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Workaround Issue 397 using 'if' in Cheetah template to avoid hidden parameters

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This commit is contained in:
Peter Cock
2010-10-13 11:27:08 +01:00
parent 22fb64823a
commit 5f6112ecfa
5 changed files with 32 additions and 54 deletions
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tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
+6 -9
View File
@@ -12,11 +12,12 @@ blastn
#end if
-task $blast_type
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.strand
-out $output1
$out_format
-num_threads 8
#if $adv_opts.adv_opts_selector=="advanced":
$adv_opts.filter_query
$adv_opts.strand
## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
## Note -max_target_seqs overrides -num_descriptions and -num_alignments
#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
@@ -26,6 +27,8 @@ $out_format
-word_size $adv_opts.word_size
#end if
$adv_opts.ungapped
## End of advanced options:
#end if
</command>
<inputs>
<param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
@@ -78,13 +81,7 @@ $adv_opts.ungapped
<option value="basic" selected="True">Hide Advanced Options</option>
<option value="advanced">Show Advanced Options</option>
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<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="basic" />
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
+6 -12
View File
@@ -12,11 +12,12 @@ blastp
#end if
-task $blast_type
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.matrix
-out $output1
$out_format
-num_threads 8
#if $adv_opts.adv_opts_selector=="advanced":
$adv_opts.filter_query
$adv_opts.matrix
## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
## Note -max_target_seqs overrides -num_descriptions and -num_alignments
#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
@@ -27,6 +28,8 @@ $out_format
#end if
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
## End of advanced options:
#end if
</command>
<inputs>
<param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>
@@ -73,16 +76,7 @@ $out_format
<option value="basic" selected="True">Hide Advanced Options</option>
<option value="advanced">Show Advanced Options</option>
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<param name="matrix" type="hidden" value="" />
<param name="max_hits" type="hidden" value="" />
<param name="word_size" type="hidden" value="" />
<!--
Ungapped disabled for now, see comments below
<param name="ungapped" type="hidden" value="" />
-->
</when>
<when value="basic" />
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+7 -11
View File
@@ -11,12 +11,13 @@ blastx
-subject "$db_opts.subject"
#end if
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.strand
$adv_opts.matrix
-out $output1
$out_format
-num_threads 8
#if $adv_opts.adv_opts_selector=="advanced":
$adv_opts.filter_query
$adv_opts.strand
$adv_opts.matrix
## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
## Note -max_target_seqs overrides -num_descriptions and -num_alignments
#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
@@ -26,6 +27,8 @@ $out_format
-word_size $adv_opts.word_size
#end if
$adv_opts.ungapped
## End of advanced options:
#end if
</command>
<inputs>
<param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
@@ -68,14 +71,7 @@ $adv_opts.ungapped
<option value="basic" selected="True">Hide Advanced Options</option>
<option value="advanced">Show Advanced Options</option>
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<param name="strand" type="hidden" value="" />
<param name="matrix" type="hidden" value="" />
<param name="max_hits" type="hidden" value="" />
<param name="word_size" type="hidden" value="" />
<param name="ungapped" type="hidden" value="" />
</when>
<when value="basic" />
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
+6 -12
View File
@@ -11,11 +11,12 @@ tblastn
-subject "$db_opts.subject"
#end if
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.matrix
-out $output1
$out_format
-num_threads 8
#if $adv_opts.adv_opts_selector=="advanced":
$adv_opts.filter_query
$adv_opts.matrix
## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
## Note -max_target_seqs overrides -num_descriptions and -num_alignments
#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
@@ -26,6 +27,8 @@ $out_format
#end if
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
## End of advanced options:
#end if
</command>
<inputs>
<param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>
@@ -68,16 +71,7 @@ $out_format
<option value="basic" selected="True">Hide Advanced Options</option>
<option value="advanced">Show Advanced Options</option>
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<param name="matrix" type="hidden" value="" />
<param name="max_hits" type="hidden" value="" />
<param name="word_size" type="hidden" value="" />
<!--
Ungapped disabled for now, see comments below
<param name="ungapped" type="hidden" value="" />
-->
</when>
<when value="basic" />
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+7 -10
View File
@@ -11,12 +11,13 @@ tblastx
-subject "$db_opts.subject"
#end if
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.strand
$adv_opts.matrix
-out $output1
$out_format
-num_threads 8
#if $adv_opts.adv_opts_selector=="advanced":
$adv_opts.filter_query
$adv_opts.strand
$adv_opts.matrix
## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
## Note -max_target_seqs overrides -num_descriptions and -num_alignments
#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
@@ -24,6 +25,8 @@ $out_format
#end if
#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
-word_size $adv_opts.word_size
#end if
## End of advanced options:
#end if
</command>
<inputs>
@@ -67,13 +70,7 @@ $out_format
<option value="basic" selected="True">Hide Advanced Options</option>
<option value="advanced">Show Advanced Options</option>
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<param name="strand" type="hidden" value="" />
<param name="matrix" type="hidden" value="" />
<param name="max_hits" type="hidden" value="" />
<param name="word_size" type="hidden" value="" />
</when>
<when value="basic" />
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />