| Previous changeset 0:3e0660c2fb2c (2015-09-24) Next changeset 2:1bb80c25b379 (2015-09-24) |
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added:
meta_velvet.xml |
| b |
| diff -r 3e0660c2fb2c -r 0591d844bd08 meta_velvet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/meta_velvet.xml Thu Sep 24 10:41:51 2015 -0400 |
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| b'@@ -0,0 +1,419 @@\n+<tool id="velvet_test" name="velvet_test" version="3.0 (2013-4-30)">\n+\n+\t<macros>\n+\t\t<import>velvet_macro.xml</import>\n+\t</macros>\n+\t<description>Run velvet or meta-velvetg assembly.</description>\n+\n+ <command interpreter="perl">velvet.pl\n+\n+ $meta\n+\n+\t\t#for $i, $library in enumerate( $shortPaired )\n+\n+\t\t\t#set $libNumber = $i + 1\n+\n+\t\t\t#if $libNumber == 1\n+\n+\t\t\t\t#set $libNumber = \'\'\n+\n+\t\t\t#end if\n+\n+\t\t\t#if not $library.ins_length.value is None\n+\n+\t\t\t-ins_length$libNumber $library.ins_length\n+\n+\t\t\t#end if\n+\n+\t\t\t#if not $library.ins_length_sd.value is None\n+\n+\t\t\t-ins_length_sd$libNumber $library.ins_length_sd\n+\n+\t\t\t#end if\n+\n+ -shortPaired$libNumber\n+\n+\t\t\t@PAIRED_FILES_OPTIONS@\n+\n+\t\t#end for\n+\n+\t\t#for $i, $library in enumerate( $short )\n+\n+\t\t\t#set $libNumber = $i + 1\n+\n+\t\t\t#if $libNumber == 1\n+\n+\t\t\t\t#set $libNumber = \'\'\n+\n+\t\t\t#end if\n+\n+\t\t\t-short$libNumber\n+\n+\t\t\t@UNPAIRED_FILES_OPTIONS@\n+\n+\t\t#end for\n+\n+\t\t#for $i, $library in enumerate( $longPaired )\n+\n+\t\t\t#if not $library.ins_length.value is None\n+\n+\t\t\t-ins_length_long $library.ins_length\n+\n+\t\t\t#end if\n+\n+\t\t\t#if not $library.ins_length_sd.value is None\n+\n+\t\t\t-ins_length_long_sd $library.ins_length_sd\n+\n+\t\t\t#end if\n+\n+ -longPaired\n+\n+\t\t\t@PAIRED_FILES_OPTIONS@\n+\n+\t\t#end for\n+\n+\t\t#for $i, $library in enumerate( $long )\n+\n+\t\t\t-long\n+\n+\t\t\t@UNPAIRED_FILES_OPTIONS@\n+\n+\t\t#end for\n+\n+ #if not $hash_length.value == \'\'\n+\n+ -hash_length $hash_length\n+\n+ #end if\n+\n+ $strand_specific\n+\n+ #if not $cov_cutoff.value == \'\'\n+\n+ -cov_cutoff $cov_cutoff\n+\n+ #end if\n+\n+ $read_trkg\n+\n+ #if not $min_contig_lgth.value is None\n+\n+\t\t-min_contig_lgth $min_contig_lgth\n+\n+\t\t#end if\n+\n+ $amos_file\n+\n+ #if not $exp_cov.value == \'\'\n+\n+\t\t-exp_cov $exp_cov\n+\n+\t\t#end if\n+\n+ #if not $long_cov_cutoff.value == \'\'\n+\n+\t\t-long_cov_cutoff $long_cov_cutoff\n+\n+\t\t#end if\n+\n+ $scaffolding\n+\n+ #if not $max_branch_length.value is None\n+\n+\t\t-max_branch_length $max_branch_length\n+\n+\t\t#end if\n+\n+ #if not $max_divergence.value is None\n+\n+\t\t-max_divergence $max_divergence\n+\n+\t\t#end if\n+\n+ #if not $max_gap_count.value is None\n+\n+\t\t-max_gap_count $max_gap_count\n+\n+\t\t#end if\n+\n+ #if not $min_pair_count.value is None\n+\n+\t\t-min_pair_count $min_pair_count\n+\n+\t\t#end if\n+\n+ #if not $max_coverage.value is None\n+\n+\t\t-max_coverage $max_coverage\n+\n+\t\t#end if\n+\n+ #if not $coverage_mask.value is None\n+\n+\t\t-coverage_mask $coverage_mask\n+\n+\t\t#end if\n+\n+ #if not $long_mult_cutoff.value is None\n+\n+ -long_mult_cutoff $long_mult_cutoff\n+\n+\t\t#end if\n+\n+ $unused_reads\n+\n+ $alignments\n+\n+ $exportFiltered\n+\n+ #if not $paired_exp_fraction.value is None\n+\n+ -paired_exp_fraction $paired_exp_fraction\n+\n+\t\t#end if\n+\n+ $shortMatePaired\n+\n+ $conserveLong\n+\n+ $discard_chimera\n+\n+ #if not $max_chimera_rate.value is None\n+\n+ -max_chimera_rate $max_chimera_rate\n+\n+\t\t#end if\n+\n+ #if not $repeat_cov_sd.value is None\n+\n+ -repeat_cov_sd $repeat_cov_sd\n+\n+\t\t#end if\n+\n+ #if not $min_split_length.value is None\n+\n+ -min_split_length $min_split_length\n+\n+\t\t#end if\n+\n+ #if not $valid_connections.value is None\n+\n+ -valid_connections $valid_connections\n+\n+\t\t#end if\n+\n+ #if not $noise_connections.value is None\n+\n+ -noise_connections $noise_connections\n+\n+\t\t#end if\n+\n+ $use_connections\n+\n+ $report_split_detail\n+\n+ $report_subgraph\n+\n+ #if not $exp_covs.value == \'\'\n+\n+ -exp_covs $exp_covs\n+\n+\t\t#end if\n+\n+ #if not $min_peak_cov.value is None\n+\n+ -min_peak_cov $min_peak_cov\n+\n+\t\t#end if\n+\n+ #if not $max_peak_cov.value is None\n+\n+ -max_peak_cov $max_peak_cov\n+\n+\t\t#end if\n+\n+ #if not $histo_bin_width.value is None\n+\n+ -histo_bin_width $histo_bin_width\n+\n+\t\t#end if\n+\n+ #if not $histo_sn_ratio.value is None\n+\n+ -histo_sn_ratio $histo_sn_ratio\n+\n+\t\t#end if\n+\n+ </command>\n+\n+ <inputs>\n+\n+\t\t<param name="hash_length" type="text" value="31" label="Hash length : integer <= 150 OR m,M,s with m (min km'..b' <param name="valid_connections" type="integer" optional="true" label="META-VELVETG - Minimum allowable number of consistent paired-end connections. Default: 1 (-valid_connections)"/>\n+ <param name="noise_connections" type="integer" optional="true" label="META-VELVETG - Maximum allowable number of inconsistent paired-end connections. Default: 0 (-noise_connections)"/>\n+\n+ <param name="use_connections" type="select" label="META-VELVETG - Use paired-end connections for graph splitting. Default: yes (-use_connections)">\n+ <option value="">Yes</option>\n+ <option value="-use_connections no">No</option>\n+ </param>\n+\n+ <param name="report_split_detail" type="select" label="META-VELVETG - Report sequences around repeat nodes. Default: no (-report_split_detail)">\n+ <option value="">No</option>\n+ <option value="-report_split_detail yes">Yes</option>\n+ </param>\n+\n+ <param name="report_subgraph" type="select" label="META-VELVETG - Report node sequences for each subgraph. Default: no (-report_subgraph)">\n+ <option value="">No</option>\n+ <option value="-report_subgraph yes">Yes</option>\n+ </param>\n+\n+ <param name="exp_covs" type="text" optional="true" label="META-VELVETG - Expected coverages for each species in microbiome. Default: auto (-exp_covs)"/>\n+\n+ <param name="min_peak_cov" type="float" optional="true" label="META-VELVETG - Minimum peak coverage. Default: 0 (-min_peak_cov)"/>\n+ <param name="max_peak_cov" type="float" optional="true" label="META-VELVETG - Maximum peak coverage. Default: 500 (-max_peak_cov)"/>\n+ <param name="histo_bin_width" type="float" optional="true" label="META-VELVETG - Bin width of peak coverage histogram. Default: 1 (-histo_bin_width)"/>\n+ <param name="histo_sn_ratio" type="float" optional="true" label="META-VELVETG - Signal-noise ratio to remove peak noises. Default: 10 (-histo_sn_ratio)"/>\n+\n+ </inputs>\n+\n+\t<outputs>\n+\n+ <data format="fasta" name="meta_velvet_contigs" from_work_dir="meta-velvetg.contigs.fa" label="${tool.name} on ${on_string}: meta-velvetg.contigs.fasta">\n+ <filter>(meta == \'\')</filter>\n+ </data>\n+\n+ <data format="fasta" name="velvet_contigs" from_work_dir="contigs.fa" label="${tool.name} on ${on_string}: contigs.fasta">\n+ <filter>(meta == \'-nometa\')</filter>\n+ </data>\n+\n+ <data format="fasta" name="velvet_singlets" from_work_dir="Singlets.fasta" label="${tool.name} on ${on_string}: singlets.fasta">\n+ <filter>(unused_reads == \'-unused_reads yes\')</filter>\n+ </data>\n+\n+ <data format="txt" name="meta-velvetg.asm.afg" from_work_dir="meta-velvetg.asm.afg" label="${tool.name} on ${on_string}: meta-velvetg.asm.afg">\n+ <filter>((meta == \'\') and (amos_file == \'-amos_file yes\'))</filter>\n+ </data>\n+\n+ <data format="txt" name="velvet_asm.afg" from_work_dir="velvet_asm.afg" label="${tool.name} on ${on_string}: velvet_asm.afg">\n+ <filter>((meta == \'-nometa\') and (amos_file == \'-amos_file yes\'))</filter>\n+ </data>\n+\n+ <data format="tabular" name="stats.txt" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats.txt">\n+ <filter>(meta == \'-nometa\')</filter>\n+ </data>\n+\n+ <data format="tabular" name="meta-velvetg.split-stats.txt" from_work_dir="meta-velvetg.split-stats.txt" label="${tool.name} on ${on_string}: meta-velvetg.split-stats.txt">\n+ <filter>(meta == \'\')</filter>\n+ </data>\n+\n+ <data format="txt" name="LastGraph" from_work_dir="LastGraph" label="${tool.name} on ${on_string}: LastGraph">\n+ <filter>(meta == \'-nometa\')</filter>\n+ </data>\n+\n+ <data format="txt" name="meta-velvetg.LastGraph" from_work_dir="meta-velvetg.LastGraph" label="${tool.name} on ${on_string}: meta-velvetg.LastGraph">\n+ <filter>(meta == \'\')</filter>\n+ </data>\n+\n+ <data format="tabular" name="meta-velvetg.Graph2-stats.txt" from_work_dir="meta-velvetg.Graph2-stats.txt" label="${tool.name} on ${on_string}: meta-velvetg.Graph2-stats.txt">\n+ <filter>(meta == \'\')</filter>\n+ </data>\n+\n+ </outputs>\n+\n+</tool>\n' |