflines" value="true" /> + <param name="qcov_hsp_perc" value="25" /> + </conditional> <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> </test> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-8" /> <param name="blast_type" value="blastp" /> - <param name="out_format" value="ext" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM62" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="" /> - <param name="parse_deflines" value="true" /> - <param name="qcov_hsp_perc" value="25" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <conditional name="matrix_gapcosts"> + <param name="matrix" value="BLOSUM62" /> + </conditional> + <param name="max_hits" value="0" /> + <!-- <param name="word_size" value="" /> --> + <param name="parse_deflines" value="true" /> + <param name="qcov_hsp_perc" value="25" /> + </conditional> <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-8" /> <param name="blast_type" value="blastp" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_peptides.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="200000" /> <param name="blast_type" value="blastp-short" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastp_rhodopsin_peptides_vs_four_human.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-8"/> <param name="blast_type" value="blastp" /> - <param name="out_format" value="6"/> - <param name="adv_opts_selector" value="advanced"/> - <param name="window_size" value="35" /> - <param name="matrix" value="BLOSUM62" /> - <param name="gap_costs" value="-gapopen 11 -gapextend 1"/> - <param name="comp_based_stats" value="3" /> + <conditional name="output"> + <param name="out_format" value="6"/> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced"/> + <param name="window_size" value="35" /> + <conditional name="matrix_gapcosts"> + <param name="matrix" value="BLOSUM62" /> + <param name="gap_costs" value="-gapopen 11 -gapextend 1"/> + </conditional> + <param name="comp_based_stats" value="3" /> + </conditional> <output name="output1" file="blastp_rhodopsin_adv_vs_four_human.tabular" ftype="tabular" /> </test> </tests> @@ -183,14 +226,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Mar 26 16:47:10 2025 +0000 @@ -4,9 +4,8 @@ <token name="@BINARY@">blastx</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="parallelism" /> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces blastx @@ -31,7 +30,7 @@ @ADV_COMP_BASED_STATS@ ## End of advanced options: #end if - </command> + ]]></command> <inputs> <expand macro="nucl_query" /> @@ -68,58 +67,90 @@ <tests> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="5" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="5" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> </test> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="ext" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="cols" /> - <param name="std_cols" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" /> - <param name="ext_cols" value="sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" /> - <param name="ids_cols" value="qgi,qacc,qaccver,sallseqid,sgi,sallgi,sacc,saccver,sallacc,stitle" /> - <param name="misc_cols" value="sstrand,frames,btop,qcovs,qcovhsp" /> - <param name="tax_cols" value="staxids,sscinames,scomnames,sblastnames,sskingdoms" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="cols" /> + <param name="std_cols" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" /> + <param name="ext_cols" value="sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" /> + <param name="ids_cols" value="qgi,qacc,qaccver,sallseqid,sgi,sallgi,sacc,saccver,sallacc,stitle" /> + <param name="misc_cols" value="sstrand,frames,btop,qcovs,qcovhsp" /> + <param name="tax_cols" value="staxids,sscinames,scomnames,sblastnames,sskingdoms" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="blastx_rhodopsin_vs_four_human_all.tabular" ftype="tabular" /> </test> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="matrix" value="BLOSUM62" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <conditional name="matrix_gapcosts"> + <param name="matrix" value="BLOSUM62" /> + </conditional> + </conditional> <output name="output1" file="blastx_rhodopsin_adv_vs_four_human.tabular" ftype="tabular" /> </test> </tests> @@ -142,14 +173,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Wed Mar 26 16:47:10 2025 +0000 @@ -5,7 +5,7 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces convert2blastmask @@ -15,7 +15,7 @@ $parse_seqids -out '$outfile' -outfmt $outformat - </command> + ]]></command> <inputs> <param name="infile" argument="-in" type="data" format="fasta" label="Masked FASTA file"/> <param argument="-masking_algorithm" type="select" label="Used masking algorithm"> @@ -76,12 +76,6 @@ .