# HG changeset patch
# User eskirton@lbl.gov
# Date 1324525373 28800
# Node ID bf1f8bc4abe6e7c128ddfc54cf5664d7fab4bdc5
# Parent  2d86d5b112e89117f5bda7a7df0f784a157b278d
minor updates for v2.6

diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runAssembly.xml
--- a/runAssembly.xml	Thu Jul 14 22:14:07 2011 -0400
+++ b/runAssembly.xml	Wed Dec 21 19:42:53 2011 -0800
@@ -1,6 +1,6 @@
-<tool id="runAssembly" name="runAssembly" version="1.0.0" force_history_refresh='True'>
+<tool id="runAssembly" name="runAssembly" version="1.0.1" force_history_refresh="True">
 <description>De novo assembly of Roche/454 reads using Newbler</description>
-<command interpreter='perl'>runAssembly_wrapper.pl
+<command interpreter="perl">runAssembly_wrapper.pl
 $newbler_metrics.extra_files_path
 $newbler_metrics
 $read_status
@@ -17,11 +17,13 @@
 $scaffolds_fasta
 $scaffolds_qual
 $scaffolds_agp
+$contig_scaffolds_agp
 $tag_pair_align
 $trim_status
 $large_contigs_fasta
 $large_contigs_qual
-$newbler_exe -o $newbler_metrics.extra_files_path
+runAssembly
+-o $newbler_metrics.extra_files_path
 -cpu 8 
 $rip 
 -e $e 
@@ -63,137 +65,135 @@
 #end for
 </command>
 <inputs>
-    <!-- NEWBLER VERSION -->
-    <param name='newbler_exe' type='select' display='radio' label='Newbler version'>
-        <option value='/jgi/tools/454/rig-DataProcessing_2.3/bin/runAssembly'>2.3</option>
-        <option value='/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runAssembly'>2.4</option>
-        <option value='/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runAssembly' selected='true'>2.5</option>
-    </param>
-
     <!-- READSEQ INFILES -->
     <repeat name="sff_inputs" title="Unpaired Reads Sff Files">
         <param name="sff_input" type="data" format="sff" label="SE Sff file"/>
     </repeat>
-    <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">
-        <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>
+    <repeat name="sanger_inputs" title="Unpaired Reads Fasta/Fastq Files">
+        <param name="sanger_input" type="data" format="fasta,fastqsanger" label="SE Fasta/Fastq file"/>
     </repeat>
     <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">
         <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>
     </repeat>
-    <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">
-        <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>
+    <repeat name="sanger_paired_inputs" title="Paired Reads Fasta/Fastq Files">
+        <param name="sanger_paired_input" type="data" format="fasta,fastqsanger" label="PE Fasta/Fastq file"/>
     </repeat>
-    <param name='paired_reads' type='select' display='radio' label='[-paired_reads] If supplying paired reads (above), do you want paired-read info?'>
-        <option value='false'>no</option>
-        <option value='true'>[-paired_reads] yes</option>
+    <param name="paired_reads" type="select" display="radio" label="[-paired_reads] If supplying paired reads (above), do you want paired-read info?">
+        <option value="false">no</option>
+        <option value="true">[-paired_reads] yes</option>
     </param>
-    <param name='pair' type='select' display='radio' label='[-pair] Output pairwise overlaps'>
-        <option value=''>no</option>
-        <option value='-pair'>[-pair] yes</option>
+    <param name="pair" type="select" display="radio" label="[-pair] Output pairwise overlaps">
+        <option value="">no</option>
+        <option value="-pair">[-pair] yes</option>
     </param>
     
-    <param name='l' type="integer" value='500' label="[-l] This option sets the minimum length for a contig to appear in the 454LargeContigs.fna file"/>
+    <param name="l" type="integer" value="500" label="[-l] This option sets the minimum length for a contig to appear in the 454LargeContigs.fna file"/>
 
    <!-- OPTIONAL ARGUMENTS -->
-    <param name='mcf' type='data' format='tabular' optional='true' label='[-mcf] Specify non-default MID config file' />
-    <param name='fi' type='data' format='txt' optional='true' label='[-fi] Include filter file to be specified' />
-    <param name='fe' type='data' format='txt' optional='true' label='[-fe] Exclude filter file to be specified' />
-    <param name='vt' type='data' format='fasta' optional='true' label="[-vt] This option specifies a vector trimming database, or FASTA file of sequences to be used to trim the ends of input reads (for cloning vectors, primers, adapters or other end sequences)" />
-    <param name='vs' type='data' format='fasta' optional='true' label="[-vs] This option specifies a vector screening database, or FASTA file of sequences to be used to screen the input reads for contaminants.  Reads that completely align against the screening database are trimmed completely (so that it is not used in the computation), but otherwise the read trimpoints are not changed" />
+    <param name="mcf" type="data" format="tabular" optional="true" label="[-mcf] Specify non-default MID config file" />
+    <param name="fi" type="data" format="txt" optional="true" label="[-fi] Include filter file to be specified" />
+    <param name="fe" type="data" format="txt" optional="true" label="[-fe] Exclude filter file to be specified" />
+    <param name="vt" type="data" format="fasta" optional="true" label="[-vt] This option specifies a vector trimming database, or FASTA file of sequences to be used to trim the ends of input reads (for cloning vectors, primers, adapters or other end sequences)" />
+    <param name="vs" type="data" format="fasta" optional="true" label="[-vs] This option specifies a vector screening database, or FASTA file of sequences to be used to screen the input reads for contaminants.  Reads that completely align against the screening database are trimmed completely (so that it is not used in the computation), but otherwise the read trimpoints are not changed" />
         
     <!-- READ TRIMMING -->
-    <param name='minlen' type='integer' value='20' label='[-minlen] Minimum length of reads to use (15-45 allowed)'/>
-    <param name='notrim' type='boolean' truevalue='-notrim' falsevalue='' checked='false' label='[-notrim] Do not perform default quality and primer trimming of input reads'/>
-    <param name='tr' type='select' display='radio' label='[-tr] Output trimmed reads'>
-        <option value=''>no</option>
-        <option value='-tr'>[-tr] yes</option>
+    <param name="minlen" type="integer" value="20" label="[-minlen] Minimum length of reads to use (15-45 allowed)"/>
+    <param name="notrim" type="boolean" truevalue="-notrim" falsevalue="" checked="false" label="[-notrim] Do not perform default quality and primer trimming of input reads"/>
+    <param name="tr" type="select" display="radio" label="[-tr] Output trimmed reads">
+        <option value="">no</option>
+        <option value="-tr">[-tr] yes</option>
     </param>
-    <param name='nor' type='boolean' truevalue='-nor' falsevalue='' label='[-nor] Turn off the automatic rescore function for read quality scores'/>
-    <param name='ud' type='boolean' truevalue='-ud' falsevalue='' label='[-ud] Treat each read separately, with no grouping of duplicates'/>
+    <param name="nor" type="boolean" truevalue="-nor" falsevalue="" label="[-nor] Turn off the automatic rescore function for read quality scores"/>
+    <param name="ud" type="boolean" truevalue="-ud" falsevalue="" label="[-ud] Treat each read separately, with no grouping of duplicates"/>
 
     <!-- ALIGNMENT PARAMETERS -->
-    <param name='ss' type='integer' value='12' label='[-ss] Seed step parameter - The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection. Allow values: 1 or greater'/>
-    <param name='sl' type='integer' value='16' label='[-sl] Seed length parameter - The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the "k" value of the k-mer matching). Allowed values: 6-16'/>
-    <param name='sc' type='integer' value='1' label='[-sc] Seed count parameter - The number of seeds required in a window before an extension is made. Allowed values: 1 or greater'/>
-    <param name='ml' type="text" value='40' label="[-ml] Minimum overlap length - The minimum length of overlaps used for the pairwise alignment step. The value can either be a minimum length in bases or a percentage of read length. In the case of a percentage, simply include '%' immediately following the numeric value. Allowed values: 1 or greater"/>
-    <param name='mi' type="integer" value='90' label="[-mi] Minimum overlap identity - The percent identity of overlaps used for the pairwise alignment step. Allowed values: 0 or greater"/>
-    <param name='ais' type='integer' value='2' label='[-ais] Alignment identity score - When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Allowed values: 0 or greater'/>
+    <param name="ss" type="integer" value="12" label="[-ss] Seed step parameter - The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection. Allow values: 1 or greater"/>
+    <param name="sl" type="integer" value="16" label="[-sl] Seed length parameter - The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the 'k' value of the k-mer matching). Allowed values: 6-16"/>
+    <param name="sc" type="integer" value="1" label="[-sc] Seed count parameter - The number of seeds required in a window before an extension is made. Allowed values: 1 or greater"/>
+    <param name="ml" type="text" value="40" label="[-ml] Minimum overlap length - The minimum length of overlaps used for the pairwise alignment step. The value can either be a minimum length in bases or a percentage of read length. In the case of a percentage, simply include '%' immediately following the numeric value. Allowed values: 1 or greater"/>
+    <param name="mi" type="integer" value="90" label="[-mi] Minimum overlap identity - The percent identity of overlaps used for the pairwise alignment step. Allowed values: 0 or greater"/>
+    <param name="ais" type="integer" value="2" label="[-ais] Alignment identity score - When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Allowed values: 0 or greater"/>
 
     <!-- ASSEMBLY OPTIONS -->
-    <param name='e' type="integer" value='0' label="[-e] This option tells the assembler that the expected depth of the data is at a certain level.  The assembler has been optimized for datasets in the 10-50x oversampling size, and this option helps the assembler with datasets that have a higher oversampling level.  A value of 0 resets the assembler computation to use its default algorithms"/>
-    <param name='large' type='boolean' truevalue='-large' falsevalue='' checked='false' label='[-large] Check if large or complex genome'/>
+    <param name="e" type="integer" value="0" label="[-e] This option tells the assembler that the expected depth of the data is at a certain level.  The assembler has been optimized for datasets in the 10-50x oversampling size, and this option helps the assembler with datasets that have a higher oversampling level.  A value of 0 resets the assembler computation to use its default algorithms"/>
+    <param name="large" type="boolean" truevalue="-large" falsevalue="" checked="false" label="[-large] Check if large or complex genome"/>
+    <param name="scaffold" type="boolean" truevalue="-scaffold" falsevalue="" checked="true" label="[-scaffold] Output scaffolds"
+        help="Select this option to output scaffoldContigs to Fasta and Qual files. When selected, the contents of 454Scaffolds.txt will represent scaffoldContigs and gaps rather than the contigs found in the allContigs file. An additional file, 454ContigScaffolds.txt, will be produced that is identical to the 454Scaffolds.txt file produced without this option. The scaffoldContig names found in the 454Scaffolds.txt file represent the scaffoldContigs found in the 454ScaffoldContigs Fasta and Qual files." />
 
