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diff meta_velvet.xml @ 1:0591d844bd08 draft

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author stheil
date Thu, 24 Sep 2015 10:41:51 -0400
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children 34ea8f113018
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/meta_velvet.xml	Thu Sep 24 10:41:51 2015 -0400
@@ -0,0 +1,419 @@
+<tool id="velvet_test" name="velvet_test" version="3.0 (2013-4-30)">
+
+	<macros>
+		<import>velvet_macro.xml</import>
+	</macros>
+	<description>Run velvet or meta-velvetg assembly.</description>
+
+  <command interpreter="perl">velvet.pl
+
+    $meta
+
+		#for $i, $library in enumerate( $shortPaired )
+
+			#set $libNumber = $i + 1
+
+			#if $libNumber == 1
+
+				#set $libNumber = ''
+
+			#end if
+
+			#if not $library.ins_length.value is None
+
+			-ins_length$libNumber $library.ins_length
+
+			#end if
+
+			#if not $library.ins_length_sd.value is None
+
+			-ins_length_sd$libNumber $library.ins_length_sd
+
+			#end if
+
+      -shortPaired$libNumber
+
+			@PAIRED_FILES_OPTIONS@
+
+		#end for
+
+		#for $i, $library in enumerate( $short )
+
+			#set $libNumber = $i + 1
+
+			#if $libNumber == 1
+
+				#set $libNumber = ''
+
+			#end if
+
+			-short$libNumber
+
+			@UNPAIRED_FILES_OPTIONS@
+
+		#end for
+
+		#for $i, $library in enumerate( $longPaired )
+
+			#if not $library.ins_length.value is None
+
+			-ins_length_long $library.ins_length
+
+			#end if
+
+			#if not $library.ins_length_sd.value is None
+
+			-ins_length_long_sd $library.ins_length_sd
+
+			#end if
+
+      -longPaired
+
+			@PAIRED_FILES_OPTIONS@
+
+		#end for
+
+		#for $i, $library in enumerate( $long )
+
+			-long
+
+			@UNPAIRED_FILES_OPTIONS@
+
+		#end for
+
+    #if not $hash_length.value == ''
+
+    -hash_length $hash_length
+
+    #end if
+
+    $strand_specific
+
+    #if not $cov_cutoff.value == ''
+
+    -cov_cutoff $cov_cutoff
+
+    #end if
+
+    $read_trkg
+
+    #if not $min_contig_lgth.value is None
+
+		-min_contig_lgth $min_contig_lgth
+
+		#end if
+
+    $amos_file
+
+    #if not $exp_cov.value == ''
+
+		-exp_cov $exp_cov
+
+		#end if
+
+    #if not $long_cov_cutoff.value == ''
+
+		-long_cov_cutoff $long_cov_cutoff
+
+		#end if
+
+    $scaffolding
+
+    #if not $max_branch_length.value is None
+
+		-max_branch_length $max_branch_length
+
+		#end if
+
+    #if not $max_divergence.value is None
+
+		-max_divergence $max_divergence
+
+		#end if
+
+    #if not $max_gap_count.value is None
+
+		-max_gap_count $max_gap_count
+
+		#end if
+
+    #if not $min_pair_count.value is None
+
+		-min_pair_count $min_pair_count
+
+		#end if
+
+    #if not $max_coverage.value is None
+
+		-max_coverage $max_coverage
+
+		#end if
+
+    #if not $coverage_mask.value is None
+
+		-coverage_mask $coverage_mask
+
+		#end if
+
+    #if not $long_mult_cutoff.value is None
+
+    -long_mult_cutoff $long_mult_cutoff
+
+		#end if
+
+    $unused_reads
+
+    $alignments
+
+    $exportFiltered
+
+    #if not $paired_exp_fraction.value is None
+
+    -paired_exp_fraction $paired_exp_fraction
+
+		#end if
+
+    $shortMatePaired
+
+    $conserveLong
+
+    $discard_chimera
+
+    #if not $max_chimera_rate.value is None
+
+    -max_chimera_rate $max_chimera_rate
+
+		#end if
+
+    #if not $repeat_cov_sd.value is None
+
+    -repeat_cov_sd $repeat_cov_sd
+
+		#end if
+
+    #if not $min_split_length.value is None
+
+    -min_split_length $min_split_length
+
+		#end if
+
+    #if not $valid_connections.value is None
+
+    -valid_connections $valid_connections
+
+		#end if
+