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Wed Mar 26 16:47:10 2025 +0000 @@ -6,7 +6,7 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces dustmasker @@ -14,12 +14,18 @@ -in '${db_opts.database.fields.path}' -infmt blastdb #elif $db_opts.db_opts_selector == "histdb": -in '${os.path.join($db_opts.histdb.files_path, "blastdb")}' -infmt blastdb -#else: - -in '$subject' -infmt fasta +#else + -in + #if $subject.ext == "fasta" + '$subject' + #else + <(gunzip -c '$subject') + #end if + -infmt fasta #end if -out '$outfile' -window $window -level $level -linker $linker -outfmt $outformat - </command> + ]]></command> <inputs> <expand macro="input_conditional_nucleotide_db" /> <param argument="-window" type="integer" value="64" label="DUST window length" /> @@ -49,8 +55,10 @@ </outputs> <tests> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + </conditional> <param name="window" value="64" /> <param name="level" value="20" /> <param name="linker" value="1" /> @@ -58,8 +66,10 @@ <output name="outfile" file="dustmasker_three_human.fasta" /> </test> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" /> + </conditional> <param name="window" value="64" /> <param name="level" value="20" /> <param name="linker" value="1" /> @@ -67,8 +77,10 @@ <output name="outfile" file="dustmasker_three_human.maskinfo-asn1-binary" /> </test> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + </conditional> <param name="window" value="64" /> <param name="level" value="20" /> <param name="linker" value="1" /> @@ -88,12 +100,6 @@ .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ .. _DUST: https://www.ncbi.nlm.nih.gov/pubmed/16796549 -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_macros.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Wed Mar 26 16:47:10 2025 +0000 @@ -1,18 +1,24 @@ <macros> - <token name="@TOOL_VERSION@">2.14.1</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 --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> + <token name="@TOOL_VERSION@">2.16.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> + + <xrefs> + <xref type="bio.tools">blast</xref> + </xrefs> + + <xml name="preamble"> + <expand macro="requirements"> + <yield/> + </expand> + <version_command>@BINARY@ -version</version_command> </xml> - <xml name="preamble"> + <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">blast</requirement> <yield /> </requirements> - <version_command>@BINARY@ -version</version_command> </xml> <xml name="nucl_query"> @@ -769,19 +775,6 @@ #end if ]]></token> - <token name="@REFERENCES@"><![CDATA[ -Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015). -NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39 -https://doi.org/10.1186/s13742-015-0080-7 - -Christiam Camacho et al. (2009). -BLAST+: architecture and applications. -*BMC Bioinformatics* 15;10:421. -https://doi.org/10.1186/1471-2105-10-421 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus - ]]></token> <xml name="blast_citations"> <citations> <citation type="doi">10.1093/nar/25.17.3389</citation>
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Mar 26 16:47:10 2025 +0000 @@ -167,7 +167,7 @@ </repeat> </conditional> <param name="title" value="Just 4 human proteins" /> - <param name="parse_seqids" value="" /> + <param name="parse_seqids" value="false" /> <param name="hash_index" value="true" /> <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp"> <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" /> @@ -188,10 +188,12 @@ </repeat> </conditional> <param name="title" value="Just 4 human proteins" /> - <param name="parse_seqids" value="" /> + <param name="parse_seqids" value="false" /> <param name="hash_index" value="true" /> - <param name="taxselect" value="id" /> - <param name="taxid" value="9606" /> + <conditional name="tax"> + <param name="taxselect" value="id" /> + <param name="taxid" value="9606" /> + </conditional> <output name="outfile" compare="contains" file="four_human_proteins_taxid.fasta.log.txt" ftype="blastdbp"> <extra_files type="file" value="four_human_proteins_taxid.fasta.phr" name="blastdb.phr" /> <extra_files type="file" value="four_human_proteins_taxid.fasta.pin" name="blastdb.pin" compare="sim_size" delta="0" /> @@ -211,7 +213,7 @@ </repeat> </conditional> <param name="title" value="Just 4 human proteins" /> - <param name="parse_seqids" value="" /> + <param name="parse_seqids" value="false" /> <param name="hash_index" value="true" /> <param name="mask_data_file" value="segmasker_four_human.maskinfo-asn1" ftype="maskinfo-asn1" /> <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp"> @@ -236,10 +238,12 @@ </repeat> </conditional> <param name="title" value="Just 3 human mRNA sequences" /> - <param name="parse_seqids" value="" /> + <param name="parse_seqids" value="false" /> <param name="hash_index" value="true" /> - <param name="taxselect" value="id" /> - <param name="taxid" value="9606" /> + <conditional name="tax"> + <param name="taxselect" value="id" /> + <param name="taxid" value="9606" /> + </conditional> <output name="outfile" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn"> <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" /> <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" compare="sim_size" delta="8" /> @@ -262,10 +266,12 @@ </repeat> </conditional> <param name="title" value="Just 3 human mRNA sequences" /> - <param name="parse_seqids" value="" /> + <param name="parse_seqids" value="false" /> <param name="hash_index" value="true" /> - <param name="taxselect" value="id" /> - <param name="taxid" value="9606" /> + <conditional name="tax"> + <param name="taxselect" value="id" /> + <param name="taxid" value="9606" /> + </conditional> <output