     <!-- OUTPUT OPTIONS -->
-    <param name='no' type='select' display='radio' label='[-no] Do complete assembly'>
-        <option value=''>do complete assembly</option>
-        <option value='-no'>[-no] do not assemble; do alignments only</option>
+    <param name="no" type="select" display="radio" label="[-no] Do complete assembly">
+        <option value="">do complete assembly</option>
+        <option value="-no">[-no] do not assemble; do alignments only</option>
     </param>
-    <param name='qo' type='boolean' truevalue='' falsevalue='-qo' checked='false' label='[-qo] Generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy'/>
-    <param name='a' type="integer" value='100' label="[-a] This option sets the minimum length for a contig to appear in the 454AllContigs.fna file."/>
-    <param name='rip' type='boolean' truevalue='' falsevalue='-rip' checked='false' label='[-rip] Output each read in only one contig'/>
-    <param name='info' type='select' display='radio' label='Output Alignment Info'>
-        <option value='-info'>[-info] yes</option>
-        <option value='-infoall'>[-infoall] yes, including 0-coverage positions</option>
+    <param name="qo" type="boolean" truevalue="" falsevalue="-qo" checked="false" label="[-qo] Generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy"/>
+    <param name="a" type="integer" value="100" label="[-a] This option sets the minimum length for a contig to appear in the 454AllContigs.fna file."/>
+    <param name="rip" type="boolean" truevalue="" falsevalue="-rip" checked="false" label="[-rip] Output each read in only one contig"/>
+    <param name="info" type="select" display="radio" label="Output Alignment Info">
+        <option value="-info">[-info] yes</option>
+        <option value="-infoall">[-infoall] yes, including 0-coverage positions</option>
     </param>
-    <param name='ace' type='select' display='radio' label='Produce Ace assembly file'>
-        <option value=''>no</option>
-        <option value='-ace'>[-ace] yes</option>
-        <option value='-ace -consed'>[-consed] yes, in consed dir</option>
+    <param name="ace" type="select" display="radio" label="Produce Ace assembly file">
+        <option value="">no</option>
+        <option value="-ace">[-ace] yes</option>
+        <option value="-ace -consed">[-consed] yes, in consed dir</option>
     </param>
 </inputs>
 
 <outputs>
-    <data name='newbler_metrics' format='txt' />
-    <data name='read_status' format='tabular' label='Read Status'/>
-    <data name='trimmed_reads_fasta' format='fasta' label='Trimmed Reads (Fasta)'>
-        <filter>tr == '-tr'</filter>
+    <data name="newbler_metrics" format="txt" />
+    <data name="read_status" format="tabular" label="${tool.name} on $on_string: Read Status"/>
+    <data name="trimmed_reads_fasta" format="fasta" label="${tool.name} on $on_string: Trimmed Reads (Fasta)">
+        <filter>tr == "-tr"</filter>
     </data>
-    <data name='trimmed_reads_qual' format='qual454' label='Trimmed Reads (Qual)'>
-        <filter>tr == '-tr'</filter>
+    <data name="trimmed_reads_qual" format="qual454" label="${tool.name} on $on_string: Trimmed Reads (Qual)">
+        <filter>tr == "-tr"</filter>
     </data>
-    <!-- the following produced only if no != '-no' -->
-    <data name='alignment_info' format='tabular' label='Alignment Info'>
-        <filter>no != '-no'</filter>
+    <!-- the following produced only if no != "-no" -->
+    <data name="alignment_info" format="tabular" label="${tool.name} on $on_string: Alignment Info">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='all_contigs_fasta' format='fasta' label='All Contigs (Fasta)'>
-        <filter>no != '-no'</filter>
+    <data name="all_contigs_fasta" format="fasta" label="${tool.name} on $on_string: All Contigs (Fasta)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='all_contigs_qual' format='qual454' label='All Contigs (Qual454)'>
-        <filter>no != '-no'</filter>
+    <data name="all_contigs_qual" format="qual454" label="${tool.name} on $on_string: All Contigs (Qual454)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='contigs_ace' format='ace' label='Contigs (Ace)'>
-        <filter>ace == '-ace' and no != '-no'</filter>
+    <data name="contigs_ace" format="ace" label="${tool.name} on $on_string: Contigs (Ace)">
+        <filter>ace == "-ace" and no != "-no"</filter>
     </data>
-    <data name='contigs_consed_ace' format='ace' label='Contigs (Consed/Ace)'>
-        <filter>ace == '-ace -consed' and no != '-no'</filter>
+    <data name="contigs_consed_ace" format="ace" label="${tool.name} on $on_string: Contigs (Consed/Ace)">
+        <filter>ace == "-ace -consed" and no != "-no"</filter>
     </data>
 
-    <data name='contig_graph' format='txt' label='Contig Graph'/>
-    <data name='large_contigs_fasta' format='fasta' label='Large Contigs (Fasta)'>
-        <filter>no != '-no'</filter>
+    <data name="contig_graph" format="txt" label="${tool.name} on $on_string: Contig Graph"/>
+    <data name="large_contigs_fasta" format="fasta" label="${tool.name} on $on_string: Large Contigs (Fasta)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='large_contigs_qual' format='qual454' label='Large Contigs (Qual454)'>
-        <filter>no != '-no'</filter>
+    <data name="large_contigs_qual" format="qual454" label="${tool.name} on $on_string: Large Contigs (Qual454)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='pair_align' format='txt' label='Pairwise Alignments'>
-        <filter>pair == '-pair' and no != '-no'</filter>
+    <data name="pair_align" format="txt" label="${tool.name} on $on_string: Pairwise Alignments">
+        <filter>pair == "-pair" and no != "-no"</filter>
     </data>
-    <data name='pair_status' format='tabular' label='Paired-End Read Status'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="pair_status" format="tabular" label="${tool.name} on $on_string: Paired-End Read Status">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_fasta' format='fasta' label='Scaffolds (Fasta)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="scaffolds_fasta" format="fasta" label="${tool.name} on $on_string: Scaffolds (Fasta)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_qual' format='qual454' label='Scaffolds (Qual454)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="scaffolds_qual" format="qual454" label="${tool.name} on $on_string: Scaffolds (Qual454)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_agp' format='tabular' label='Scaffolds (Agp)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Scaffolds (Agp)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='tag_pair_align' format='txt' label='Tag Pair Alignments'>
-        <filter>pair == '-pair' and paired_reads == 'true' and no != '-no'</filter>
+    <data name="contig_scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Contig Scaffolds(Agp)">
+        <filter>scaffold is True</filter>
     </data>
-    <data name='trim_status' format='tabular' label='Trim Status'/>
+    <data name="tag_pair_align" format="txt" label="${tool.name} on $on_string: Tag Pair Alignments">
+        <filter>pair == "-pair" and paired_reads == "true" and no != "-no"</filter>
+    </data>
+    <data name="trim_status" format="tabular" label="${tool.name} on $on_string: Trim Status"/>
 
 </outputs>
 <help>
diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runAssembly_cDNA.xml
--- a/runAssembly_cDNA.xml	Thu Jul 14 22:14:07 2011 -0400
+++ b/runAssembly_cDNA.xml	Wed Dec 21 19:42:53 2011 -0800
@@ -1,4 +1,4 @@
-<tool id="runAssembly_cDNA" name="runAssembly cDNA" version="1.0.0" force_history_refresh='True'>
+<tool id="runAssembly_cDNA" name="runAssembly cDNA" version="1.0.1" force_history_refresh='True'>
 <description>De novo assembly of Roche/454 cDNA reads using Newbler</description>
 <command interpreter='perl'>runAssembly_cDNA_wrapper.pl
 $newbler_metrics.extra_files_path
@@ -17,6 +17,7 @@
 $scaffolds_fasta
 $scaffolds_qual
 $scaffolds_agp
+$contig_scaffolds_agp
 $tag_pair_align
 $trim_status
 $isotigs_ace
@@ -24,7 +25,8 @@
 $isotigs_qual
 $isotigs_agp
 $isotigs_layout
-$newbler_exe -o $newbler_metrics.extra_files_path
+runAssembly
+-o $newbler_metrics.extra_files_path
 -cpu 8 
 $rip 
 -e $e 
@@ -70,149 +72,147 @@
 #end for
 </command>
 <inputs>
-    <!-- NEWBLER VERSION -->
-    <param name='newbler_exe' type='select' display='radio' label='Newbler version'>
-        <option value='/jgi/tools/454/rig-DataProcessing_2.3/bin/runAssembly'>2.3</option>
-        <option value='/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runAssembly'>2.4</option>
-        <option value='/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runAssembly' selected='true'>2.5</option>
-    </param>
-
     <!-- READSEQ INFILES -->
     <repeat name="sff_inputs" title="Unpaired Reads Sff Files">
         <param name="sff_input" type="data" format="sff" label="SE Sff file"/>
     </repeat>
-    <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">
-        <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>
+    <repeat name="sanger_inputs" title="Unpaired Reads Fasta/Fastq Files">
+        <param name="sanger_input" type="data" format="fasta,fastqsanger" label="SE Fasta/Fastq file"/>
     </repeat>
     <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">
         <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>
     </repeat>
-    <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">
-        <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>
+    <repeat name="sanger_paired_inputs" title="Paired Reads Fasta/Fastq Files">
+        <param name="sanger_paired_input" type="data" format="fasta,fastqsanger" label="PE Fasta/Fastq file"/>
     </repeat>
-    <param name='paired_reads' type='select' display='radio' label='[-paired_reads] If supplying paired reads (above), do you want paired-read info?'>
-        <option value='false'>no</option>
-        <option value='true'>[-paired_reads] yes</option>
+    <param name="paired_reads" type="select" display="radio" label="[-paired_reads] If supplying paired reads (above), do you want paired-read info?">
+        <option value="false">no</option>
+        <option value="true">[-paired_reads] yes</option>
     </param>
-    <param name='pair' type='select' display='radio' label='[-pair] Output pairwise overlaps'>
-        <option value=''>no</option>
-        <option value='-pair'>[-pair] yes</option>
+    <param name="pair" type="select" display="radio" label="[-pair] Output pairwise overlaps">
+        <option value="">no</option>
+        <option value="-pair">[-pair] yes</option>
     </param>
     
