# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock@googlemail.com> # Date 1286796719 -3600 # Node ID 9f172e4713edbf4d6a22f10ad01867710cce6b00 # Parent d8da4f7bb0f5e1d43b371e4e52fb688ad816e5bf Support query anchored and HTML output --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -15,7 +15,7 @@ blastn $adv_opts.filter_query $adv_opts.strand -out $output1 --outfmt $out_format +$out_format -num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments @@ -60,11 +60,16 @@ blastn </param><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"> - <option value="6">Tabular</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> + <option value="-outfmt 6" selected="True">Tabular</option> + <option value="-outfmt 5">BLAST XML</option> + <option value="-outfmt 0">Pairwise text</option> + <option value="-outfmt 0 -html">Pairwise HTML</option> + <option value="-outfmt 2">Query-anchored text</option> + <option value="-outfmt 2 -html">Query-anchored HTML</option> + <option value="-outfmt 4">Flat query-anchored text</option> + <option value="-outfmt 4 -html">Flat query-anchored HTML</option><!-- - <option value="11">BLAST archive format (ASN.1)</option> + <option value="-outfmt 11">BLAST archive format (ASN.1)</option> --></param><conditional name="adv_opts"> @@ -102,10 +107,13 @@ blastn <outputs><data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"><change_format> - <when input="out_format" value="0" format="txt"/> - </change_format> - <change_format> - <when input="out_format" value="5" format="blastxml"/> + <when input="out_format" value="-outfmt 0" format="txt"/> + <when input="out_format" value="-outfmt 0 -html" format="html"/> + <when input="out_format" value="-outfmt 2" format="txt"/> + <when input="out_format" value="-outfmt 2 -html" format="html"/> + <when input="out_format" value="-outfmt 4" format="txt"/> + <when input="out_format" value="-outfmt 4 -html" format="html"/> + <when input="out_format" value="-outfmt 5" format="blastxml"/></change_format></data></outputs> @@ -147,7 +155,7 @@ Algorithms include blastn, megablast, an **Output format** -The default output of this tool is tabular, containing 12 columns: +Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns: 1. Id of your sequence 2. GI of the database hit @@ -162,6 +170,14 @@ 10. End position in database hit 11. E-value 12. Bit score +The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + ------- **References** --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -15,7 +15,7 @@ blastp $adv_opts.filter_query $adv_opts.matrix -out $output1 --outfmt $out_format +$out_format -num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments @@ -55,11 +55,16 @@ blastp </param><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"> - <option value="6">Tabular</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> + <option value="-outfmt 6" selected="True">Tabular</option> + <option value="-outfmt 5">BLAST XML</option> + <option value="-outfmt 0">Pairwise text</option> + <option value="-outfmt 0 -html">Pairwise HTML</option> + <option value="-outfmt 2">Query-anchored text</option> + <option value="-outfmt 2 -html">Query-anchored HTML</option> + <option value="-outfmt 4">Flat query-anchored text</option> + <option value="-outfmt 4 -html">Flat query-anchored HTML</option><!-- - <option value="11">BLAST archive format (ASN.1)</option> + <option value="-outfmt 11">BLAST archive format (ASN.1)</option> --></param><conditional name="adv_opts"> @@ -110,10 +115,13 @@ blastp <outputs><data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"><change_format> - <when input="out_format" value="0" format="txt"/> - </change_format> - <change_format> - <when input="out_format" value="5" format="blastxml"/> + <when input="out_format" value="-outfmt 0" format="txt"/> + <when input="out_format" value="-outfmt 0 -html" format="html"/> + <when input="out_format" value="-outfmt 2" format="txt"/> + <when input="out_format" value="-outfmt 2 -html" format="html"/> + <when input="out_format" value="-outfmt 4" format="txt"/> + <when input="out_format" value="-outfmt 4 -html" format="html"/> + <when input="out_format" value="-outfmt 5" format="blastxml"/></change_format></data></outputs> @@ -140,7 +148,7 @@ using the NCBI BLAST+ blastp command lin **Output format** -The default output of this tool is tabular, containing 12 columns: +Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns: 1. Id of your sequence 2. GI of the database hit @@ -155,6 +163,14 @@ 10. End position in database hit 11. E-value 12. Bit score +The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + ------- **References** --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -15,7 +15,7 @@ tblastx $adv_opts.strand $adv_opts.matrix -out $output1 --outfmt $out_format +$out_format -num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments @@ -49,11 +49,16 @@ tblastx </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"> - <option value="6">Tabular</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> + <option value="-outfmt 6" selected="True">Tabular</option> + <option value="-outfmt 5">BLAST XML</option> + <option value="-outfmt 0">Pairwise text</option> + <option value="-outfmt 0 -html">Pairwise HTML</option> + <option value="-outfmt 2">Query-anchored text</option> + <option value="-outfmt 2 -html">Query-anchored HTML</option> + <option value="-outfmt 4">Flat query-anchored text</option> + <option value="-outfmt 4 -html">Flat query-anchored HTML</option><!-- - <option value="11">BLAST archive format (ASN.1)</option> + <option value="-outfmt 11">BLAST archive format (ASN.1)</option> --></param><conditional name="adv_opts"> @@ -100,10 +105,13 @@ tblastx <outputs><data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}"><change_format> - <when input="out_format" value="0" format="txt"/> - </change_format> - <change_format> - <when input="out_format" value="5" format="blastxml"/> + <when input="out_format" value="-outfmt 0" format="txt"/> + <when input="out_format" value="-outfmt 0 -html" format="html"/> + <when input="out_format" value="-outfmt 2" format="txt"/> + <when input="out_format" value="-outfmt 2 -html" format="html"/> + <when input="out_format" value="-outfmt 4" format="txt"/> + <when input="out_format" value="-outfmt 4 -html" format="html"/> + <when input="out_format" value="-outfmt 5" format="blastxml"/></change_format></data></outputs> @@ -122,7 +130,7 @@ tblastx --><param name="evalue_cutoff" value="10.0" /><param name="filter_query" value="yes" /> - <param name="out_format" value="6" /> + <param name="out_format" value="-outfmt 6" /><output name="output1" file="megablast_wrapper_test1.out"/></test></tests> @@ -143,7 +151,7 @@ using the NCBI BLAST+ tblastx command li **Output format** -The default output of this tool is tabular, containing 12 columns: +Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns: 1. Id of your sequence 2. GI of the database hit @@ -158,6 +166,14 @@ 10. End position in database hit 11. E-value 12. Bit score +The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + ------- **References** --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -15,7 +15,7 @@ blastx $adv_opts.strand $adv_opts.matrix -out $output1 --outfmt $out_format +$out_format -num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments @@ -50,11 +50,16 @@ blastx </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"> - <option value="6">Tabular</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> + <option value="-outfmt 6" selected="True">Tabular</option> + <option value="-outfmt 5">BLAST XML</option> + <option value="-outfmt 0">Pairwise text</option> + <option value="-outfmt 0 -html">Pairwise HTML</option> + <option value="-outfmt 2">Query-anchored text</option> + <option value="-outfmt 2 -html">Query-anchored HTML</option> + <option value="-outfmt 4">Flat query-anchored text</option> + <option value="-outfmt 4 -html">Flat query-anchored HTML</option><!-- - <option value="11">BLAST archive format (ASN.1)</option> + <option value="-outfmt 11">BLAST archive format (ASN.1)</option> --></param><conditional name="adv_opts"> @@ -103,10 +108,13 @@ blastx <outputs><data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}"><change_format> - <when input="out_format" value="0" format="txt"/> - </change_format> - <change_format> - <when input="out_format" value="5" format="blastxml"/> + <when input="out_format" value="-outfmt 0" format="txt"/> + <when input="out_format" value="-outfmt 0 -html" format="html"/> + <when input="out_format" value="-outfmt 2" format="txt"/> + <when input="out_format" value="-outfmt 2 -html" format="html"/> + <when input="out_format" value="-outfmt 4" format="txt"/> + <when input="out_format" value="-outfmt 4 -html" format="html"/> + <when input="out_format" value="-outfmt 5" format="blastxml"/></change_format></data></outputs> @@ -133,7 +141,7 @@ using the NCBI BLAST+ blastx command lin **Output format** -The default output of this tool is tabular, containing 12 columns: +Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns: 1. Id of your sequence 2. GI of the database hit @@ -148,6 +156,14 @@ 10. End position in database hit 11. E-value 12. Bit score +The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + ------- **References** --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -14,7 +14,7 @@ tblastn $adv_opts.filter_query $adv_opts.matrix -out $output1 --outfmt $out_format +$out_format -num_threads 8 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string ## Note -max_target_seqs overrides -num_descriptions and -num_alignments @@ -50,11 +50,16 @@ tblastn </conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format"> - <option value="6">Tabular</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> + <option value="-outfmt 6" selected="True">Tabular</option> + <option value="-outfmt 5">BLAST XML</option> + <option value="-outfmt 0">Pairwise text</option> + <option value="-outfmt 0 -html">Pairwise HTML</option> + <option value="-outfmt 2">Query-anchored text</option> + <option value="-outfmt 2 -html">Query-anchored HTML</option> + <option value="-outfmt 4">Flat query-anchored text</option> + <option value="-outfmt 4 -html">Flat query-anchored HTML</option><!-- - <option value="11">BLAST archive format (ASN.1)</option> + <option value="-outfmt 11">BLAST archive format (ASN.1)</option> --></param><conditional name="adv_opts"> @@ -105,10 +110,13 @@ tblastn <outputs><data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"><change_format> - <when input="out_format" value="0" format="txt"/> - </change_format> - <change_format> - <when input="out_format" value="5" format="blastxml"/> + <when input="out_format" value="-outfmt 0" format="txt"/> + <when input="out_format" value="-outfmt 0 -html" format="html"/> + <when input="out_format" value="-outfmt 2" format="txt"/> + <when input="out_format" value="-outfmt 2 -html" format="html"/> + <when input="out_format" value="-outfmt 4" format="txt"/> + <when input="out_format" value="-outfmt 4 -html" format="html"/> + <when input="out_format" value="-outfmt 5" format="blastxml"/></change_format></data></outputs> @@ -135,7 +143,7 @@ using the NCBI BLAST+ tblastn command li **Output format** -The default output of this tool is tabular, containing 12 columns: +Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns: 1. Id of your sequence 2. GI of the database hit @@ -150,6 +158,14 @@ 10. End position in database hit 11. E-value 12. Bit score +The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + ------- **References**