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comparison runAssembly_cDNA.xml @ 3:bf1f8bc4abe6 default tip

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minor updates for v2.6
author eskirton@lbl.gov
date Wed, 21 Dec 2011 19:42:53 -0800
parents 2d86d5b112e8
children
comparison
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2:2d86d5b112e8 3:bf1f8bc4abe6
1 <tool id="runAssembly_cDNA" name="runAssembly cDNA" version="1.0.0" force_history_refresh='True'> 1 <tool id="runAssembly_cDNA" name="runAssembly cDNA" version="1.0.1" force_history_refresh='True'>
2 <description>De novo assembly of Roche/454 cDNA reads using Newbler</description> 2 <description>De novo assembly of Roche/454 cDNA reads using Newbler</description>
3 <command interpreter='perl'>runAssembly_cDNA_wrapper.pl 3 <command interpreter='perl'>runAssembly_cDNA_wrapper.pl
4 $newbler_metrics.extra_files_path 4 $newbler_metrics.extra_files_path
5 $newbler_metrics 5 $newbler_metrics
6 $read_status 6 $read_status
15 $pair_align 15 $pair_align
16 $pair_status 16 $pair_status
17 $scaffolds_fasta 17 $scaffolds_fasta
18 $scaffolds_qual 18 $scaffolds_qual
19 $scaffolds_agp 19 $scaffolds_agp
20 $contig_scaffolds_agp
20 $tag_pair_align 21 $tag_pair_align
21 $trim_status 22 $trim_status
22 $isotigs_ace 23 $isotigs_ace
23 $isotigs_fasta 24 $isotigs_fasta
24 $isotigs_qual 25 $isotigs_qual
25 $isotigs_agp 26 $isotigs_agp
26 $isotigs_layout 27 $isotigs_layout
27 $newbler_exe -o $newbler_metrics.extra_files_path 28 runAssembly
29 -o $newbler_metrics.extra_files_path
28 -cpu 8 30 -cpu 8
29 $rip 31 $rip
30 -e $e 32 -e $e
31 -mi $mi 33 -mi $mi
32 -ml $ml 34 -ml $ml
68 #for $i in $sanger_inputs 70 #for $i in $sanger_inputs
69 ${i.sanger_input} 71 ${i.sanger_input}
70 #end for 72 #end for
71 </command> 73 </command>
72 <inputs> 74 <inputs>
73 <!-- NEWBLER VERSION -->
74 <param name='newbler_exe' type='select' display='radio' label='Newbler version'>
75 <option value='/jgi/tools/454/rig-DataProcessing_2.3/bin/runAssembly'>2.3</option>
76 <option value='/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runAssembly'>2.4</option>
77 <option value='/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runAssembly' selected='true'>2.5</option>
78 </param>
79
80 <!-- READSEQ INFILES --> 75 <!-- READSEQ INFILES -->
81 <repeat name="sff_inputs" title="Unpaired Reads Sff Files"> 76 <repeat name="sff_inputs" title="Unpaired Reads Sff Files">
82 <param name="sff_input" type="data" format="sff" label="SE Sff file"/> 77 <param name="sff_input" type="data" format="sff" label="SE Sff file"/>
83 </repeat> 78 </repeat>
84 <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files"> 79 <repeat name="sanger_inputs" title="Unpaired Reads Fasta/Fastq Files">
85 <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/> 80 <param name="sanger_input" type="data" format="fasta,fastqsanger" label="SE Fasta/Fastq file"/>
86 </repeat> 81 </repeat>
87 <repeat name="sff_paired_inputs" title="Paired Reads Sff Files"> 82 <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">
88 <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/> 83 <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>
89 </repeat> 84 </repeat>
90 <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files"> 85 <repeat name="sanger_paired_inputs" title="Paired Reads Fasta/Fastq Files">
91 <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/> 86 <param name="sanger_paired_input" type="data" format="fasta,fastqsanger" label="PE Fasta/Fastq file"/>
92 </repeat> 87 </repeat>
93 <param name='paired_reads' type='select' display='radio' label='[-paired_reads] If supplying paired reads (above), do you want paired-read info?'> 88 <param name="paired_reads" type="select" display="radio" label="[-paired_reads] If supplying paired reads (above), do you want paired-read info?">
94 <option value='false'>no</option> 89 <option value="false">no</option>
95 <option value='true'>[-paired_reads] yes</option> 90 <option value="true">[-paired_reads] yes</option>
96 </param> 91 </param>
97 <param name='pair' type='select' display='radio' label='[-pair] Output pairwise overlaps'> 92 <param name="pair" type="select" display="radio" label="[-pair] Output pairwise overlaps">
98 <option value=''>no</option> 93 <option value="">no</option>
99 <option value='-pair'>[-pair] yes</option> 94 <option value="-pair">[-pair] yes</option>