+    #if not $noise_connections.value is None
+
+    -noise_connections $noise_connections
+
+		#end if
+
+    $use_connections
+
+    $report_split_detail
+
+    $report_subgraph
+
+    #if not $exp_covs.value == ''
+
+    -exp_covs $exp_covs
+
+		#end if
+
+    #if not $min_peak_cov.value is None
+
+    -min_peak_cov $min_peak_cov
+
+		#end if
+
+    #if not $max_peak_cov.value is None
+
+    -max_peak_cov $max_peak_cov
+
+		#end if
+
+    #if not $histo_bin_width.value is None
+
+    -histo_bin_width $histo_bin_width
+
+		#end if
+
+    #if not $histo_sn_ratio.value is None
+
+    -histo_sn_ratio $histo_sn_ratio
+
+		#end if
+
+  </command>
+
+  <inputs>
+
+		<param name="hash_length" type="text" value="31" label="Hash length : integer &lt;= 150 OR m,M,s with m (min kmer length) &lt; M (max kmer length) &lt;= 150 and s is a step number"/>
+
+    <param name="meta" type="select" label="Perform a metagenomic assembly using meta-velvetg">
+			<option value="">Yes</option>
+			<option value="-nometa">No</option>
+		</param>
+
+		<repeat name="shortPaired" max="2" title="Short paired reads library">
+			<expand macro="paired_library_options" />
+		</repeat>
+
+		<repeat name="short" max="2" title="Short unpaired reads library">
+			<expand macro="unpaired_library_options" />
+		</repeat>
+
+		<repeat name="longPaired" max="1" title="Long paired reads library">
+			<expand macro="paired_library_options" />
+		</repeat>
+
+		<repeat name="long" max="1" title="Long unpaired reads library">
+			<expand macro="unpaired_library_options" />
+		</repeat>
+
+		<param name="reference" type="data" format="fasta" optional="true" label="VELVETH - Reference file (-reference)"/>
+
+    <param name="strand_specific" type="select" label="VELVETH - Strand specific transcriptome sequencing data. Default: No (-strand_specific)">
+      <option value="">No</option>
+      <option value="-strand_specific">Yes</option>
+    </param>
+
+    <param name="cov_cutoff" type="text" optional="true" label="VELVETG - Coverage cutoff. Float or auto (-cov_cutoff)"/>
+
+    <param name="read_trkg" type="select" label="VELVETG - Tracking of short read positions in assembly. Default: no tracking (-read_trkg)">
+      <option value="">No</option>
+      <option value="-read_trkg yes">Yes</option>
+    </param>
+
+    <param name="min_contig_lgth" type="integer" optional="true" label="VELVETG - Minimum contig length. Default: hash length * 2 (-min_contig_lgth)"/>
+
+    <param name="amos_file" type="select" label="VELVETG - Export assembly to AMOS file. Default: no export (-amos_file)">
+      <option value="">No</option>
+      <option value="-amos_file yes">Yes</option>
+    </param>
+
+    <param name="exp_cov" type="text" optional="true" label="VELVETG - Expected coverage of unique regions (float or auto). In case of metagenomic analysis it will be set to auto (-exp_cov)"/>
+    <param name="long_cov_cutoff" type="text" optional="true" label="VELVETG - Cutoff for removal of nodes with low long-read coverage (-long_cov_cutoff)"/>
+
+    <param name="scaffolding" type="select" label="VELVETG - Scaffolding of contigs used paired end information. Default: on (-scaffolding)">
+			<option value="">Yes</option>
+			<option value="-scaffolding no">No</option>
+		</param>
+
+    <param name="max_branch_length" type="integer" optional="true" label="VELVETG - Maximum length in base pair of bubble. Default: 100 (-max_branch_length)"/>
+    <param name="max_divergence" type="float" optional="true" label="VELVETG - Maximum divergence rate between two branches in a bubble. Default: 0.2 (-max_divergence)"/>