-    <param name='it' type='integer' value='100' label='[-it] Specify the maximum number of isotigs in an isogroup. Maximum is 10,000.'/>
-    <param name='ig' type='integer' value='500' label='[-ig] Specify the maximum number of contigs in an isogroup.'/>
-    <param name='icc' type='integer' value='100' label='[-icc] Specify the maximum number of contigs in an isotig. Maximum is 200 and corresponds to the recursion depth during graph traversal'/>
-    <param name='icl' type='integer' value='3' label='[-icl] Specify the minimum length a contig must be to be part of an isotig. Minimum is 3bp.'/>
+    <param name="it" type="integer" value="100" label="[-it] Specify the maximum number of isotigs in an isogroup. Maximum is 10,000."/>
+    <param name="ig" type="integer" value="500" label="[-ig] Specify the maximum number of contigs in an isogroup."/>
+    <param name="icc" type="integer" value="100" label="[-icc] Specify the maximum number of contigs in an isotig. Maximum is 200 and corresponds to the recursion depth during graph traversal"/>
+    <param name="icl" type="integer" value="3" label="[-icl] Specify the minimum length a contig must be to be part of an isotig. Minimum is 3bp."/>
 
    <!-- OPTIONAL ARGUMENTS -->
-    <param name='mcf' type='data' format='tabular' optional='true' label='[-mcf] Specify non-default MID config file' />
-    <param name='fi' type='data' format='txt' optional='true' label='[-fi] Include filter file to be specified' />
-    <param name='fe' type='data' format='txt' optional='true' label='[-fe] Exclude filter file to be specified' />
-    <param name='vt' type='data' format='fasta' optional='true' label="[-vt] This option specifies a vector trimming database, or FASTA file of sequences to be used to trim the ends of input reads (for cloning vectors, primers, adapters or other end sequences)" />
-    <param name='vs' type='data' format='fasta' optional='true' label="[-vs] This option specifies a vector screening database, or FASTA file of sequences to be used to screen the input reads for contaminants.  Reads that completely align against the screening database are trimmed completely (so that it is not used in the computation), but otherwise the read trimpoints are not changed" />
+    <param name="mcf" type="data" format="tabular" optional="true" label="[-mcf] Specify non-default MID config file" />
+    <param name="fi" type="data" format="txt" optional="true" label="[-fi] Include filter file to be specified" />
+    <param name="fe" type="data" format="txt" optional="true" label="[-fe] Exclude filter file to be specified" />
+    <param name="vt" type="data" format="fasta" optional="true" label="[-vt] This option specifies a vector trimming database, or FASTA file of sequences to be used to trim the ends of input reads (for cloning vectors, primers, adapters or other end sequences)" />
+    <param name="vs" type="data" format="fasta" optional="true" label="[-vs] This option specifies a vector screening database, or FASTA file of sequences to be used to screen the input reads for contaminants.  Reads that completely align against the screening database are trimmed completely (so that it is not used in the computation), but otherwise the read trimpoints are not changed" />
  
     <!-- READ TRIMMING -->
-    <param name='minlen' type='integer' value='20' label='[-minlen] Minimum length of reads to use (15-45 allowed)'/>
-    <param name='notrim' type='boolean' truevalue='-notrim' falsevalue='' checked='false' label='[-notrim] Do not perform default quality and primer trimming of input reads'/>
-    <param name='tr' type='select' display='radio' label='[-tr] Output trimmed reads'>
-        <option value=''>no</option>
-        <option value='-tr'>[-tr] yes</option>
+    <param name="minlen" type="integer" value="20" label="[-minlen] Minimum length of reads to use (15-45 allowed)"/>
+    <param name="notrim" type="boolean" truevalue="-notrim" falsevalue="" checked="false" label="[-notrim] Do not perform default quality and primer trimming of input reads"/>
+    <param name="tr" type="select" display="radio" label="[-tr] Output trimmed reads">
+        <option value="">no</option>
+        <option value="-tr">[-tr] yes</option>
     </param>
-    <param name='nor' type='boolean' truevalue='-nor' falsevalue='' label='[-nor] Turn off the automatic rescore function for read quality scores'/>
-    <param name='ud' type='boolean' truevalue='-ud' falsevalue='' label='[-ud] Treat each read separately, with no grouping of duplicates'/>
+    <param name="nor" type="boolean" truevalue="-nor" falsevalue="" label="[-nor] Turn off the automatic rescore function for read quality scores"/>
+    <param name="ud" type="boolean" truevalue="-ud" falsevalue="" label="[-ud] Treat each read separately, with no grouping of duplicates"/>
 
     <!-- ALIGNMENT PARAMETERS -->
-    <param name='ss' type='integer' value='12' label='[-ss] Seed step parameter - The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection. Allow values: 1 or greater'/>
-    <param name='sl' type='integer' value='16' label='[-sl] Seed length parameter - The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the "k" value of the k-mer matching). Allowed values: 6-16'/>
-    <param name='sc' type='integer' value='1' label='[-sc] Seed count parameter - The number of seeds required in a window before an extension is made. Allowed values: 1 or greater'/>
-    <param name='ml' type="text" value='40' label="[-ml] Minimum overlap length - The minimum length of overlaps used for the pairwise alignment step. The value can either be a minimum length in bases or a percentage of read length. In the case of a percentage, simply include '%' immediately following the numeric value. Allowed values: 1 or greater"/>
-    <param name='mi' type="integer" value='90' label="[-mi] Minimum overlap identity - The percent identity of overlaps used for the pairwise alignment step. Allowed values: 0 or greater"/>
-    <param name='ais' type='integer' value='2' label='[-ais] Alignment identity score - When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Allowed values: 0 or greater'/>
+    <param name="ss" type="integer" value="12" label="[-ss] Seed step parameter - The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection. Allow values: 1 or greater"/>
+    <param name="sl" type="integer" value="16" label="[-sl] Seed length parameter - The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the 'k' value of the k-mer matching). Allowed values: 6-16"/>
+    <param name="sc" type="integer" value="1" label="[-sc] Seed count parameter - The number of seeds required in a window before an extension is made. Allowed values: 1 or greater"/>
+    <param name="ml" type="text" value="40" label="[-ml] Minimum overlap length - The minimum length of overlaps used for the pairwise alignment step. The value can either be a minimum length in bases or a percentage of read length. In the case of a percentage, simply include '%' immediately following the numeric value. Allowed values: 1 or greater"/>
+    <param name="mi" type="integer" value="90" label="[-mi] Minimum overlap identity - The percent identity of overlaps used for the pairwise alignment step. Allowed values: 0 or greater"/>
+    <param name="ais" type="integer" value="2" label="[-ais] Alignment identity score - When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Allowed values: 0 or greater"/>
 
     <!-- ASSEMBLY OPTIONS -->
-    <param name='e' type="integer" value='0' label="[-e] This option tells the assembler that the expected depth of the data is at a certain level.  The assembler has been optimized for datasets in the 10-50x oversampling size, and this option helps the assembler with datasets that have a higher oversampling level.  A value of 0 resets the assembler computation to use its default algorithms"/>
-    <param name='large' type='boolean' truevalue='-large' falsevalue='' checked='false' label='[-large] Check if large or complex genome'/>
+    <param name="e" type="integer" value="0" label="[-e] This option tells the assembler that the expected depth of the data is at a certain level.  The assembler has been optimized for datasets in the 10-50x oversampling size, and this option helps the assembler with datasets that have a higher oversampling level.  A value of 0 resets the assembler computation to use its default algorithms"/>
+    <param name="large" type="boolean" truevalue="-large" falsevalue="" checked="false" label="[-large] Check if large or complex genome"/>
+    <param name="scaffold" type="boolean" truevalue="-scaffold" falsevalue="" checked="true" label="[-scaffold] Output scaffolds"
+        help="Select this option to output scaffoldContigs to Fasta and Qual files. When selected, the contents of 454Scaffolds.txt will represent scaffoldContigs and gaps rather than the contigs found in the allContigs file. An additional file, 454ContigScaffolds.txt, will be produced that is identical to the 454Scaffolds.txt file produced without this option. The scaffoldContig names found in the 454Scaffolds.txt file represent the scaffoldContigs found in the 454ScaffoldContigs Fasta and Qual files." />
 
     <!-- OUTPUT OPTIONS -->
-    <param name='no' type='select' display='radio' label='[-no] Do complete assembly'>
-        <option value=''>do complete assembly</option>
-        <option value='-no'>[-no] do not assemble; do alignments only</option>
+    <param name="no" type="select" display="radio" label="[-no] Do complete assembly">
+        <option value="">do complete assembly</option>
+        <option value="-no">[-no] do not assemble; do alignments only</option>
     </param>
-    <param name='qo' type='boolean' truevalue='' falsevalue='-qo' checked='false' label='[-qo] Generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy'/>
-    <param name='a' type="integer" value='100' label="[-a] This option sets the minimum length for a contig to appear in the 454AllContigs.fna file."/>
-    <param name='rip' type='boolean' truevalue='' falsevalue='-rip' checked='false' label='[-rip] Output each read in only one contig'/>
-    <param name='info' type='select' display='radio' label='Output Alignment Info'>
-        <option value='-info'>[-info] yes</option>
-        <option value='-infoall'>[-infoall] yes, including 0-coverage positions</option>
+    <param name="qo" type="boolean" truevalue="" falsevalue="-qo" checked="false" label="[-qo] Generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy"/>
+    <param name="a" type="integer" value="100" label="[-a] This option sets the minimum length for a contig to appear in the 454AllContigs.fna file."/>
+    <param name="rip" type="boolean" truevalue="" falsevalue="-rip" checked="false" label="[-rip] Output each read in only one contig"/>
+    <param name="info" type="select" display="radio" label="Output Alignment Info">
+        <option value="-info">[-info] yes</option>
+        <option value="-infoall">[-infoall] yes, including 0-coverage positions</option>
     </param>
-    <param name='ace' type='select' display='radio' label='Produce Ace assembly file'>
-        <option value=''>no</option>
-        <option value='-ace'>[-ace] yes</option>
-        <option value='-ace -consed'>[-consed] yes, in consed dir</option>
+    <param name="ace" type="select" display="radio" label="Produce Ace assembly file">
+        <option value="">no</option>
+        <option value="-ace">[-ace] yes</option>
+        <option value="-ace -consed">[-consed] yes, in consed dir</option>
     </param>
 </inputs>
 
