| Previous changeset 23:9e483194ebf6 (2017-09-15) Next changeset 25:cc9baedbc059 (2017-09-15) |
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Commit message:
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit dc88568c900086550ce206dd83bad65e991df743-dirty |
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modified:
tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml |
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| diff -r 9e483194ebf6 -r 3b4efe26da79 tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Fri Sep 15 07:52:22 2017 -0400 +++ b/tools/ncbi_blast_plus/README.rst Fri Sep 15 10:02:56 2017 -0400 |
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| @@ -244,9 +244,10 @@ (internal change only). v0.2.01 - Use ``<command detect_errors="aggressive">`` (internal change only). - Single quote command line arguments (internal change only). - - Show the BLAST option corresponding to each tool parameter - - Add ``-max_hsps`` option - - Add ``-use_sw_tback`` option for BLASTP + - Show BLAST command line argument corresponding to each tool + parameter (contribution from Nicola Soranzo). + - Add ``-max_hsps`` option (contribution from Nicola Soranzo). + - Add ``-use_sw_tback`` option for BLASTP (Nicola Soranzo). ======= ====================================================================== |
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| diff -r 9e483194ebf6 -r 3b4efe26da79 tools/ncbi_blast_plus/blastxml_to_tabular.xml --- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Fri Sep 15 07:52:22 2017 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Fri Sep 15 10:02:56 2017 -0400 |
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| @@ -134,7 +134,7 @@ </test> </tests> <help> - + **What it does** NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of |
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| diff -r 9e483194ebf6 -r 3b4efe26da79 tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Fri Sep 15 07:52:22 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Fri Sep 15 10:02:56 2017 -0400 |
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| @@ -32,7 +32,7 @@ </test> </tests> <help> - + **What it does** Calls the NCBI BLAST+ blastdbcmd command line tool with the -info |
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| diff -r 9e483194ebf6 -r 3b4efe26da79 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Fri Sep 15 07:52:22 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Fri Sep 15 10:02:56 2017 -0400 |
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| @@ -105,7 +105,7 @@ </test> </tests> <help> - + **What it does** Extracts FASTA formatted sequences from a BLAST database @@ -138,5 +138,5 @@ @REFERENCES@ </help> - <expand macro="blast_citations" /> + <expand macro="blast_citations" /> </tool> |
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| diff -r 9e483194ebf6 -r 3b4efe26da79 tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Fri Sep 15 07:52:22 2017 -0400 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Fri Sep 15 10:02:56 2017 -0400 |
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| @@ -174,7 +174,7 @@ <option value="file">FASTA file from your history (see warning note below)</option> </param> <when value="db"> - <param name="database" type="select" multiple="true" label="Nucleotide BLAST database"> + <param name="database" argument="-db" type="select" multiple="true" label="Nucleotide BLAST database"> <options from_data_table="blastdb" /> </param> <param name="histdb" type="hidden" value="" /> @@ -182,13 +182,13 @@ </when> <when value="histdb"> <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> + <param name="histdb" argument="-db" type="data" format="blastdbn" label="Nucleotide BLAST database" /> <param name="subject" type="hidden" value="" /> </when> <when value="file"> <param name="database" type="hidden" value="" /> <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + <param argument="subject" type="data" format="fasta" label="Nucleotide FASTA subject file to use instead of a database"/> </when> </conditional> </xml> @@ -200,7 +200,7 @@ <option value="file">FASTA file from your history (see warning note below)</option> </param> <when value="db"> - <param name="database" type="select" multiple="true" label="Protein BLAST database"> + <param name="database" argument="db" type="select" multiple="true" label="Protein BLAST database"> <options from_data_table="blastdb_p" /> </param> <param name="histdb" type="hidden" value="" /> @@ -208,13 +208,13 @@ </when> <when value="histdb"> <param name="database" type="hidden" value="" /> - <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> + <param name="histdb" argument="db" type="data" format="blastdbp" label="Protein BLAST database" /> <param name="subject" type="hidden" value="" /> </when> <when value="file"> <param name="database" type="hidden" value="" /> <param name="histdb" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> + <param argument="subject" type="data" format="fasta" label="Protein FASTA subject file to use instead of a database"/> </when> </conditional> </xml> |