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Add -ungapped for blastn and blastx (having trouble with blastp and tblastn, not in tblastx)

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This commit is contained in:
Peter Cock
2010-10-08 17:18:58 +01:00
parent df6fa45575
commit 581b8cc917
4 changed files with 30 additions and 0 deletions
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tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
+3
View File
@@ -25,6 +25,7 @@ $adv_opts.strand
#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
-word_size $adv_opts.word_size
#end if
$adv_opts.ungapped
</command>
<inputs>
<param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
@@ -76,6 +77,7 @@ $adv_opts.strand
<param name="strand" type="hidden" value="" />
<param name="max_hits" type="hidden" value="" />
<param name="word_size" type="hidden" value="" />
<param name="ungapped" type="hidden" value="" />
</when>
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
@@ -93,6 +95,7 @@ $adv_opts.strand
<param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4.">
<validator type="in_range" min="0" />
</param>
<param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
+12
View File
@@ -25,6 +25,8 @@ $adv_opts.matrix
#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
-word_size $adv_opts.word_size
#end if
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
</command>
<inputs>
<param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>
@@ -70,6 +72,10 @@ $adv_opts.matrix
<param name="matrix" type="hidden" value="" />
<param name="max_hits" type="hidden" value="" />
<param name="word_size" type="hidden" value="" />
<!--
Ungapped disabled for now, see comments below
<param name="ungapped" type="hidden" value="" />
-->
</when>
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
@@ -92,6 +98,12 @@ $adv_opts.matrix
<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>
<!--
Can't use '-ungapped' on its own, error back is:
Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
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" />
-->
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+3
View File
@@ -25,6 +25,7 @@ $adv_opts.matrix
#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
-word_size $adv_opts.word_size
#end if
$adv_opts.ungapped
</command>
<inputs>
<param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
@@ -67,6 +68,7 @@ $adv_opts.matrix
<param name="matrix" type="hidden" value="" />
<param name="max_hits" type="hidden" value="" />
<param name="word_size" type="hidden" value="" />
<param name="ungapped" type="hidden" value="" />
</when>
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
@@ -94,6 +96,7 @@ $adv_opts.matrix
<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="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
+12
View File
@@ -24,6 +24,8 @@ $adv_opts.matrix
#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
-word_size $adv_opts.word_size
#end if
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
</command>
<inputs>
<param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>
@@ -65,6 +67,10 @@ $adv_opts.matrix
<param name="matrix" type="hidden" value="" />
<param name="max_hits" type="hidden" value="" />
<param name="word_size" type="hidden" value="" />
<!--
Ungapped disabled for now, see comments below
<param name="ungapped" type="hidden" value="" />
-->
</when>
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
@@ -87,6 +93,12 @@ $adv_opts.matrix
<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>
<!--
Can't use '-ungapped' on its own, error back is:
Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
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" />
-->
</when>
</conditional>
</inputs>