 <outputs>
-    <data name='newbler_metrics' format='txt' />
-    <data name='read_status' format='tabular' label='Read Status'/>
-    <data name='trimmed_reads_fasta' format='fasta' label='Trimmed Reads (Fasta)'>
-        <filter>tr == '-tr'</filter>
+    <data name="newbler_metrics" format="txt" />
+    <data name="read_status" format="tabular" label="${tool.name} on $on_string: Read Status"/>
+    <data name="trimmed_reads_fasta" format="fasta" label="${tool.name} on $on_string: Trimmed Reads (Fasta)">
+        <filter>tr == "-tr"</filter>
     </data>
-    <data name='trimmed_reads_qual' format='qual454' label='Trimmed Reads (Qual)'>
-        <filter>tr == '-tr'</filter>
+    <data name="trimmed_reads_qual" format="qual454" label="${tool.name} on $on_string: Trimmed Reads (Qual)">
+        <filter>tr == "-tr"</filter>
     </data>
-    <!-- the following produced only if no != '-no' -->
-    <data name='alignment_info' format='tabular' label='Alignment Info'>
-        <filter>no != '-no'</filter>
+    <!-- the following produced only if no != "-no" -->
+    <data name="alignment_info" format="tabular" label="${tool.name} on $on_string: Alignment Info">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='all_contigs_fasta' format='fasta' label='All Contigs (Fasta)'>
-        <filter>no != '-no'</filter>
+    <data name="all_contigs_fasta" format="fasta" label="${tool.name} on $on_string: All Contigs (Fasta)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='all_contigs_qual' format='qual454' label='All Contigs (Qual454)'>
-        <filter>no != '-no'</filter>
+    <data name="all_contigs_qual" format="qual454" label="${tool.name} on $on_string: All Contigs (Qual454)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='contigs_ace' format='ace' label='Contigs (Ace)'>
-        <filter>ace == '-ace' and no != '-no'</filter>
+    <data name="contigs_ace" format="ace" label="${tool.name} on $on_string: Contigs (Ace)">
+        <filter>ace == "-ace" and no != "-no"</filter>
     </data>
-    <data name='contigs_consed_ace' format='ace' label='Contigs (Consed/Ace)'>
-        <filter>ace == '-ace -consed' and no != '-no'</filter>
+    <data name="contigs_consed_ace" format="ace" label="${tool.name} on $on_string: Contigs (Consed/Ace)">
+        <filter>ace == "-ace -consed" and no != "-no"</filter>
     </data>
 
-    <data name='contig_graph' format='txt' label='Contig Graph'/>
-    <data name='pair_align' format='txt' label='Pairwise Alignments'>
-        <filter>pair == '-pair' and no != '-no'</filter>
+    <data name="contig_graph" format="txt" label="${tool.name} on $on_string: Contig Graph"/>
+    <data name="pair_align" format="txt" label="${tool.name} on $on_string: Pairwise Alignments">
+        <filter>pair == "-pair" and no != "-no"</filter>
     </data>
-    <data name='pair_status' format='tabular' label='Paired-End Read Status'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="pair_status" format="tabular" label="${tool.name} on $on_string: Paired-End Read Status">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_fasta' format='fasta' label='Scaffolds (Fasta)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="scaffolds_fasta" format="fasta" label="${tool.name} on $on_string: Scaffolds (Fasta)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
+    </data>
+    <data name="scaffolds_qual" format="qual454" label="${tool.name} on $on_string: Scaffolds (Qual454)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_qual' format='qual454' label='Scaffolds (Qual454)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Scaffolds (Agp)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_agp' format='tabular' label='Scaffolds (Agp)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="contig_scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Contig Scaffolds(Agp)">
+        <filter>scaffold is True</filter>
     </data>
-    <data name='tag_pair_align' format='txt' label='Tag Pair Alignments'>
-        <filter>pair == '-pair' and paired_reads == 'true' and no != '-no'</filter>
+    <data name="tag_pair_align" format="txt" label="${tool.name} on $on_string: Tag Pair Alignments">
+        <filter>pair == "-pair" and paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='trim_status' format='tabular' label='Trim Status'/>
+    <data name="trim_status" format="tabular" label="${tool.name} on $on_string: Trim Status"/>
 
-    <data name='isotigs_ace' format='ace' label='Isotigs (Ace)'>
-        <filter>ace != '' and no != '-no'</filter>
+    <data name="isotigs_ace" format="ace" label="${tool.name} on $on_string: Isotigs (Ace)">
+        <filter>ace != "" and no != "-no"</filter>
     </data>
-    <data name='isotigs_fasta' format='fasta' label='Isotigs (Fasta)'>
-        <filter>no != '-no'</filter>
+    <data name="isotigs_fasta" format="fasta" label="${tool.name} on $on_string: Isotigs (Fasta)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='isotigs_qual' format='qual454' label='Isotigs (Qual454)'>
-        <filter>no != '-no'</filter>
+    <data name="isotigs_qual" format="qual454" label="${tool.name} on $on_string: Isotigs (Qual454)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='isotigs_agp' format='tabular' label='Isotigs (Agp)'>
-        <filter>no != '-no'</filter>
+    <data name="isotigs_agp" format="tabular" label="${tool.name} on $on_string: Isotigs (Agp)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='isotigs_layout' format='txt' label='Isotig Layout'>
-        <filter>no != '-no'</filter>
+    <data name="isotigs_layout" format="txt" label="${tool.name} on $on_string: Isotig Layout">
+        <filter>no != "-no"</filter>
     </data>
 
 </outputs>
diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runAssembly_cDNA_wrapper.pl
--- a/runAssembly_cDNA_wrapper.pl	Thu Jul 14 22:14:07 2011 -0400
+++ b/runAssembly_cDNA_wrapper.pl	Wed Dec 21 19:42:53 2011 -0800
@@ -22,6 +22,7 @@
 my $scaffolds_fasta=shift @ARGV;
 my $scaffolds_qual=shift @ARGV;
 my $scaffolds_agp=shift @ARGV;
+my $contig_scaffolds_agp=shift @ARGV;
 my $tag_pair_align=shift @ARGV;
 my $trim_status=shift @ARGV;
 my $isotigs_ace=shift @ARGV;
@@ -35,9 +36,8 @@
 my @cmd=removeUnusedOptions(@ARGV);
 
 # RUN COMMAND
-# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
 my $stderr;
-eval { $stderr=`@cmd 2>&1`; };
+eval { $stderr=`runAssembly @cmd 2>&1`; };
 if ( $@ ) {
     print STDERR "Newbler ERROR: $stderr\n";
     `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
@@ -59,6 +59,7 @@
 get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta);
 get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual);
 get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp);
+get_outfile("$outdir/454ContigScaffolds.txt", $contig_scaffolds_agp);
 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
 get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);
diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runAssembly_wrapper.pl
--- a/runAssembly_wrapper.pl	Thu Jul 14 22:14:07 2011 -0400
+++ b/runAssembly_wrapper.pl	Wed Dec 21 19:42:53 2011 -0800
@@ -22,6 +22,7 @@
 my $scaffolds_fasta=shift @ARGV;
 my $scaffolds_qual=shift @ARGV;
 my $scaffolds_agp=shift @ARGV;
+my $contig_scaffolds_agp=shift @ARGV;
 my $tag_pair_align=shift @ARGV;
 my $trim_status=shift @ARGV;
 my $large_contigs_fasta=shift @ARGV;
@@ -32,9 +33,8 @@
 my @cmd=removeUnusedOptions(@ARGV);
 
 # RUN COMMAND
-# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
 my $stderr;
-eval { $stderr=`@cmd 2>&1`; };
+eval { $stderr=`runAssembly @cmd 2>&1`; };
 if ( $@ ) {
     print STDERR "Newbler ERROR: $stderr\n";
     `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
@@ -56,6 +56,7 @@
 get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta);
 get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual);
 get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp);
+get_outfile("$outdir/454ContigScaffolds.txt", $contig_scaffolds_agp);
 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
 get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta);
diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runMapping.xml
--- a/runMapping.xml	Thu Jul 14 22:14:07 2011 -0400
+++ b/runMapping.xml	Wed Dec 21 19:42:53 2011 -0800
@@ -1,4 +1,4 @@
-<tool id="runMapping" name="runMapping" version="1.0.0">
+<tool id="runMapping" name="runMapping" version="1.0.1">
 <description>Map Roche/454 reads to a reference using Newbler</description>
 <command interpreter='perl'>runMapping_wrapper.pl
 $newbler_metrics.extra_files_path
@@ -19,10 +19,12 @@
 $trimmed_reads_fasta
 $trimmed_reads_qual
 $contigs_ace
+$contigs_bam
 $large_contigs_fasta
 $large_contigs_qual
 $gene_status
-$newbler_exe -o $newbler_metrics.extra_files_path
+runAssembly
+-o $newbler_metrics.extra_files_path
 -cpu 8 
 -a $a
 -e $e 
@@ -34,6 +36,7 @@
 $notrim 
 $tr 
 $ace 
+$bam
 $no 
 $qo 
 $nor 
@@ -70,155 +73,152 @@
 #end for
 </command>
 <inputs>
-    <!-- NEWBLER VERSION -->
-    <param name='newbler_exe' type='select' display='radio' label='Newbler version'>
-        <option value='/jgi/tools/454/rig-DataProcessing_2.3/bin/runMapping'>2.3</option>
-        <option value='/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runMapping'>2.4</option>
-        <option value='/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runMapping' selected='true'>2.5</option>
-    </param>
-
     <!-- READSEQ INFILES -->
     <repeat name="sff_inputs" title="Unpaired Reads Sff Files">
         <param name="sff_input" type="data" format="sff" label="SE Sff file"/>
     </repeat>
-    <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">
-        <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>
+    <repeat name="sanger_inputs" title="Unpaired Reads Fasta/Fastq Files">
+        <param name="sanger_input" type="data" format="fasta,fastqsanger" label="SE Fasta/Fastq file"/>
     </repeat>
     <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">
         <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>
     </repeat>
-    <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">
-        <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>
+    <repeat name="sanger_paired_inputs" title="Paired Reads Fasta/Fastq Files">
+        <param name="sanger_paired_input" type="data" format="fasta,fastqsanger" label="PE Fasta/Fastq file"/>
     </repeat>
-    <param name='paired_reads' type='select' display='radio' label='[-paired_reads] If supplying paired reads (above), do you want paired-read info?'>
-        <option value='false'>no</option>
-        <option value='true'>[-paired_reads] yes</option>
+    <param name="paired_reads" type="select" display="radio" label="[-paired_reads] If supplying paired reads (above), do you want paired-read info?">
+        <option value="false">no</option>
+        <option value="true">[-paired_reads] yes</option>
     </param>
-    <param name='pair' type='select' display='radio' label='[-pair] Output pairwise overlaps'>
-        <option value=''>no</option>
-        <option value='-pair'>[-pair] yes</option>
+    <param name="pair" type="select" display="radio" label="[-pair] Output pairwise overlaps">
+        <option value="">no</option>
+        <option value="-pair">[-pair] yes</option>
     </param>
  