100 </param> 95 </param>
101 96
102 <param name='it' type='integer' value='100' label='[-it] Specify the maximum number of isotigs in an isogroup. Maximum is 10,000.'/> 97 <param name="it" type="integer" value="100" label="[-it] Specify the maximum number of isotigs in an isogroup. Maximum is 10,000."/>
103 <param name='ig' type='integer' value='500' label='[-ig] Specify the maximum number of contigs in an isogroup.'/> 98 <param name="ig" type="integer" value="500" label="[-ig] Specify the maximum number of contigs in an isogroup."/>
104 <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'/> 99 <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"/>
105 <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.'/> 100 <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."/>
106 101
107 <!-- OPTIONAL ARGUMENTS --> 102 <!-- OPTIONAL ARGUMENTS -->
108 <param name='mcf' type='data' format='tabular' optional='true' label='[-mcf] Specify non-default MID config file' /> 103 <param name="mcf" type="data" format="tabular" optional="true" label="[-mcf] Specify non-default MID config file" />
109 <param name='fi' type='data' format='txt' optional='true' label='[-fi] Include filter file to be specified' /> 104 <param name="fi" type="data" format="txt" optional="true" label="[-fi] Include filter file to be specified" />
110 <param name='fe' type='data' format='txt' optional='true' label='[-fe] Exclude filter file to be specified' /> 105 <param name="fe" type="data" format="txt" optional="true" label="[-fe] Exclude filter file to be specified" />
111 <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)" /> 106 <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)" />
112 <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" /> 107 <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" />
113 108
114 <!-- READ TRIMMING --> 109 <!-- READ TRIMMING -->
115 <param name='minlen' type='integer' value='20' label='[-minlen] Minimum length of reads to use (15-45 allowed)'/> 110 <param name="minlen" type="integer" value="20" label="[-minlen] Minimum length of reads to use (15-45 allowed)"/>
116 <param name='notrim' type='boolean' truevalue='-notrim' falsevalue='' checked='false' label='[-notrim] Do not perform default quality and primer trimming of input reads'/> 111 <param name="notrim" type="boolean" truevalue="-notrim" falsevalue="" checked="false" label="[-notrim] Do not perform default quality and primer trimming of input reads"/>
117 <param name='tr' type='select' display='radio' label='[-tr] Output trimmed reads'> 112 <param name="tr" type="select" display="radio" label="[-tr] Output trimmed reads">
118 <option value=''>no</option> 113 <option value="">no</option>
119 <option value='-tr'>[-tr] yes</option> 114 <option value="-tr">[-tr] yes</option>
120 </param> 115 </param>
121 <param name='nor' type='boolean' truevalue='-nor' falsevalue='' label='[-nor] Turn off the automatic rescore function for read quality scores'/> 116 <param name="nor" type="boolean" truevalue="-nor" falsevalue="" label="[-nor] Turn off the automatic rescore function for read quality scores"/>
122 <param name='ud' type='boolean' truevalue='-ud' falsevalue='' label='[-ud] Treat each read separately, with no grouping of duplicates'/> 117 <param name="ud" type="boolean" truevalue="-ud" falsevalue="" label="[-ud] Treat each read separately, with no grouping of duplicates"/>
123 118
124 <!-- ALIGNMENT PARAMETERS --> 119 <!-- ALIGNMENT PARAMETERS -->
125 <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'/> 120 <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"/>
126 <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'/> 121 <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"/>
127 <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'/> 122 <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"/>
128 <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"/> 123 <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"/>
129 <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"/> 124 <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"/>
130 <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'/> 125 <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"/>
131 126
132 <!-- ASSEMBLY OPTIONS --> 127 <!-- ASSEMBLY OPTIONS -->
133 <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"/> 128 <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"/>
