| Previous changeset 38:2be8f8cc13de (2018-10-23) Next changeset 40:fe0c28b3673e (2018-11-09) |
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Commit message:
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 022191902de1bae6ac6570b33284287c4854ae76-dirty |
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modified:
tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml |
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added:
test-data/rhodopsin_nucs.blastdbcmd.txt |
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| diff -r 2be8f8cc13de -r 5dd84f7ab575 test-data/rhodopsin_nucs.blastdbcmd.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rhodopsin_nucs.blastdbcmd.txt Tue Oct 23 12:59:33 2018 -0400 |
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| @@ -0,0 +1,7 @@ +gi|57163782|ref|NM_001009242.1| +gi|2734705|gb|U59921.1|BBU59921 "1 -" + +gi|283855845|gb|GQ290303.1| 1-4301 + +gi|283855822|gb|GQ290312.1| "1-983" +gi|18148870|dbj|AB062417.1| "1 -" + +gi|12583664|dbj|AB043817.1| "1--" + |
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| diff -r 2be8f8cc13de -r 5dd84f7ab575 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Tue Oct 23 10:40:59 2018 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Tue Oct 23 12:59:33 2018 -0400 |
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| @@ -55,7 +55,7 @@ <option value="prompt">User entered</option> </param> <when value="file"> - <param name="entries" argument="-entry_batch" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line (i.e. single column tabular file)"/> + <param name="entries" argument="-entry_batch" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line, optionally with space separated range, strand, and algorithm."/> </when> <when value="prompt"> <param name="entries" argument="-entry" type="text" optional="false" area="true" size="10x30" label="Sequence identifier(s)" help="Comma or new line separated list"/> @@ -88,6 +88,15 @@ <output name="seq" file="rhodopsin_nucs.no_gi.fasta" ftype="fasta" /> </test> <test> + <!-- This uses various start end frame combinations but all recover full sequence --> + <param name="db_opts|db_type" value="nucl" /> + <param name="db_opts|database" value="rhodopsin_nucs" /> + <param name="id_opts|id_type" value="file" /> + <param name="id_opts|entries" value="rhodopsin_nucs.blastdbcmd.txt" ftype="txt" /> + <param name="outfmt" value="original" /> + <output name="seq" file="rhodopsin_nucs.no_gi.fasta" ftype="fasta" /> + </test> + <test> <param name="db_opts|db_type" value="nucl" /> <param name="db_opts|database" value="rhodopsin_nucs" /> <param name="id_opts|id_type" value="prompt" /> @@ -111,6 +120,12 @@ Extracts FASTA formatted sequences from a BLAST database using the NCBI BLAST+ blastdbcmd command line tool. +When giving a text file of entries, use one line per sequence. +Optional valies should be space separate - the simplest syntax +is ``identifier start-end`` (where ``end`` can be just ``-``), +or ``identifier start-end strand`` (wheere the strand given as +either ``+`` or ``-``). + .. class:: warningmark **BLAST assigned identifiers** |