     <!-- SOURCE DNA TYPE -->
-    <param name='l' type="integer" value='500' label="[-l] This option sets the minimum length for a contig to appear in the 454LargeContigs.fna file"/>
+    <param name="l" type="integer" value="500" label="[-l] This option sets the minimum length for a contig to appear in the 454LargeContigs.fna file"/>
 
     <!-- INPUTS SPECIFIC TO MAPPING -->
-    <repeat name='ref_inputs' title='Reference Sequence'>
-        <param name='ref_input' type='data' format='fasta' label='Fasta file'/>
+    <repeat name="ref_inputs" title="Reference Sequence">
+        <param name="ref_input" type="data" format="fasta" label="Fasta file"/>
     </repeat>
-    <param name='ref_type' type='select' display='radio' label='Reference type'>
-        <option value='-gref'>[-gref] Genomic reference sequence</option>
-        <option value='-cref'>[-cref] cDNA reference sequence</option>
+    <param name="ref_type" type="select" display="radio" label="Reference type">
+        <option value="-gref">[-gref] Genomic reference sequence</option>
+        <option value="-cref">[-cref] cDNA reference sequence</option>
     </param>
-    <param name='rst' type='integer' value='12' label='[-rst] Repeat score threshold parameter. Allowed values: 0 or greater'/>
-    <param name='hsl' type='integer' value='70' label='[-hsl] Hit-per-seed limit parameter'/>
-    <param name='srv' type='boolean' truevalue='-srv' falsevalue='' checked='false' label='[-srv] Single read variant output'/>
+    <param name="rst" type="integer" value="12" label="[-rst] Repeat score threshold parameter. Allowed values: 0 or greater"/>
+    <param name="hsl" type="integer" value="70" label="[-hsl] Hit-per-seed limit parameter"/>
+    <param name="srv" type="boolean" truevalue="-srv" falsevalue="" checked="false" label="[-srv] Single read variant output"/>
 
    <!-- OPTIONAL ARGUMENTS -->
    <!-- NYI
-    <param name='accno' type='data' format='tabular' optional='true' label='[-accno] Specify annotation data. Required only if reference sequence headers do not contain gene=NAME pairs' />
-    <param name='annot' type='data' format='tabular' optional='true' label='[-annot] Supply gene, transcript, and protein information' />
+    <param name="accno" type="data" format="tabular" optional="true" label="[-accno] Specify annotation data. Required only if reference sequence headers do not contain gene=NAME pairs" />
+    <param name="annot" type="data" format="tabular" optional="true" label="[-annot] Supply gene, transcript, and protein information" />
     -->
-    <param name='mcf' type='data' format='tabular' optional='true' label='[-mcf] Specify non-default MID config file' />
-    <param name='fi' type='data' format='txt' optional='true' label='[-fi] Include filter file to be specified' />
-    <param name='fe' type='data' format='txt' optional='true' label='[-fe] Exclude filter file to be specified' />
-    <param name='vt' type='data' format='fasta' optional='true' label="[-vt] This option specifies a vector trimming database, or FASTA file of sequences to be used to trim the ends of input reads (for cloning vectors, primers, adapters or other end sequences)" />
-    <param name='vs' type='data' format='fasta' optional='true' label="[-vs] This option specifies a vector screening database, or FASTA file of sequences to be used to screen the input reads for contaminants.  Reads that completely align against the screening database are trimmed completely (so that it is not used in the computation), but otherwise the read trimpoints are not changed" />
+    <param name="mcf" type="data" format="tabular" optional="true" label="[-mcf] Specify non-default MID config file" />
+    <param name="fi" type="data" format="txt" optional="true" label="[-fi] Include filter file to be specified" />
+    <param name="fe" type="data" format="txt" optional="true" label="[-fe] Exclude filter file to be specified" />
+    <param name="vt" type="data" format="fasta" optional="true" label="[-vt] This option specifies a vector trimming database, or FASTA file of sequences to be used to trim the ends of input reads (for cloning vectors, primers, adapters or other end sequences)" />
+    <param name="vs" type="data" format="fasta" optional="true" label="[-vs] This option specifies a vector screening database, or FASTA file of sequences to be used to screen the input reads for contaminants.  Reads that completely align against the screening database are trimmed completely (so that it is not used in the computation), but otherwise the read trimpoints are not changed" />
  
 
     <!-- READ TRIMMING -->
-    <param name='minlen' type='integer' value='20' label='[-minlen] Minimum length of reads to use (15-45 allowed)'/>
-    <param name='notrim' type='boolean' truevalue='-notrim' falsevalue='' checked='false' label='[-notrim] Do not perform default quality and primer trimming of input reads'/>
-    <param name='tr' type='select' display='radio' label='[-tr] Output trimmed reads'>
-        <option value=''>no</option>
-        <option value='-tr'>[-tr] yes</option>
+    <param name="minlen" type="integer" value="20" label="[-minlen] Minimum length of reads to use (15-45 allowed)"/>
+    <param name="notrim" type="boolean" truevalue="-notrim" falsevalue="" checked="false" label="[-notrim] Do not perform default quality and primer trimming of input reads"/>
+    <param name="tr" type="select" display="radio" label="[-tr] Output trimmed reads">
+        <option value="">no</option>
+        <option value="-tr">[-tr] yes</option>
     </param>
-    <param name='nor' type='boolean' truevalue='-nor' falsevalue='' label='[-nor] Turn off the automatic rescore function for read quality scores'/>
-    <param name='ud' type='boolean' truevalue='-ud' falsevalue='' label='[-ud] Treat each read separately, with no grouping of duplicates'/>
+    <param name="nor" type="boolean" truevalue="-nor" falsevalue="" label="[-nor] Turn off the automatic rescore function for read quality scores"/>
+    <param name="ud" type="boolean" truevalue="-ud" falsevalue="" label="[-ud] Treat each read separately, with no grouping of duplicates"/>
 
     <!-- ALIGNMENT PARAMETERS -->
-    <param name='ss' type='integer' value='12' label='[-ss] Seed step parameter - The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection. Allow values: 1 or greater'/>
-    <param name='sl' type='integer' value='16' label='[-sl] Seed length parameter - The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the "k" value of the k-mer matching). Allowed values: 6-16'/>
-    <param name='sc' type='integer' value='1' label='[-sc] Seed count parameter - The number of seeds required in a window before an extension is made. Allowed values: 1 or greater'/>
-    <param name='ml' type="text" value='40' label="[-ml] Minimum overlap length - The minimum length of overlaps used for the pairwise alignment step. The value can either be a minimum length in bases or a percentage of read length. In the case of a percentage, simply include '%' immediately following the numeric value. Allowed values: 1 or greater"/>
-    <param name='mi' type="integer" value='90' label="[-mi] Minimum overlap identity - The percent identity of overlaps used for the pairwise alignment step. Allowed values: 0 or greater"/>
-    <param name='ais' type='integer' value='2' label='[-ais] Alignment identity score - When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Allowed values: 0 or greater'/>
+    <param name="ss" type="integer" value="12" label="[-ss] Seed step parameter - The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection. Allow values: 1 or greater"/>
+    <param name="sl" type="integer" value="16" label="[-sl] Seed length parameter - The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the 'k' value of the k-mer matching). Allowed values: 6-16"/>
+    <param name="sc" type="integer" value="1" label="[-sc] Seed count parameter - The number of seeds required in a window before an extension is made. Allowed values: 1 or greater"/>
+    <param name="ml" type="text" value="40" label="[-ml] Minimum overlap length - The minimum length of overlaps used for the pairwise alignment step. The value can either be a minimum length in bases or a percentage of read length. In the case of a percentage, simply include '%' immediately following the numeric value. Allowed values: 1 or greater"/>
+    <param name="mi" type="integer" value="90" label="[-mi] Minimum overlap identity - The percent identity of overlaps used for the pairwise alignment step. Allowed values: 0 or greater"/>
+    <param name="ais" type="integer" value="2" label="[-ais] Alignment identity score - When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Allowed values: 0 or greater"/>
 
     <!-- ASSEMBLY OPTIONS -->
-    <param name='e' type="integer" value='0' label="[-e] This option tells the assembler that the expected depth of the data is at a certain level.  The assembler has been optimized for datasets in the 10-50x oversampling size, and this option helps the assembler with datasets that have a higher oversampling level.  A value of 0 resets the assembler computation to use its default algorithms"/>
+    <param name="e" type="integer" value="0" label="[-e] This option tells the assembler that the expected depth of the data is at a certain level.  The assembler has been optimized for datasets in the 10-50x oversampling size, and this option helps the assembler with datasets that have a higher oversampling level.  A value of 0 resets the assembler computation to use its default algorithms"/>
 