name="outfile" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn"> <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" /> <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" compare="sim_size" delta="8" /> @@ -296,12 +302,6 @@ For this reason, it's best to apply all masks at once to minimize the number of unnecessary intermediate databases. --> -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Wed Mar 26 16:47:10 2025 +0000 @@ -5,9 +5,9 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive" strict="true"> + <command detect_errors="aggressive" strict="true"><![CDATA[ ##Unlike makeblastdb, makeprofiledb needs directory to exist already: -mkdir -p $outfile.files_path && +mkdir -p $outfile.files_path && makeprofiledb -blastdb_version 4 -out '${os.path.join($outfile.files_path, "blastdb")}' @@ -35,13 +35,13 @@ -exclude_invalid $exclude_invalid -logfile '$outfile' - </command> + ]]></command> <configfiles> - <configfile name="infiles"> + <configfile name="infiles"><![CDATA[ #for $infile in $input_file ${infile} #end for - </configfile> + ]]></configfile> </configfiles> <inputs> <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="pssm-asn1" @@ -89,7 +89,9 @@ <test> <param name="input_file" value="cd00003.smp,cd00008.smp" ftype="pssm-asn1" /> <param name="title" value="Just 2 PSSM matrices" /> - <param name="contain_pssm_scores_type" value="yes" /> + <conditional name="contain_pssm_scores"> + <param name="contain_pssm_scores_type" value="yes" /> + </conditional> <output name="outfile" file="empty_file.dat" ftype="blastdbd" > <extra_files type="file" value="cd00003_and_cd00008.phr" name="blastdb.phr" /> <extra_files type="file" value="cd00003_and_cd00008.pin" name="blastdb.pin" compare="sim_size" delta="8" /> @@ -116,13 +118,6 @@ .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Mar 26 16:47:10 2025 +0000 @@ -4,9 +4,8 @@ <token name="@BINARY@">deltablast</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="parallelism" /> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces rpsblast @@ -26,7 +25,7 @@ @ADV_WINDOW_SIZE@ ## End of advanced options: #end if - </command> + ]]></command> <inputs> <expand macro="prot_query" /> @@ -47,18 +46,20 @@ </inputs> <outputs> <data name="output1" format="tabular" label="rpsblast on ${on_string}"> - <expand macro="output_change_format" /> - </data> </outputs> <tests> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="db" /> - <param name="database" value="cd00003_and_cd00008" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="db" /> + <param name="database" value="cd00003_and_cd00008" /> + </conditional> <param name="evalue_cutoff" value="1e-8" /> - <param name="out_format" value="6" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> <output name="output1" file="empty_file.dat" ftype="tabular" /> </test> </tests> @@ -109,14 +110,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Wed Mar 26 16:47:10 2025 +0000 @@ -4,9 +4,8 @@ <token name="@BINARY@">rpstblastn</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="parallelism" /> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces rpstblastn @@ -26,7 +25,7 @@ @ADV_QCOV_HSP_PERC@ ## End of advanced options: #end if - </command> + ]]></command> <inputs> <expand macro="nucl_query" /> @@ -53,10 +52,14 @@ <tests> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="db" /> - <param name="database" value="cd00003_and_cd00008" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="db" /> + <param name="database" value="cd00003_and_cd00008" /> + </conditional> <param name="evalue_cutoff" value="1e-8" /> - <param name="out_format" value="6" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> <output name="output1" file="empty_file.dat" ftype="tabular" /> </test> </tests> @@ -107,14 +110,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Wed Mar 26 16:47:10 2025 +0000 @@ -5,7 +5,7 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces segmasker @@ -21,7 +21,7 @@ -locut $locut -hicut $hicut -outfmt $outformat - </command> + ]]></command> <inputs> <expand macro="input_conditional_protein_db" /> <param name="window" type="integer" value="12" label="SEG window length" help="(-window)" /> @@ -51,8 +51,10 @@ </outputs> <tests> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + </conditional> <param name="window" value="12" /> <param name="locut" value="2.2" /> <param name="hicut" value="2.5" /> @@ -60,8 +62,10 @@ <output name="outfile" file="segmasker_four_human.fasta" /> </test> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + </conditional> <param name="window" value="12" /> <param name="locut" value="2.2" /> <param name="hicut" value="2.5" /> @@ -69,8 +73,10 @@ <output name="outfile" file="segmasker_four_human.maskinfo-asn1-binary" /> </test> <test> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + </conditional> <param name="window" value="12" /> <param name="locut" value="2.2" /> <param name="hicut" value="2.5" /> @@ -90,12 +96,6 @@ .