# 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 1287758911 -3600 # Node ID a6cd0223a53b4f9498a0dde69dcef53387188e5f # Parent 082399b4681b878d20a727150832ef30679b7e1c Add -parse_deflines switch to BLAST+ wrappers

--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -27,6 +27,7 @@ blastn -word_size $adv_opts.word_size #end if $adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -99,6 +100,7 @@ blastn <validator type="in_range" min="0" /></param><param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs>

--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -28,6 +28,7 @@ blastp #end if ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -104,6 +105,7 @@ blastp Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> --> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs>

--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -26,6 +26,7 @@ tblastx #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -97,6 +98,7 @@ tblastx <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."><validator type="in_range" min="0" /></param> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs>

--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -27,6 +27,7 @@ blastx -word_size $adv_opts.word_size #end if $adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -99,6 +100,7 @@ blastx <validator type="in_range" min="0" /></param><param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs>

--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -27,6 +27,7 @@ tblastn #end if ##Ungapped disabled for now - see comments below ##$adv_opts.ungapped +$adv_opts.parse_deflines ## End of advanced options: #end if </command> @@ -99,6 +100,7 @@ tblastn Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.' <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> --> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/></when></conditional></inputs>