     <!-- OUTPUT OPTIONS -->
-    <param name='no' type='select' display='radio' label='[-no] Do complete assembly'>
-        <option value=''>do complete assembly</option>
-        <option value='-no'>[-no] do not assemble; do alignments only</option>
+    <param name="no" type="select" display="radio" label="[-no] Do complete assembly">
+        <option value="">do complete assembly</option>
+        <option value="-no">[-no] do not assemble; do alignments only</option>
     </param>
-    <param name='qo' type='boolean' truevalue='' falsevalue='-qo' checked='false' label='[-qo] Generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy'/>
-    <param name='a' type="integer" value='100' label="[-a] This option sets the minimum length for a contig to appear in the 454AllContigs.fna file."/>
-    <param name='info' type='select' display='radio' label='Output Alignment Info'>
-        <option value='-info'>[-info] yes</option>
-        <option value='-infoall'>[-infoall] yes, including 0-coverage positions</option>
+    <param name="qo" type="boolean" truevalue="" falsevalue="-qo" checked="false" label="[-qo] Generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy"/>
+    <param name="a" type="integer" value="100" label="[-a] This option sets the minimum length for a contig to appear in the 454AllContigs.fna file."/>
+    <param name="info" type="select" display="radio" label="Output Alignment Info">
+        <option value="-info">[-info] yes</option>
+        <option value="-infoall">[-infoall] yes, including 0-coverage positions</option>
     </param>
-    <param name='ace' type='select' display='radio' label='Produce Ace assembly file'>
-        <option value=''>no</option>
-        <option value='-ace'>[-ace] yes</option>
+    <param name="ace" type="select" display="radio" label="Produce Ace assembly file">
+        <option value="">no</option>
+        <option value="-ace">[-ace] yes</option>
     </param>
+    <param name="bam" type="boolean" truevalue="-bam" falsevalue="-nobam" checked="true" label="[-bam] Produce Bam alignments file" />
 </inputs>
 
 <outputs>
     <!-- the following are common to runMapping and runAssembly -->
-    <data name='newbler_metrics' format='txt' />
-    <data name='read_status' format='tabular' label='Read Status'/>
-    <data name='trimmed_reads_fasta' format='fasta' label='Trimmed Reads (Fasta)'>
-        <filter>tr == '-tr'</filter>
+    <data name="newbler_metrics" format="txt" />
+    <data name="read_status" format="tabular" label="${tool.name} on $on_string: Read Status"/>
+    <data name="trimmed_reads_fasta" format="fasta" label="${tool.name} on $on_string: Trimmed Reads (Fasta)">
+        <filter>tr == "-tr"</filter>
     </data>
-    <data name='trimmed_reads_qual' format='qual454' label='Trimmed Reads (Qual)'>
-        <filter>tr == '-tr'</filter>
+    <data name="trimmed_reads_qual" format="qual454" label="${tool.name} on $on_string: Trimmed Reads (Qual)">
+        <filter>tr == "-tr"</filter>
     </data>
-    <!-- the following produced only if no != '-no' -->
-    <data name='alignment_info' format='tabular' label='Alignment Info'/>
-    <data name='all_contigs_fasta' format='fasta' label='All Contigs (Fasta)'>
-        <filter>no != '-no'</filter>
+    <!-- the following produced only if no != "-no" -->
+    <data name="alignment_info" format="tabular" label="${tool.name} on $on_string: Alignment Info"/>
+    <data name="all_contigs_fasta" format="fasta" label="${tool.name} on $on_string: All Contigs (Fasta)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='all_contigs_qual' format='qual454' label='All Contigs (Qual454)'>
-        <filter>no != '-no'</filter>
+    <data name="all_contigs_qual" format="qual454" label="${tool.name} on $on_string: All Contigs (Qual454)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='contigs_ace' format='ace' label='Contigs (Ace)'>
-        <filter>ace == '-ace' and no != '-no'</filter>
+    <data name="contigs_ace" format="ace" label="${tool.name} on $on_string: Contigs (Ace)">
+        <filter>ace == "-ace" and no != "-no"</filter>
     </data>
-    <data name='large_contigs_fasta' format='fasta' label='Large Contigs (Fasta)'>
-        <filter>no != '-no'</filter>
+    <data name="contigs_bam" format="bam" label="${tool.name} on $on_string: Contigs (Bam)">
+        <filter>bam is True and no != "-no"</filter>
     </data>
-    <data name='large_contigs_qual' format='qual454' label='Large Contigs (Qual454)'>
-        <filter>no != '-no'</filter>
+    <data name="large_contigs_fasta" format="fasta" label="${tool.name} on $on_string: Large Contigs (Fasta)">
+        <filter>no != "-no"</filter>
+    </data>
+    <data name="large_contigs_qual" format="qual454" label="${tool.name} on $on_string: Large Contigs (Qual454)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='pair_align' format='txt' label='Pairwise Alignments'>
-        <filter>pair == '-pair' and no != '-no'</filter>
+    <data name="pair_align" format="txt" label="${tool.name} on $on_string: Pairwise Alignments">
+        <filter>pair == "-pair" and no != "-no"</filter>
     </data>
-    <data name='pair_status' format='tabular' label='Paired-End Read Status'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="pair_status" format="tabular" label="${tool.name} on $on_string: Paired-End Read Status">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_fasta' format='fasta' label='Scaffolds (Fasta)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="scaffolds_fasta" format="fasta" label="${tool.name} on $on_string: Scaffolds (Fasta)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_qual' format='qual454' label='Scaffolds (Qual454)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="scaffolds_qual" format="qual454" label="${tool.name} on $on_string: Scaffolds (Qual454)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_agp' format='tabular' label='Scaffolds (Agp)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Scaffolds (Agp)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='tag_pair_align' format='txt' label='Tag Pair Alignments'>
-        <filter>pair == '-pair' and paired_reads == 'true' and no != '-no'</filter>
+    <data name="tag_pair_align" format="txt" label="${tool.name} on $on_string: Tag Pair Alignments">
+        <filter>pair == "-pair" and paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='trim_status' format='tabular' label='Trim Status'/>
+    <data name="trim_status" format="tabular" label="${tool.name} on $on_string: Trim Status"/>
 
     <!-- THE FOLLOWING ARE LIMITED TO MAPPING -->
-    <data name='all_diffs' format='tabular' label='All Diffs'/>
-    <data name='all_struct_vars' format='tabular' label='All Struct Vars'/>
-    <data name='hc_diff' format='tabular' label='High Confidence Diff'/>
-    <data name='hc_struct_vars' format='tabular' label='High Confidence Struct Vars'/>
-    <data name='gene_status' format='tabular' label='Gene Status'/>
-    <data name='mapping_qc' format='xls' label='Mapping QC (Excel)'/>
-    <data name='ref_status' format='tabular' label='Ref Status'/>
+    <data name="all_diffs" format="tabular" label="${tool.name} on $on_string: All Diffs"/>
+    <data name="all_struct_vars" format="tabular" label="${tool.name} on $on_string: All Struct Vars"/>
+    <data name="hc_diff" format="tabular" label="${tool.name} on $on_string: High Confidence Diff"/>
+    <data name="hc_struct_vars" format="tabular" label="${tool.name} on $on_string: High Confidence Struct Vars"/>
+    <data name="gene_status" format="tabular" label="${tool.name} on $on_string: Gene Status"/>
+    <data name="mapping_qc" format="xls" label="${tool.name} on $on_string: Mapping QC (Excel)"/>
+    <data name="ref_status" format="tabular" label="${tool.name} on $on_string: Ref Status"/>
 
 </outputs>
 <help>
diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runMapping_cDNA.xml
--- a/runMapping_cDNA.xml	Thu Jul 14 22:14:07 2011 -0400
+++ b/runMapping_cDNA.xml	Wed Dec 21 19:42:53 2011 -0800
@@ -1,4 +1,4 @@
-<tool id="runMapping_cDNA" name="runMapping cDNA" version="1.0.0">
+<tool id="runMapping_cDNA" name="runMapping cDNA" version="1.0.1">
 <description>Map Roche/454 reads to a reference using Newbler</description>
 <command interpreter='perl'>runMapping_cDNA_wrapper.pl
 $newbler_metrics.extra_files_path
@@ -25,7 +25,8 @@
 $isotigs_qual
 $isotigs_agp
 $isotigs_layout
-$newbler_exe -o $newbler_metrics.extra_files_path
+runAssembly
+-o $newbler_metrics.extra_files_path
 -cpu 8 
 -a $a
 -e $e 
@@ -78,167 +79,160 @@
 #end for
 </command>
 <inputs>
-    <!-- NEWBLER VERSION -->
-    <param name='newbler_exe' type='select' display='radio' label='Newbler version'>
-        <option value='/jgi/tools/454/rig-DataProcessing_2.3/bin/runMapping'>2.3</option>
-        <option value='/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runMapping'>2.4</option>
-        <option value='/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runMapping' selected='true'>2.5</option>
-    </param>
-
     <!-- READSEQ INFILES -->
     <repeat name="sff_inputs" title="Unpaired Reads Sff Files">
         <param name="sff_input" type="data" format="sff" label="SE Sff file"/>
     </repeat>
-    <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">
-        <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>
+    <repeat name="sanger_inputs" title="Unpaired Reads Fasta/Fastq Files">
+        <param name="sanger_input" type="data" format="fasta,fastqsanger" label="SE Fasta/Fastq file"/>
     </repeat>
     <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">
         <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>
     </repeat>
-    <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">
-        <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>
+    <repeat name="sanger_paired_inputs" title="Paired Reads Fasta/Fastq Files">
+        <param name="sanger_paired_input" type="data" format="fasta,fastqsanger" label="PE Fasta/Fastq file"/>
     </repeat>
-    <param name='paired_reads' type='select' display='radio' label='[-paired_reads] If supplying paired reads (above), do you want paired-read info?'>
-        <option value='false'>no</option>
-        <option value='true'>[-paired_reads] yes</option>
+    <param name="paired_reads" type="select" display="radio" label="[-paired_reads] If supplying paired reads (above), do you want paired-read info?">
+        <option value="false">no</option>
+        <option value="true">[-paired_reads] yes</option>
     </param>
-    <param name='pair' type='select' display='radio' label='[-pair] Output pairwise overlaps'>
-        <option value=''>no</option>
-        <option value='-pair'>[-pair] yes</option>
+    <param name="pair" type="select" display="radio" label="[-pair] Output pairwise overlaps">
+        <option value="">no</option>
+        <option value="-pair">[-pair] yes</option>
     </param>
  