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ .. _SEG: https://www.ncbi.nlm.nih.gov/pubmed/8743706 -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Mar 26 16:47:10 2025 +0000 @@ -4,9 +4,8 @@ <token name="@BINARY@">tblastn</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="parallelism" /> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces tblastn @@ -31,7 +30,7 @@ @ADV_COMP_BASED_STATS@ ## End of advanced options: #end if - </command> + ]]></command> <inputs> <expand macro="prot_query" /> @@ -72,80 +71,120 @@ <tests> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="5" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM80" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="" /> - <param name="parse_deflines" value="false" /> + <conditional name="output"> + <param name="out_format" value="5" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <conditional name="matrix_gapcosts"> + <param name="matrix" value="BLOSUM80" /> + </conditional> + <param name="max_hits" value="0" /> + <!-- <param name="word_size" value="" /> https://github.com/galaxyproject/galaxy/issues/19908 --> + <param name="parse_deflines" value="false" /> + </conditional> <output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" /> </test> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="ext" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM80" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="" /> - <param name="parse_deflines" value="false" /> + <conditional name="output"> + <param name="out_format" value="ext" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <conditional name="matrix_gapcosts"> + <param name="matrix" value="BLOSUM80" /> + </conditional> + <param name="max_hits" value="0" /> + <!-- <param name="word_size" value="" /> --> + <param name="parse_deflines" value="false" /> + </conditional> <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> </test> <test> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM80" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="" /> - <param name="parse_deflines" value="false" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <conditional name="matrix_gapcosts"> + <param name="matrix" value="BLOSUM80" /> + </conditional> + <param name="max_hits" value="0" /> + <!-- <param name="word_size" value="" /> --> + <param name="parse_deflines" value="false" /> + </conditional> <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> </test> <test> <!-- Same as above, but parse deflines --> <!-- Note back on BLAST 2.2.25+ - 2.2.27+ made no difference --> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM80" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="" /> - <param name="parse_deflines" value="true" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <conditional name="matrix_gapcosts"> + <param name="matrix" value="BLOSUM80" /> + </conditional> + <param name="max_hits" value="0" /> + <!-- <param name="word_size" value="" /> --> + <param name="parse_deflines" value="true" /> + </conditional> <output name="output1" file="tblastn_four_human_vs_rhodopsin_deflines.tabular" ftype="tabular" /> </test> <test> <!-- As of BLAST 2.5.0+ the full path appears twice, so get small diff --> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="database" value="" /> + </conditional> <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="0 -html" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM80" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="" /> - <param name="parse_deflines" value="false" /> + <conditional name="output"> + <param name="out_format" value="0 -html" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <conditional name="matrix_gapcosts"> + <param name="matrix" value="BLOSUM80" /> + </conditional> + <param name="max_hits" value="0" /> + <!-- <param name="word_size" value="" /> --> + <param name="parse_deflines" value="false" /> + </conditional> <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" lines_diff="10" /> </test> </tests> @@ -168,14 +207,6 @@ @CLI_OPTIONS@ ------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Feb 22 15:07:36 2024 +0000 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Mar 26 16:47:10 2025 +0000 @@ -4,9 +4,8 @@ <token name="@BINARY@">tblastx</token> <import>ncbi_macros.xml</import> </macros> - <expand macro="parallelism" /> <expand macro="preamble" /> - <command detect_errors="aggressive"> + <command detect_errors="aggressive"><![CDATA[ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces tblastx @@ -28,7 +27,7 @@ @ADV_THRESHOLD@ ## End of advanced options: #end if - </command> + ]]></command> <inputs> <expand macro="nucl_query" /> @@ -61,12 +60,18 @@ <tests> <test> <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> - <param name="database" value="" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="file" /> + <param name="database" value="" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + </conditional> <param name="evalue_cutoff" value="1e-40" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="basic" /> + <conditional name="output"> + <param name="out_format" value="6" /> + </conditional> + <conditional name="adv_opts"> + <param name="adv_opts_selector" value="basic" /> + </conditional> <output name="output1" file="tblastx_rhodopsin_vs_three_human.tabular" ftype="tabular" /> </test> </tests> @@ -89,14 +94,6 @@ @CLI_OPTIONS@ -------- - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following papers: - -@REFERENCES@ </help> <expand macro="blast_citations" /> </tool>