134 <param name='large' type='boolean' truevalue='-large' falsevalue='' checked='false' label='[-large] Check if large or complex genome'/> 129 <param name="large" type="boolean" truevalue="-large" falsevalue="" checked="false" label="[-large] Check if large or complex genome"/>
130 <param name="scaffold" type="boolean" truevalue="-scaffold" falsevalue="" checked="true" label="[-scaffold] Output scaffolds"
131 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." />
135 132
136 <!-- OUTPUT OPTIONS --> 133 <!-- OUTPUT OPTIONS -->
137 <param name='no' type='select' display='radio' label='[-no] Do complete assembly'> 134 <param name="no" type="select" display="radio" label="[-no] Do complete assembly">
138 <option value=''>do complete assembly</option> 135 <option value="">do complete assembly</option>
139 <option value='-no'>[-no] do not assemble; do alignments only</option> 136 <option value="-no">[-no] do not assemble; do alignments only</option>
140 </param> 137 </param>
141 <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'/> 138 <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"/>
142 <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."/> 139 <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."/>
143 <param name='rip' type='boolean' truevalue='' falsevalue='-rip' checked='false' label='[-rip] Output each read in only one contig'/> 140 <param name="rip" type="boolean" truevalue="" falsevalue="-rip" checked="false" label="[-rip] Output each read in only one contig"/>
144 <param name='info' type='select' display='radio' label='Output Alignment Info'> 141 <param name="info" type="select" display="radio" label="Output Alignment Info">
145 <option value='-info'>[-info] yes</option> 142 <option value="-info">[-info] yes</option>
146 <option value='-infoall'>[-infoall] yes, including 0-coverage positions</option> 143 <option value="-infoall">[-infoall] yes, including 0-coverage positions</option>
147 </param> 144 </param>
148 <param name='ace' type='select' display='radio' label='Produce Ace assembly file'> 145 <param name="ace" type="select" display="radio" label="Produce Ace assembly file">
149 <option value=''>no</option> 146 <option value="">no</option>
150 <option value='-ace'>[-ace] yes</option> 147 <option value="-ace">[-ace] yes</option>
151 <option value='-ace -consed'>[-consed] yes, in consed dir</option> 148 <option value="-ace -consed">[-consed] yes, in consed dir</option>
152 </param> 149 </param>
153 </inputs> 150 </inputs>
154 151
155 <outputs> 152 <outputs>
156 <data name='newbler_metrics' format='txt' /> 153 <data name="newbler_metrics" format="txt" />
157 <data name='read_status' format='tabular' label='Read Status'/> 154 <data name="read_status" format="tabular" label="${tool.name} on $on_string: Read Status"/>
158 <data name='trimmed_reads_fasta' format='fasta' label='Trimmed Reads (Fasta)'> 155 <data name="trimmed_reads_fasta" format="fasta" label="${tool.name} on $on_string: Trimmed Reads (Fasta)">
159 <filter>tr == '-tr'</filter> 156 <filter>tr == "-tr"</filter>
160 </data> 157 </data>
161 <data name='trimmed_reads_qual' format='qual454' label='Trimmed Reads (Qual)'> 158 <data name="trimmed_reads_qual" format="qual454" label="${tool.name} on $on_string: Trimmed Reads (Qual)">
162 <filter>tr == '-tr'</filter> 159 <filter>tr == "-tr"</filter>
163 </data> 160 </data>
164 <!-- the following produced only if no != '-no' --> 161 <!-- the following produced only if no != "-no" -->
165 <data name='alignment_info' format='tabular' label='Alignment Info'> 162 <data name="alignment_info" format="tabular" label="${tool.name} on $on_string: Alignment Info">
166 <filter>no != '-no'</filter> 163 <filter>no != "-no"</filter>
167 </data> 164 </data>
168 <data name='all_contigs_fasta' format='fasta' label='All Contigs (Fasta)'> 165 <data name="all_contigs_fasta" format="fasta" label="${tool.name} on $on_string: All Contigs (Fasta)">
169 <filter>no != '-no'</filter> 166 <filter>no != "-no"</filter>
170 </data> 167 </data>
171 <data name='all_contigs_qual' format='qual454' label='All Contigs (Qual454)'> 168 <data name="all_contigs_qual" format="qual454" label="${tool.name} on $on_string: All Contigs (Qual454)">
172 <filter>no != '-no'</filter> 169 <filter>no != "-no"</filter>
173 </data> 170 </data>