     <!-- SOURCE DNA TYPE -->
-    <param name='it' type='integer' value='100' label='[-it] Specify the maximum number of isotigs in an isogroup. Maximum is 10,000.'/>
-    <param name='ig' type='integer' value='500' label='[-ig] Specify the maximum number of contigs in an isogroup.'/>
-    <param name='icc' type='integer' value='100' label='[-icc] Specify the maximum number of contigs in an isotig. Maximum is 200 and corresponds to the recursion depth during graph traversal'/>
-    <param name='icl' type='integer' value='3' label='[-icl] Specify the minimum length a contig must be to be part of an isotig. Minimum is 3bp.'/>
+    <param name="it" type="integer" value="100" label="[-it] Specify the maximum number of isotigs in an isogroup. Maximum is 10,000."/>
+    <param name="ig" type="integer" value="500" label="[-ig] Specify the maximum number of contigs in an isogroup."/>
+    <param name="icc" type="integer" value="100" label="[-icc] Specify the maximum number of contigs in an isotig. Maximum is 200 and corresponds to the recursion depth during graph traversal"/>
+    <param name="icl" type="integer" value="3" label="[-icl] Specify the minimum length a contig must be to be part of an isotig. Minimum is 3bp."/>
 
     <!-- INPUTS SPECIFIC TO MAPPING -->
-    <repeat name='ref_inputs' title='Reference Sequence'>
-        <param name='ref_input' type='data' format='fasta' label='Fasta file'/>
+    <repeat name="ref_inputs" title="Reference Sequence">
+        <param name="ref_input" type="data" format="fasta" label="Fasta file"/>
     </repeat>
-    <param name='ref_type' type='select' display='radio' label='Reference type'>
-        <option value='-gref'>[-gref] Genomic reference sequence</option>
-        <option value='-cref'>[-cref] cDNA reference sequence</option>
+    <param name="ref_type" type="select" display="radio" label="Reference type">
+        <option value="-gref">[-gref] Genomic reference sequence</option>
+        <option value="-cref">[-cref] cDNA reference sequence</option>
     </param>
-    <param name='rst' type='integer' value='12' label='[-rst] Repeat score threshold parameter. Allowed values: 0 or greater'/>
-    <param name='hsl' type='integer' value='70' label='[-hsl] Hit-per-seed limit parameter'/>
-    <param name='srv' type='boolean' truevalue='-srv' falsevalue='' checked='false' label='[-srv] Single read variant output'/>
+    <param name="rst" type="integer" value="12" label="[-rst] Repeat score threshold parameter. Allowed values: 0 or greater"/>
+    <param name="hsl" type="integer" value="70" label="[-hsl] Hit-per-seed limit parameter"/>
+    <param name="srv" type="boolean" truevalue="-srv" falsevalue="" checked="false" label="[-srv] Single read variant output"/>
 
    <!-- OPTIONAL ARGUMENTS -->
    <!-- NYI
-    <param name='accno' type='data' format='tabular' optional='true' label='[-accno] Specify annotation data. Required only if reference sequence headers do not contain gene=NAME pairs' />
-    <param name='annot' type='data' format='tabular' optional='true' label='[-annot] Supply gene, transcript, and protein information' />
+    <param name="accno" type="data" format="tabular" optional="true" label="[-accno] Specify annotation data. Required only if reference sequence headers do not contain gene=NAME pairs" />
+    <param name="annot" type="data" format="tabular" optional="true" label="[-annot] Supply gene, transcript, and protein information" />
     -->
-    <param name='mcf' type='data' format='tabular' optional='true' label='[-mcf] Specify non-default MID config file' />
-    <param name='fi' type='data' format='txt' optional='true' label='[-fi] Include filter file to be specified' />
-    <param name='fe' type='data' format='txt' optional='true' label='[-fe] Exclude filter file to be specified' />
-    <param name='vt' type='data' format='fasta' optional='true' label="[-vt] This option specifies a vector trimming database, or FASTA file of sequences to be used to trim the ends of input reads (for cloning vectors, primers, adapters or other end sequences)" />
-    <param name='vs' type='data' format='fasta' optional='true' label="[-vs] This option specifies a vector screening database, or FASTA file of sequences to be used to screen the input reads for contaminants.  Reads that completely align against the screening database are trimmed completely (so that it is not used in the computation), but otherwise the read trimpoints are not changed" />
+    <param name="mcf" type="data" format="tabular" optional="true" label="[-mcf] Specify non-default MID config file" />
+    <param name="fi" type="data" format="txt" optional="true" label="[-fi] Include filter file to be specified" />
+    <param name="fe" type="data" format="txt" optional="true" label="[-fe] Exclude filter file to be specified" />
+    <param name="vt" type="data" format="fasta" optional="true" label="[-vt] This option specifies a vector trimming database, or FASTA file of sequences to be used to trim the ends of input reads (for cloning vectors, primers, adapters or other end sequences)" />
+    <param name="vs" type="data" format="fasta" optional="true" label="[-vs] This option specifies a vector screening database, or FASTA file of sequences to be used to screen the input reads for contaminants.  Reads that completely align against the screening database are trimmed completely (so that it is not used in the computation), but otherwise the read trimpoints are not changed" />
  
     <!-- READ TRIMMING -->
-    <param name='minlen' type='integer' value='20' label='[-minlen] Minimum length of reads to use (15-45 allowed)'/>
-    <param name='notrim' type='boolean' truevalue='-notrim' falsevalue='' checked='false' label='[-notrim] Do not perform default quality and primer trimming of input reads'/>
-    <param name='tr' type='select' display='radio' label='[-tr] Output trimmed reads'>
-        <option value=''>no</option>
-        <option value='-tr'>[-tr] yes</option>
+    <param name="minlen" type="integer" value="20" label="[-minlen] Minimum length of reads to use (15-45 allowed)"/>
+    <param name="notrim" type="boolean" truevalue="-notrim" falsevalue="" checked="false" label="[-notrim] Do not perform default quality and primer trimming of input reads"/>
+    <param name="tr" type="select" display="radio" label="[-tr] Output trimmed reads">
+        <option value="">no</option>
+        <option value="-tr">[-tr] yes</option>
     </param>
-    <param name='nor' type='boolean' truevalue='-nor' falsevalue='' label='[-nor] Turn off the automatic rescore function for read quality scores'/>
-    <param name='ud' type='boolean' truevalue='-ud' falsevalue='' label='[-ud] Treat each read separately, with no grouping of duplicates'/>
+    <param name="nor" type="boolean" truevalue="-nor" falsevalue="" label="[-nor] Turn off the automatic rescore function for read quality scores"/>
+    <param name="ud" type="boolean" truevalue="-ud" falsevalue="" label="[-ud] Treat each read separately, with no grouping of duplicates"/>
 
     <!-- ALIGNMENT PARAMETERS -->
-    <param name='ss' type='integer' value='12' label='[-ss] Seed step parameter - The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection. Allow values: 1 or greater'/>
-    <param name='sl' type='integer' value='16' label='[-sl] Seed length parameter - The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the "k" value of the k-mer matching). Allowed values: 6-16'/>
-    <param name='sc' type='integer' value='1' label='[-sc] Seed count parameter - The number of seeds required in a window before an extension is made. Allowed values: 1 or greater'/>
-    <param name='ml' type="text" value='40' label="[-ml] Minimum overlap length - The minimum length of overlaps used for the pairwise alignment step. The value can either be a minimum length in bases or a percentage of read length. In the case of a percentage, simply include '%' immediately following the numeric value. Allowed values: 1 or greater"/>
-    <param name='mi' type="integer" value='90' label="[-mi] Minimum overlap identity - The percent identity of overlaps used for the pairwise alignment step. Allowed values: 0 or greater"/>
-    <param name='ais' type='integer' value='2' label='[-ais] Alignment identity score - When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Allowed values: 0 or greater'/>
+    <param name="ss" type="integer" value="12" label="[-ss] Seed step parameter - The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection. Allow values: 1 or greater"/>
+    <param name="sl" type="integer" value="16" label="[-sl] Seed length parameter - The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the 'k' value of the k-mer matching). Allowed values: 6-16"/>
+    <param name="sc" type="integer" value="1" label="[-sc] Seed count parameter - The number of seeds required in a window before an extension is made. Allowed values: 1 or greater"/>
+    <param name="ml" type="text" value="40" label="[-ml] Minimum overlap length - The minimum length of overlaps used for the pairwise alignment step. The value can either be a minimum length in bases or a percentage of read length. In the case of a percentage, simply include '%' immediately following the numeric value. Allowed values: 1 or greater"/>
+    <param name="mi" type="integer" value="90" label="[-mi] Minimum overlap identity - The percent identity of overlaps used for the pairwise alignment step. Allowed values: 0 or greater"/>
+    <param name="ais" type="integer" value="2" label="[-ais] Alignment identity score - When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Allowed values: 0 or greater"/>
 
     <!-- ASSEMBLY OPTIONS -->
-    <param name='e' type="integer" value='0' label="[-e] This option tells the assembler that the expected depth of the data is at a certain level.  The assembler has been optimized for datasets in the 10-50x oversampling size, and this option helps the assembler with datasets that have a higher oversampling level.  A value of 0 resets the assembler computation to use its default algorithms"/>
+    <param name="e" type="integer" value="0" label="[-e] This option tells the assembler that the expected depth of the data is at a certain level.  The assembler has been optimized for datasets in the 10-50x oversampling size, and this option helps the assembler with datasets that have a higher oversampling level.  A value of 0 resets the assembler computation to use its default algorithms"/>
 