+    <param name="max_gap_count" type="integer" optional="true" label="VELVETG - Maximum number of gaps allowed in the alignment of the two branches of a bubble. Default: 3 (-max_gap_count)"/>
+    <param name="min_pair_count" type="integer" optional="true" label="VELVETG -Minimum number of paired end connections to justify the scaffolding of two long contigs. Default: 5 (-min_pair_count)"/>
+
+    <param name="max_coverage" type="float" optional="true" label="VELVETG - Cutoff for removal of high coverage nodes AFTER tour bus. Default: no removal (-max_coverage)"/>
+    <param name="coverage_mask" type="integer" optional="true" label="VELVETG - Minimum coverage required for confident regions of contigs. Default: 1 (-coverage_mask)"/>
+    <param name="long_mult_cutoff" type="integer" optional="true" label="VELVETG -Minimum number of long reads required to merge contigs. Default: 2 (-long_mult_cutoff)"/>
+
+    <param name="unused_reads" type="select" label="VELVETG - Export unused reads in UnusedReads.fa file. Default: no (-unused_reads)">
+      <option value="">No</option>
+      <option value="-unused_reads yes">Yes</option>
+    </param>
+
+    <param name="alignments" type="select" label="VELVETG - Export a summary of contig alignment to the reference sequences. Default: no (-alignments)">
+      <option value="">No</option>
+      <option value="-alignments yes">Yes</option>
+    </param>
+
+    <param name="exportFiltered" type="select" label="VELVETG - Export the long nodes which were eliminated by the coverage filters. Default: no (-exportFiltered)">
+      <option value="">No</option>
+      <option value="-exportFiltered yes">Yes</option>
+    </param>
+
+    <param name="paired_exp_fraction" type="float" optional="true" label="VELVETG -Remove all the paired end connections which less than the specified fraction of the expected count. Default: 0.1 (-paired_exp_fraction)"/>
+
+    <param name="shortMatePaired" type="select" label="VELVETG - For mate-pair libraries, indicate that the library might be contaminated with paired-end reads. Default no (-shortMatePaired)">
+      <option value="">No</option>
+      <option value="-shortMatePaired yes">Yes</option>
+    </param>
+
+    <param name="conserveLong" type="select" label="VELVETG - Preserve sequences with long reads in them. Default no (-conserveLong)">
+      <option value="">No</option>
+      <option value="-conserveLong yes">Yes</option>
+    </param>
+
+    <param name="discard_chimera" type="select" label="META-VELVETG - Discard chimera sub-graph. Default: no (-discard_chimera)">
+      <option value="">No</option>
+      <option value="-discard_chimera yes">Yes</option>
+    </param>
+
+    <param name="max_chimera_rate" type="float" optional="true" label="META-VELVETG - Maximum allowable chimera rate. Default: 0.0 (-max_chimera_rate)"/>
+    <param name="repeat_cov_sd" type="float" optional="true" label="META-VELVETG - Standard deviation of repeat node coverages. Default: 0.1 (-repeat_cov_sd)"/>
+    <param name="min_split_length" type="integer" optional="true" label="META-VELVETG - Minimum node length required for repeat resolution. Default: 0 (-min_split_length)"/>
+    <param name="valid_connections" type="integer" optional="true" label="META-VELVETG - Minimum allowable number of consistent paired-end connections. Default: 1 (-valid_connections)"/>
+    <param name="noise_connections" type="integer" optional="true" label="META-VELVETG - Maximum allowable number of inconsistent paired-end connections. Default: 0 (-noise_connections)"/>
+