174 <data name='contigs_ace' format='ace' label='Contigs (Ace)'> 171 <data name="contigs_ace" format="ace" label="${tool.name} on $on_string: Contigs (Ace)">
175 <filter>ace == '-ace' and no != '-no'</filter> 172 <filter>ace == "-ace" and no != "-no"</filter>
176 </data> 173 </data>
177 <data name='contigs_consed_ace' format='ace' label='Contigs (Consed/Ace)'> 174 <data name="contigs_consed_ace" format="ace" label="${tool.name} on $on_string: Contigs (Consed/Ace)">
178 <filter>ace == '-ace -consed' and no != '-no'</filter> 175 <filter>ace == "-ace -consed" and no != "-no"</filter>
179 </data> 176 </data>
180 177
181 <data name='contig_graph' format='txt' label='Contig Graph'/> 178 <data name="contig_graph" format="txt" label="${tool.name} on $on_string: Contig Graph"/>
182 <data name='pair_align' format='txt' label='Pairwise Alignments'> 179 <data name="pair_align" format="txt" label="${tool.name} on $on_string: Pairwise Alignments">
183 <filter>pair == '-pair' and no != '-no'</filter> 180 <filter>pair == "-pair" and no != "-no"</filter>
184 </data> 181 </data>
185 <data name='pair_status' format='tabular' label='Paired-End Read Status'> 182 <data name="pair_status" format="tabular" label="${tool.name} on $on_string: Paired-End Read Status">
186 <filter>paired_reads == 'true' and no != '-no'</filter> 183 <filter>paired_reads == "true" and no != "-no"</filter>
187 </data> 184 </data>
188 <data name='scaffolds_fasta' format='fasta' label='Scaffolds (Fasta)'> 185 <data name="scaffolds_fasta" format="fasta" label="${tool.name} on $on_string: Scaffolds (Fasta)">
189 <filter>paired_reads == 'true' and no != '-no'</filter> 186 <filter>paired_reads == "true" and no != "-no"</filter>
190 </data> 187 </data>
191 <data name='scaffolds_qual' format='qual454' label='Scaffolds (Qual454)'> 188 <data name="scaffolds_qual" format="qual454" label="${tool.name} on $on_string: Scaffolds (Qual454)">
192 <filter>paired_reads == 'true' and no != '-no'</filter> 189 <filter>paired_reads == "true" and no != "-no"</filter>
193 </data> 190 </data>
194 <data name='scaffolds_agp' format='tabular' label='Scaffolds (Agp)'> 191 <data name="scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Scaffolds (Agp)">
195 <filter>paired_reads == 'true' and no != '-no'</filter> 192 <filter>paired_reads == "true" and no != "-no"</filter>
196 </data> 193 </data>
197 <data name='tag_pair_align' format='txt' label='Tag Pair Alignments'> 194 <data name="contig_scaffolds_agp" format="tabular" label="${tool.name} on $on_string: Contig Scaffolds(Agp)">
198 <filter>pair == '-pair' and paired_reads == 'true' and no != '-no'</filter> 195 <filter>scaffold is True</filter>
199 </data> 196 </data>
200 <data name='trim_status' format='tabular' label='Trim Status'/> 197 <data name="tag_pair_align" format="txt" label="${tool.name} on $on_string: Tag Pair Alignments">
201 198 <filter>pair == "-pair" and paired_reads == "true" and no != "-no"</filter>
202 <data name='isotigs_ace' format='ace' label='Isotigs (Ace)'> 199 </data>
203 <filter>ace != '' and no != '-no'</filter> 200 <data name="trim_status" format="tabular" label="${tool.name} on $on_string: Trim Status"/>
204 </data> 201
205 <data name='isotigs_fasta' format='fasta' label='Isotigs (Fasta)'> 202 <data name="isotigs_ace" format="ace" label="${tool.name} on $on_string: Isotigs (Ace)">
206 <filter>no != '-no'</filter> 203 <filter>ace != "" and no != "-no"</filter>
207 </data> 204 </data>
208 <data name='isotigs_qual' format='qual454' label='Isotigs (Qual454)'> 205 <data name="isotigs_fasta" format="fasta" label="${tool.name} on $on_string: Isotigs (Fasta)">
209 <filter>no != '-no'</filter> 206 <filter>no != "-no"</filter>
210 </data> 207 </data>
211 <data name='isotigs_agp' format='tabular' label='Isotigs (Agp)'> 208 <data name="isotigs_qual" format="qual454" label="${tool.name} on $on_string: Isotigs (Qual454)">
212 <filter>no != '-no'</filter> 209 <filter>no != "-no"</filter>
213 </data> 210 </data>
214 <data name='isotigs_layout' format='txt' label='Isotig Layout'> 211 <data name="isotigs_agp" format="tabular" label="${tool.name} on $on_string: Isotigs (Agp)">
215 <filter>no != '-no'</filter> 212 <filter>no != "-no"</filter>
213 </data>
214 <data name="isotigs_layout" format="txt" label="${tool.name} on $on_string: Isotig Layout">
215 <filter>no != "-no"</filter>
216 </data> 216 </data>
217 217
218 </outputs> 218 </outputs>
219 <help> 219 <help>
220 220