1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/68c34a8bd236/ changeset: 68c34a8bd236 branches: user: kanwei date: 2011-05-27 11:01:46 summary: Velvet wrapper: fix typos, tabs -> spaces, spacing affected #: 2 files (1.2 KB)
--- a/tools/sr_assembly/velvetg.xml Fri May 27 10:47:17 2011 +0200 +++ b/tools/sr_assembly/velvetg.xml Fri May 27 11:01:46 2011 +0200 @@ -1,7 +1,7 @@ <tool id="velvetg" name="velvetg" version="1.0.0"> - <description>Velvet sequence assembler for very short reads</description> - <command interpreter="python"> - velvetg_wrapper.py + <description>Velvet sequence assembler for very short reads</description> + <command interpreter="python"> + velvetg_wrapper.py '$input.extra_files_path' '$contigs' '$stats' '$LastGraph' '$velvet_asm' '$unused_reads_fasta' #if $generate_amos.afg == "yes": @@ -65,159 +65,159 @@ $reads.options.scaffolding #end if #end if - </command> - <inputs> - <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/> - <conditional name="generate_amos"> - <param name="afg" type="select" label="Generate a AMOS.afg file"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"/> - <when value="yes"/> - </conditional> + </command> + <inputs> + <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/> + <conditional name="generate_amos"> + <param name="afg" type="select" label="Generate a AMOS.afg file"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"/> + </conditional>
- <conditional name="unused_reads"> - <param name="generate_unused" type="select" label="Generate a UnusedReads fasta file"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"/> - <when value="yes"/> - </conditional> + <conditional name="unused_reads"> + <param name="generate_unused" type="select" label="Generate a UnusedReads fasta file"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"/> + </conditional>
- <conditional name="last_graph"> - <param name="generate_graph" type="select" label="Generate velvet LastGraph file"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"/> - <when value="yes"/> - </conditional> + <conditional name="last_graph"> + <param name="generate_graph" type="select" label="Generate velvet LastGraph file"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"/> + </conditional>
- <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="track short read positions" help=" tracking of short read positions in assembly"/> + <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="track short read positions" help=" tracking of short read positions in assembly"/>
- <conditional name="coverage"> - <param name="cutoff" type="select" label="Coverage cutoff" help=""> - <option value="none">None</option> - <option value="auto">Automatically Determined</option> - <option value="value">Specify Cutoff Value</option> - </param> - <when value="none"/> - <when value="auto"/> - <when value="value"> - <param name="cov_cutoff" value = "10.0" label="Remove nodes with coverage below" type="float" /> - </when> - </conditional> + <conditional name="coverage"> + <param name="cutoff" type="select" label="Coverage cutoff" help=""> + <option value="none">None</option> + <option value="auto">Automatically Determined</option> + <option value="value">Specify Cutoff Value</option> + </param> + <when value="none"/> + <when value="auto"/> + <when value="value"> + <param name="cov_cutoff" value = "10.0" label="Remove nodes with coverage below" type="float" /> + </when> + </conditional>
- <conditional name="expected"> - <param name="coverage" type="select" label="Expected Coverage of Unique Regions" help=""> - <option value="none">None</option> - <option value="auto">Automatically Determined</option> - <option value="value">Specify Expected Value</option> - </param> - <when value="none"/> - <when value="auto"/> - <when value="value"> - <param name="exp_cov" value = "10.0" label="Remove nodes with coverage below" type="float" /> - </when> - </conditional> + <conditional name="expected"> + <param name="coverage" type="select" label="Expected Coverage of Unique Regions" help=""> + <option value="none">None</option> + <option value="auto">Automatically Determined</option> + <option value="value">Specify Expected Value</option> + </param> + <when value="none"/> + <when value="auto"/> + <when value="value"> + <param name="exp_cov" value = "10.0" label="Remove nodes with coverage below" type="float" /> + </when> + </conditional>