+    <param name="use_connections" type="select" label="META-VELVETG - Use paired-end connections for graph splitting. Default: yes (-use_connections)">
+      <option value="">Yes</option>
+      <option value="-use_connections no">No</option>
+    </param>
+
+    <param name="report_split_detail" type="select" label="META-VELVETG - Report sequences around repeat nodes. Default: no (-report_split_detail)">
+      <option value="">No</option>
+      <option value="-report_split_detail yes">Yes</option>
+    </param>
+
+    <param name="report_subgraph" type="select" label="META-VELVETG - Report node sequences for each subgraph. Default: no (-report_subgraph)">
+      <option value="">No</option>
+      <option value="-report_subgraph yes">Yes</option>
+    </param>
+
+    <param name="exp_covs" type="text" optional="true" label="META-VELVETG - Expected coverages for each species in microbiome. Default: auto (-exp_covs)"/>
+
+    <param name="min_peak_cov" type="float" optional="true" label="META-VELVETG - Minimum peak coverage. Default: 0 (-min_peak_cov)"/>
+    <param name="max_peak_cov" type="float" optional="true" label="META-VELVETG - Maximum peak coverage. Default: 500 (-max_peak_cov)"/>
+    <param name="histo_bin_width" type="float" optional="true" label="META-VELVETG - Bin width of peak coverage histogram. Default: 1 (-histo_bin_width)"/>
+    <param name="histo_sn_ratio" type="float" optional="true" label="META-VELVETG - Signal-noise ratio to remove peak noises. Default: 10 (-histo_sn_ratio)"/>
+
+  </inputs>
+
+	<outputs>
+
+  <data format="fasta" name="meta_velvet_contigs" from_work_dir="meta-velvetg.contigs.fa" label="${tool.name} on ${on_string}: meta-velvetg.contigs.fasta">
+    <filter>(meta == '')</filter>
+  </data>
+
+  <data format="fasta" name="velvet_contigs" from_work_dir="contigs.fa" label="${tool.name} on ${on_string}: contigs.fasta">
+    <filter>(meta == '-nometa')</filter>
+  </data>
+
+  <data format="fasta" name="velvet_singlets" from_work_dir="Singlets.fasta" label="${tool.name} on ${on_string}: singlets.fasta">
+    <filter>(unused_reads == '-unused_reads yes')</filter>
+  </data>
+
+  <data format="txt" name="meta-velvetg.asm.afg" from_work_dir="meta-velvetg.asm.afg" label="${tool.name} on ${on_string}: meta-velvetg.asm.afg">
+    <filter>((meta == '') and (amos_file == '-amos_file yes'))</filter>
+  </data>
+
+  <data format="txt" name="velvet_asm.afg" from_work_dir="velvet_asm.afg" label="${tool.name} on ${on_string}: velvet_asm.afg">
+    <filter>((meta == '-nometa') and (amos_file == '-amos_file yes'))</filter>
+  </data>
+
+  <data format="tabular" name="stats.txt" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats.txt">
+    <filter>(meta == '-nometa')</filter>
+  </data>
+
+  <data format="tabular" name="meta-velvetg.split-stats.txt" from_work_dir="meta-velvetg.split-stats.txt" label="${tool.name} on ${on_string}: meta-velvetg.split-stats.txt">
+    <filter>(meta == '')</filter>
+  </data>
+
+  <data format="txt" name="LastGraph" from_work_dir="LastGraph" label="${tool.name} on ${on_string}: LastGraph">
+    <filter>(meta == '-nometa')</filter>
+  </data>
+
+  <data format="txt" name="meta-velvetg.LastGraph" from_work_dir="meta-velvetg.LastGraph" label="${tool.name} on ${on_string}: meta-velvetg.LastGraph">
+    <filter>(meta == '')</filter>
+  </data>
+
+  <data format="tabular" name="meta-velvetg.Graph2-stats.txt" from_work_dir="meta-velvetg.Graph2-stats.txt" label="${tool.name} on ${on_string}: meta-velvetg.Graph2-stats.txt">
+    <filter>(meta == '')</filter>
+  </data>
+
+  </outputs>
+
+</tool>