     <!-- OUTPUT OPTIONS -->
-    <param name='no' type='select' display='radio' label='[-no] Do complete assembly'>
-        <option value=''>do complete assembly</option>
-        <option value='-no'>[-no] do not assemble; do alignments only</option>
+    <param name="no" type="select" display="radio" label="[-no] Do complete assembly">
+        <option value="">do complete assembly</option>
+        <option value="-no">[-no] do not assemble; do alignments only</option>
     </param>
-    <param name='qo' type='boolean' truevalue='' falsevalue='-qo' checked='false' label='[-qo] Generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy'/>
-    <param name='a' type="integer" value='100' label="[-a] This option sets the minimum length for a contig to appear in the 454AllContigs.fna file."/>
-    <param name='info' type='select' display='radio' label='Output Alignment Info'>
-        <option value='-info'>[-info] yes</option>
-        <option value='-infoall'>[-infoall] yes, including 0-coverage positions</option>
+    <param name="qo" type="boolean" truevalue="" falsevalue="-qo" checked="false" label="[-qo] Generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy"/>
+    <param name="a" type="integer" value="100" label="[-a] This option sets the minimum length for a contig to appear in the 454AllContigs.fna file."/>
+    <param name="info" type="select" display="radio" label="Output Alignment Info">
+        <option value="-info">[-info] yes</option>
+        <option value="-infoall">[-infoall] yes, including 0-coverage positions</option>
     </param>
-    <param name='ace' type='select' display='radio' label='Produce Ace assembly file'>
-        <option value=''>no</option>
-        <option value='-ace'>[-ace] yes</option>
+    <param name="ace" type="select" display="radio" label="Produce Ace assembly file">
+        <option value="">no</option>
+        <option value="-ace">[-ace] yes</option>
     </param>
 </inputs>
 
 <outputs>
     <!-- the following are common to runMapping and runAssembly -->
-    <data name='newbler_metrics' format='txt' />
-    <data name='read_status' format='tabular' label='Read Status'/>
-    <data name='trimmed_reads_fasta' format='fasta' label='Trimmed Reads (Fasta)'>
-        <filter>tr == '-tr'</filter>
+    <data name="newbler_metrics" format="txt" />
+    <data name="read_status" format="tabular" label="${tool.name} on $on_string: Read Status"/>
+    <data name="trimmed_reads_fasta" format="fasta" label="${tool.name} on $on_string: Trimmed Reads (Fasta)">
+        <filter>tr == "-tr"</filter>
     </data>
-    <data name='trimmed_reads_qual' format='qual454' label='Trimmed Reads (Qual)'>
-        <filter>tr == '-tr'</filter>
+    <data name="trimmed_reads_qual" format="qual454" label="${tool.name} on $on_string: Trimmed Reads (Qual)">
+        <filter>tr == "-tr"</filter>
     </data>
-    <!-- the following produced only if no != '-no' -->
-    <data name='alignment_info' format='tabular' label='Alignment Info'/>
-    <data name='all_contigs_fasta' format='fasta' label='All Contigs (Fasta)'>
-        <filter>no != '-no'</filter>
+    <!-- the following produced only if no != "-no" -->
+    <data name="alignment_info" format="tabular" label="${tool.name} on $on_string: Alignment Info"/>
+    <data name="all_contigs_fasta" format="fasta" label="${tool.name} on $on_string: All Contigs (Fasta)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='all_contigs_qual' format='qual454' label='All Contigs (Qual454)'>
-        <filter>no != '-no'</filter>
+    <data name="all_contigs_qual" format="qual454" label="${tool.name} on $on_string: All Contigs (Qual454)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='contigs_ace' format='ace' label='Contigs (Ace)'>
-        <filter>ace == '-ace' and no != '-no'</filter>
+    <data name="contigs_ace" format="ace" label="${tool.name} on $on_string: Contigs (Ace)">
+        <filter>ace == "-ace" and no != "-no"</filter>
     </data>
-    <data name='pair_align' format='txt' label='Pairwise Alignments'>
-        <filter>pair == '-pair' and no != '-no'</filter>
+    <data name="pair_align" format="txt" label="${tool.name} on $on_string: Pairwise Alignments">
+        <filter>pair == "-pair" and no != "-no"</filter>
     </data>
-    <data name='pair_status' format='tabular' label='Paired-End Read Status'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="pair_status" format="tabular" label="${tool.name} on $on_string: Paired-End Read Status">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_fasta' format='fasta' label='Scaffolds (Fasta)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="scaffolds_fasta" format="fasta" label="${tool.name} on $on_string: Scaffolds (Fasta)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_qual' format='qual454' label='Scaffolds (Qual454)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="scaffolds_qual" format="qual454" label="${tool.name} on $on_string: Scaffolds (Qual454)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='scaffolds_agp' format='tabular' label='Scaffolds (Agp)'>
-        <filter>paired_reads == 'true' and no != '-no'</filter>
+    <data name="scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Scaffolds (Agp)">
+        <filter>paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='tag_pair_align' format='txt' label='Tag Pair Alignments'>
-        <filter>pair == '-pair' and paired_reads == 'true' and no != '-no'</filter>
+    <data name="tag_pair_align" format="txt" label="${tool.name} on $on_string: Tag Pair Alignments">
+        <filter>pair == "-pair" and paired_reads == "true" and no != "-no"</filter>
     </data>
-    <data name='trim_status' format='tabular' label='Trim Status'/>
+    <data name="trim_status" format="tabular" label="${tool.name} on $on_string: Trim Status"/>
 
     <!-- THE FOLLOWING ARE LIMITED TO MAPPING -->
-    <data name='all_diffs' format='tabular' label='All Diffs'/>
-    <data name='all_struct_vars' format='tabular' label='All Struct Vars'/>
-    <data name='hc_diff' format='tabular' label='High Confidence Diff'/>
-    <data name='hc_struct_vars' format='tabular' label='High Confidence Struct Vars'/>
-    <data name='gene_status' format='tabular' label='Gene Status'/>
-    <data name='mapping_qc' format='xls' label='Mapping QC (Excel)'/>
-    <data name='ref_status' format='tabular' label='Ref Status'/>
+    <data name="all_diffs" format="tabular" label="${tool.name} on $on_string: All Diffs"/>
+    <data name="all_struct_vars" format="tabular" label="${tool.name} on $on_string: All Struct Vars"/>
+    <data name="hc_diff" format="tabular" label="${tool.name} on $on_string: High Confidence Diff"/>
+    <data name="hc_struct_vars" format="tabular" label="${tool.name} on $on_string: High Confidence Struct Vars"/>
+    <data name="gene_status" format="tabular" label="${tool.name} on $on_string: Gene Status"/>
+    <data name="mapping_qc" format="xls" label="${tool.name} on $on_string: Mapping QC (Excel)"/>
+    <data name="ref_status" format="tabular" label="${tool.name} on $on_string: Ref Status"/>
 
     <!-- ISOTIGS -->
-    <data name='isotigs_ace' format='ace' label='Isotigs (Ace)'>
-        <filter>ace != '' and no != '-no'</filter>
+    <data name="isotigs_ace" format="ace" label="${tool.name} on $on_string: Isotigs (Ace)">
+        <filter>ace != "" and no != "-no"</filter>
     </data>
-    <data name='isotigs_fasta' format='fasta' label='Isotigs (Fasta)'>
-        <filter>no != '-no'</filter>
+    <data name="isotigs_fasta" format="fasta" label="${tool.name} on $on_string: Isotigs (Fasta)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='isotigs_qual' format='qual454' label='Isotigs (Qual454)'>
-        <filter>no != '-no'</filter>
+    <data name="isotigs_qual" format="qual454" label="${tool.name} on $on_string: Isotigs (Qual454)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='isotigs_agp' format='tabular' label='Isotigs (Agp)'>
-        <filter>no != '-no'</filter>
+    <data name="isotigs_agp" format="tabular" label="${tool.name} on $on_string: Isotigs (Agp)">
+        <filter>no != "-no"</filter>
     </data>
-    <data name='isotigs_layout' format='txt' label='Isotig Layout'>
-        <filter>no != '-no'</filter>
+    <data name="isotigs_layout" format="txt" label="${tool.name} on $on_string: Isotig Layout">
+        <filter>no != "-no"</filter>
     </data>
 
 </outputs>
diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runMapping_cDNA_wrapper.pl
--- a/runMapping_cDNA_wrapper.pl	Thu Jul 14 22:14:07 2011 -0400
+++ b/runMapping_cDNA_wrapper.pl	Wed Dec 21 19:42:53 2011 -0800
@@ -36,9 +36,8 @@
 my @cmd=removeUnusedOptions(@ARGV);
 
 # RUN COMMAND
-# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
 my $stderr;
-eval { $stderr=`@cmd 2>&1`; };
+eval { $stderr=`runMapping @cmd 2>&1`; };
 if ( $@ ) {
     print STDERR "Newbler ERROR: $stderr\n";
     `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
diff -r 2d86d5b112e8 -r bf1f8bc4abe6 runMapping_wrapper.pl
--- a/runMapping_wrapper.pl	Thu Jul 14 22:14:07 2011 -0400
+++ b/runMapping_wrapper.pl	Wed Dec 21 19:42:53 2011 -0800
@@ -23,6 +23,7 @@
 my $trimmed_reads_fasta=shift @ARGV;
 my $trimmed_reads_qual=shift @ARGV;
 my $contigs_ace=shift @ARGV;
+my $contigs_bam=shift @ARGV;
 my $large_contigs_fasta=shift @ARGV;
 my $large_contigs_qual=shift @ARGV;
 my $gene_status=shift @ARGV;
@@ -32,9 +33,8 @@
 my @cmd=removeUnusedOptions(@ARGV);
 
 # RUN COMMAND
-# NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
 my $stderr;
-eval { $stderr=`@cmd 2>&1`; };
+eval { $stderr=`runMapping @cmd 2>&1`; };
 if ( $@ ) {
     print STDERR "Newbler ERROR: $stderr\n";
     `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
@@ -58,6 +58,7 @@
 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
+get_outfile("$outdir/454Contigs.bam", $contigs_bam);
 get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta);
 get_outfile("$outdir/454LargeContigs.qual", $large_contigs_qual);
 get_outfile("$outdir/454GeneStatus.txt", $gene_status);