- <conditional name="contig_lgth"> - <param name="use_contig_lgth" type="select" label=" Set minimum contig length" help="minimum contig length exported to contigs.fa file (default: hash length * 2)."> - <option value="no">No</option> - <option value="yes">Yes</option> + <conditional name="contig_lgth"> + <param name="use_contig_lgth" type="select" label=" Set minimum contig length" help="minimum contig length exported to contigs.fa file (default: hash length * 2)."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="min_contig_lgth" value = "42" label="minimum contig length" type="integer" help="minimum contig length exported to contigs.fa file (default: hash length * 2)"/> + </when> + </conditional> + + <conditional name="reads"> + <param name="paired" type="select" label="Using Paired Reads"> + <option value="no">No</option> + <option value="yes" selected="${input.metadata.paired_end_reads}">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="ins_length" value = "-1" label="Insert Length in Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads"/> + <conditional name="options"> + <param name="advanced" type="select" label="Velvet Advanced Options"> + <option value="no">Use Defaults</option> + <option value="yes">Set Advanced Option Values</option></param><when value="no"/><when value="yes"> - <param name="min_contig_lgth" value = "42" label="minimum contig length" type="integer" help="minimum contig length exported to contigs.fa file (default: hash length * 2)"/> - </when> - </conditional> - - <conditional name="reads"> - <param name="paired" type="select" label="Using Paired Reads"> - <option value="no">No</option> - <option value="yes" selected="${input.metadata.paired_end_reads}">Yes</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="ins_length" value = "-1" label="Insert Length in Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads"/> - <conditional name="options"> - <param name="advanced" type="select" label="Velvet Advanced Options"> - <option value="no">Use Defaults</option> - <option value="yes">Set Advanced Option Values</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="ins_length_sd" value = "-1" label="Estimate of Standard Deviation of Paired-End Read dataset(ignored when -1)" type="integer" help="Estimate of standard deviation of Paired-End Read dataset (default: 10% of corresponding length)"/> - <param name="ins_length2" value = "-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/> - <param name="ins_length2_sd" value = "-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/> - <param name="ins_length_long" value = "-1" label="Insert Length in Long Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two long paired-end reads"/> - <param name="ins_length_long_sd" value = "-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of Long Paired-End Read dataset (default: 10% of corresponding length)"/> - <param name="max_branch_length" value = "-1" label="Maximum branch length (ignored when -1)" type="integer" help="maximum length in base pair of bubble (default: 100)"/> - <param name="max_divergence" value = "-1." label="Maximum max_divergence (between .0 and 1., ignored when -1.)" type="float" help="maximum divergence rate between two branches in a bubble (default: .2)"/> - <param name="max_gap_count" value = "-1" label="Maximum gap count (ignored when -1)" type="integer" help="maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)"/> - <param name="min_pair_count" value = "-1" label="Minimum read-pair count (ignored when -1)" type="integer" help="minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)"/> - <param name="max_coverage" value = "-1." label="Maximum coverage exclusion(ignored when -1.)" type="float" help="Exclude data that has coverage more than this maximum coverage value"/> - <param name="long_mult_cutoff" value = "-1" label="Minimum number of long reads required to merge contigs (ignored when -1)" type="integer" help="minimum number of long reads required to merge contigs (default: 2)"/> - <param name="scaffolding" type="boolean" checked="true" truevalue="-scaffolding yes" falsevalue="-scaffolding no" label="Use Scaffolding" help="Scaffold contigs that it cannot quite be connected (This results in sequences of Ns in the contigs)"/> + <param name="ins_length_sd" value = "-1" label="Estimate of Standard Deviation of Paired-End Read dataset(ignored when -1)" type="integer" help="Estimate of standard deviation of Paired-End Read dataset (default: 10% of corresponding length)"/> + <param name="ins_length2" value = "-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/> + <param name="ins_length2_sd" value = "-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/> + <param name="ins_length_long" value = "-1" label="Insert Length in Long Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two long paired-end reads"/> + <param name="ins_length_long_sd" value = "-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of Long Paired-End Read dataset (default: 10% of corresponding length)"/> + <param name="max_branch_length" value = "-1" label="Maximum branch length (ignored when -1)" type="integer" help="maximum length in base pair of bubble (default: 100)"/> + <param name="max_divergence" value = "-1." label="Maximum max_divergence (between .0 and 1., ignored when -1.)" type="float" help="maximum divergence rate between two branches in a bubble (default: .2)"/> + <param name="max_gap_count" value = "-1" label="Maximum gap count (ignored when -1)" type="integer" help="maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)"/> + <param name="min_pair_count" value = "-1" label="Minimum read-pair count (ignored when -1)" type="integer" help="minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)"/> + <param name="max_coverage" value = "-1." label="Maximum coverage exclusion(ignored when -1.)" type="float" help="Exclude data that has coverage more than this maximum coverage value"/> + <param name="long_mult_cutoff" value = "-1" label="Minimum number of long reads required to merge contigs (ignored when -1)" type="integer" help="minimum number of long reads required to merge contigs (default: 2)"/> + <param name="scaffolding" type="boolean" checked="true" truevalue="-scaffolding yes" falsevalue="-scaffolding no" label="Use Scaffolding" help="Scaffold contigs that it cannot quite be connected (This results in sequences of Ns in the contigs)"/></when> - </conditional> - </when> - </conditional> - </inputs> - <outputs> - <!-- - <data format="velvet_graph" name="LastGraph" /> - --> - <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph"> - <filter>last_graph['generate_graph'] == "yes"</filter> - </data> - <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg"> - <filter>generate_amos['afg'] == "yes"</filter> - </data> - <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads"> - <filter>unused_reads['generate_unused'] == "yes"</filter> - </data> - <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats"/> - <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs"/> - </outputs> - <requirements> - <requirement type="package">velvet</requirement> - </requirements> - <tests> - <test> - <param name="input" value="velveth_test1/output.html" ftype="velvet" > - <composite_data value='velveth_test1/Sequences' ftype="Sequences"/> - <composite_data value='velveth_test1/Roadmaps' ftype="Roadmaps"/> - <composite_data value='velveth_test1/Log'/> - </param> - <param name="afg" value="yes" /> - <param name="generate_unused" value="yes" /> - <param name="generate_graph" value="no" /> - <param name="read_trkg" value="-read_trkg no" /> - <param name="cutoff" value="auto" /> - <param name="coverage" value="auto" /> - <param name="use_contig_lgth" value="no" /> - <param name="paired" value="no" /> - <!-- - <output name="LastGraph" file="velvetg_test1/lastgraph.txt" compare="diff"/> - --> - <output name="velvet_asm" file="velvetg_test1/amos.afg" compare="diff"/> - <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" compare="diff"/> - <output name="stats" file="velvetg_test1/stats.csv" compare="diff"/> - <output name="contigs" file="velvetg_test1/contigs.fa" compare="diff"/> - </test> - </tests> - <help> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <!-- + <data format="velvet_graph" name="LastGraph" /> + --> + <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph"> + <filter>last_graph['generate_graph'] == "yes"</filter> + </data> + <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg"> + <filter>generate_amos['afg'] == "yes"</filter> + </data> + <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads"> + <filter>unused_reads['generate_unused'] == "yes"</filter> + </data> + <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats"/> + <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs"/> + </outputs> + <requirements> + <requirement type="package">velvet</requirement> + </requirements> + <tests> + <test> + <param name="input" value="velveth_test1/output.html" ftype="velvet" > + <composite_data value='velveth_test1/Sequences' ftype="Sequences"/> + <composite_data value='velveth_test1/Roadmaps' ftype="Roadmaps"/> + <composite_data value='velveth_test1/Log'/> + </param> + <param name="afg" value="yes" /> + <param name="generate_unused" value="yes" /> + <param name="generate_graph" value="no" /> + <param name="read_trkg" value="-read_trkg no" /> + <param name="cutoff" value="auto" /> + <param name="coverage" value="auto" /> + <param name="use_contig_lgth" value="no" /> + <param name="paired" value="no" /> + <!-- + <output name="LastGraph" file="velvetg_test1/lastgraph.txt" compare="diff"/> + --> + <output name="velvet_asm" file="velvetg_test1/amos.afg" compare="diff"/> + <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" compare="diff"/> + <output name="stats" file="velvetg_test1/stats.csv" compare="diff"/> + <output name="contigs" file="velvetg_test1/contigs.fa" compare="diff"/> + </test> + </tests> + <help> **Velvet Overview**
Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
-Read the Velvet `documentation`__ for details on using the Vevlet Assembler. +Read the Velvet `documentation`__ for details on using the Velvet Assembler.
.. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
@@ -238,7 +238,7 @@ **Contigs**
The *contigs.fa* file. -This fasta file contains the sequences of the contigs longer than 2k, where k is the word-length used in velveth. If you have specified a min contig lgth threshold, then the contigs shorter than that value are omitted. +This fasta file contains the sequences of the contigs longer than 2k, where k is the word-length used in velveth. If you have specified a min contig length threshold, then the contigs shorter than that value are omitted. Note that the length and coverage information provided in the header of each contig should therefore be understood in k-mers and in k-mer coverage (cf. 5.1) respectively. The N's in the sequence correspond to gaps between scaffolded contigs. The number of N's corresponds to the estimated length of the gap. For reasons of compatibility with the archives, any gap shorter than 10bp is represented by a sequence of 10 N's.
@@ -297,5 +297,5 @@ directory/LastGraph : special formatted file with all the information on the final graph directory/velvet_asm.afg : (if requested) AMOS compatible assembly file
- </help> + </help></tool>
--- a/tools/sr_assembly/velveth.xml Fri May 27 10:47:17 2011 +0200 +++ b/tools/sr_assembly/velveth.xml Fri May 27 11:01:46 2011 +0200 @@ -1,79 +1,79 @@ <tool id="velveth" name="velveth" version="1.0.0"> - <description>Prepare a dataset for the Velvet velvetg Assembler</description> - <command interpreter="python"> - velveth_wrapper.py + <description>Prepare a dataset for the Velvet velvetg Assembler</description> + <command interpreter="python"> + velveth_wrapper.py '$out_file1' '$out_file1.extra_files_path' $hash_length $strand_specific #for $i in $inputs - ${i.file_format} - ${i.read_type} - ${i.input} + ${i.file_format} + ${i.read_type} + ${i.input} #end for - </command> - <inputs> - <param label="Hash Length" name="hash_length" type="select" help="k-mer length in base pairs of the words being hashed."> - <option value="11">11</option> - <option value="13">13</option> - <option value="15">15</option> - <option value="17">17</option> - <option value="19">19</option> - <option value="21" selected="yes">21</option> - <option value="23">23</option> - <option value="25">25</option> - <option value="27">27</option> - <option value="29">29</option> - </param> - <param name="strand_specific" type="boolean" checked="false" truevalue="-strand_specific" falsevalue="" label="Use strand specific transcriptome sequencing" help="If you are using a strand specific transcriptome sequencing protocol, you may wish to use this option for better results."/> - <repeat name="inputs" title="Input Files"> - <param label="file format" name="file_format" type="select"> - <option value="-fasta" selected="yes">fasta</option> - <option value="-fastq">fastq</option> - <option value="-eland">eland</option> - <option value="-gerald">gerald</option> - </param> - <param label="read type" name="read_type" type="select"> - <option value="-short" selected="yes">short reads</option> - <option value="-shortPaired">shortPaired reads</option> - <option value="-short2">short2 reads</option> - <option value="-shortPaired2">shortPaired2 reads</option> - <option value="-long">long reads</option> - <option value="-longPaired">longPaired reads</option> - </param> + </command> + <inputs> + <param label="Hash Length" name="hash_length" type="select" help="k-mer length in base pairs of the words being hashed."> + <option value="11">11</option> + <option value="13">13</option> + <option value="15">15</option> + <option value="17">17</option> + <option value="19">19</option> + <option value="21" selected="yes">21</option> + <option value="23">23</option> + <option value="25">25</option> + <option value="27">27</option> + <option value="29">29</option> + </param> + <param name="strand_specific" type="boolean" checked="false" truevalue="-strand_specific" falsevalue="" label="Use strand specific transcriptome sequencing" help="If you are using a strand specific transcriptome sequencing protocol, you may wish to use this option for better results."/> + <repeat name="inputs" title="Input Files"> + <param label="file format" name="file_format" type="select"> + <option value="-fasta" selected="yes">fasta</option> + <option value="-fastq">fastq</option> + <option value="-eland">eland</option> + <option value="-gerald">gerald</option> + </param> + <param label="read type" name="read_type" type="select"> + <option value="-short" selected="yes">short reads</option> + <option value="-shortPaired">shortPaired reads</option> + <option value="-short2">short2 reads</option> + <option value="-shortPaired2">shortPaired2 reads</option> + <option value="-long">long reads</option> + <option value="-longPaired">longPaired reads</option> + </param>
- <param name="input" type="data" format="fasta,fastq,eland,gerald" label="Dataset"/> - </repeat> - </inputs> - <outputs> - <data format="velvet" name="out_file1" /> - </outputs> - <requirements> - <requirement type="package">velvet</requirement> - </requirements> - <tests> - <test> - <param name="hash_length" value="21" /> - <param name="read_type" value="-shortPaired" /> - <!-- <repeat name="inputs"> --> - <param name="file_format" value="fasta" /> - <param name="read_type" value="shortPaired reads" /> - <param name="input" value="velvet_test_reads.fa" ftype="fasta" /> - <!-- </repeat> --> - <param name="strand_specific" value="" /> - <output name="out_file1" file="velveth_test1/output.html" lines_diff="4"> - <extra_files type="file" name='Sequences' value="velveth_test1/Sequences" compare="diff" /> - <extra_files type="file" name='Roadmaps' value="velveth_test1/Roadmaps" compare="diff" /> - </output> - </test> - </tests> - <help> + <param name="input" type="data" format="fasta,fastq,eland,gerald" label="Dataset"/> + </repeat> + </inputs> + <outputs> + <data format="velvet" name="out_file1" /> + </outputs> + <requirements> + <requirement type="package">velvet</requirement> + </requirements> + <tests> + <test> + <param name="hash_length" value="21" /> + <param name="read_type" value="-shortPaired" /> + <!-- <repeat name="inputs"> --> + <param name="file_format" value="fasta" /> + <param name="read_type" value="shortPaired reads" /> + <param name="input" value="velvet_test_reads.fa" ftype="fasta" /> + <!-- </repeat> --> + <param name="strand_specific" value="" /> + <output name="out_file1" file="velveth_test1/output.html" lines_diff="4"> + <extra_files type="file" name='Sequences' value="velveth_test1/Sequences" compare="diff" /> + <extra_files type="file" name='Roadmaps' value="velveth_test1/Roadmaps" compare="diff" /> + </output> + </test> + </tests> + <help> **Velvet Overview**
Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
-Read the Velvet `documentation`__ for details on using the Vevlet Assembler. +Read the Velvet `documentation`__ for details on using the Velvet Assembler.
.. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
@@ -124,5 +124,5 @@ long (for Sanger, 454 or even reference sequences) longPaired
- </help> + </help></tool>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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