Mercurial > repos > devteam > velvet
diff velvetg.xml @ 2:8d09f8be269e draft
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
| author | iuc |
|---|---|
| date | Tue, 16 Jun 2020 12:58:20 -0400 |
| parents | 5da9a0e2fb2d |
| children |
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--- a/velvetg.xml Wed Feb 12 11:16:32 2020 -0500 +++ b/velvetg.xml Tue Jun 16 12:58:20 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.1"> +<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.2"> <description>Velvet sequence assembler for very short reads</description> <macros> <import>macros.xml</import> @@ -9,102 +9,85 @@ velvetg 2>&1 | grep "Version" | sed -e 's/Version //' ]]></version_command> <command><![CDATA[ -ln -s '$input.extra_files_path'/Roadmaps && -ln -s '$input.extra_files_path'/Sequences && -velvetg . -#if $generate_amos.afg == "yes": - -amos_file $generate_amos.afg -#end if -#if $unused_reads.generate_unused == "yes": - -unused_reads $unused_reads.generate_unused -#end if -$read_trkg -#if $coverage.cutoff == "auto": - -cov_cutoff auto -#elif $coverage.cutoff == "value": - -cov_cutoff $coverage.cov_cutoff -#end if -#if $expected.coverage == "auto": - -exp_cov auto -#elif $expected.coverage == "value": - -exp_cov $expected.exp_cov -#end if -#if $contig_lgth.use_contig_lgth == "yes": - -min_contig_lgth $contig_lgth.min_contig_lgth -#end if -#if $reads.paired == "yes": - #if int($reads.ins_length) > 0: - -ins_length $reads.ins_length - #end if - #if $reads.options.advanced == "yes": - #if int($reads.options.ins_length_sd) > 0: - -ins_length_sd $reads.options.ins_length_sd - #end if - #if int($reads.options.ins_length2) > 0: - -ins_length2 $reads.options.ins_length2 - #end if - #if int($reads.options.ins_length2_sd) > 0: - -ins_length2_sd $reads.options.ins_length2_sd - #end if - #if int($reads.options.ins_length_long) > 0: - -ins_length_long $reads.options.ins_length_long - #end if - #if int($reads.options.ins_length_long_sd) > 0: - -ins_length_long_sd $reads.options.ins_length_long_sd - #end if - #if int($reads.options.max_branch_length) > 0: - -max_branch_length $reads.options.max_branch_length - #end if - #if int($reads.options.max_divergence) > 0: - -max_divergence $reads.options.max_divergence - #end if - #if int($reads.options.max_gap_count) > 0: - -max_gap_count $reads.options.max_gap_count - #end if - #if int($reads.options.min_pair_count) > 0: - -min_pair_count $reads.options.min_pair_count - #end if - #if int($reads.options.max_coverage) > 0: - -max_coverage $reads.options.max_coverage - #end if - #if int($reads.options.long_mult_cutoff) > 0: - -long_mult_cutoff $reads.options.long_mult_cutoff - #end if - $reads.options.scaffolding - #end if -#end if + ln -s '$input.extra_files_path'/Roadmaps && + ln -s '$input.extra_files_path'/Sequences && + velvetg . + #if 'amos' in $add_out: + -amos_file yes + #end if + #if 'unused' in $add_out: + -unused_reads yes + #end if + $read_trkg + #if $coverage.cutoff == "auto": + -cov_cutoff auto + #elif $coverage.cutoff == "value": + -cov_cutoff $coverage.cov_cutoff + #end if + #if $expected.coverage == "auto": + -exp_cov auto + #elif $expected.coverage == "value": + -exp_cov $expected.exp_cov + #end if + #if $contig_lgth.use_contig_lgth == "yes": + -min_contig_lgth $contig_lgth.min_contig_lgth + #end if + #if $reads.paired == "yes": + #if int($reads.ins_length) > 0: + -ins_length $reads.ins_length + #end if + #if $reads.options.advanced == "yes": + #if int($reads.options.ins_length_sd) > 0: + -ins_length_sd $reads.options.ins_length_sd + #end if + #if int($reads.options.ins_length2) > 0: + -ins_length2 $reads.options.ins_length2 + #end if + #if int($reads.options.ins_length2_sd) > 0: + -ins_length2_sd $reads.options.ins_length2_sd + #end if + #if int($reads.options.ins_length3) > 0: + -ins_length3 $reads.options.ins_length3 + #end if + #if int($reads.options.ins_length3_sd) > 0: + -ins_length3_sd $reads.options.ins_length3_sd + #end if + #if int($reads.options.ins_length4) > 0: + -ins_length4 $reads.options.ins_length4 + #end if + #if int($reads.options.ins_length4_sd) > 0: + -ins_length4_sd $reads.options.ins_length4_sd + #end if + #if int($reads.options.ins_length_long) > 0: + -ins_length_long $reads.options.ins_length_long + #end if + #if int($reads.options.ins_length_long_sd) > 0: + -ins_length_long_sd $reads.options.ins_length_long_sd + #end if + #if int($reads.options.max_branch_length) > 0: + -max_branch_length $reads.options.max_branch_length + #end if + #if int($reads.options.max_divergence) > 0: + -max_divergence $reads.options.max_divergence + #end if + #if int($reads.options.max_gap_count) > 0: + -max_gap_count $reads.options.max_gap_count + #end if + #if int($reads.options.min_pair_count) > 0: + -min_pair_count $reads.options.min_pair_count + #end if + #if int($reads.options.max_coverage) > 0: + -max_coverage $reads.options.max_coverage + #end if + #if int($reads.options.long_mult_cutoff) > 0: + -long_mult_cutoff $reads.options.long_mult_cutoff + #end if + $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> - - <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> - - <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="Tracking of short read positions in assembly" help="Generates Graph2 dataset" /> - <conditional name="coverage"> <param name="cutoff" type="select" label="Coverage cutoff" help=""> <option value="none">None</option> @@ -117,7 +100,17 @@ <param name="cov_cutoff" value="10.0" label="Remove nodes with coverage below" type="float" /> </when> </conditional> - + <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="Tracking of short read positions in assembly" help="Generates Graph2 dataset" /> + <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="expected"> <param name="coverage" type="select" label="Expected Coverage of Unique Regions" help=""> <option value="none">None</option> @@ -131,16 +124,11 @@ </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> - </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> + <param name="add_out" type="select" multiple="true" optional="true" label="Additional outputs" help=""> + <option value="amos">Generate a AMOS.afg file</option> + <option value="unused">Generate a UnusedReads fasta file</option> + <option value="lastgraph">Generate velvet LastGraph file</option> + </param> <conditional name="reads"> <param name="paired" type="select" label="Using Paired Reads"> @@ -160,6 +148,10 @@ <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_length3" 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_length3_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_length4" 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_length4_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)"/> @@ -169,50 +161,53 @@ <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> +<!-- TODO +-coverage_mask +-paired_exp_fraction +-alignments +-exportFiltered +-clean +-very_clean +-shortMatePaired--> </inputs> <outputs> <data format="txt" name="Graph2" label="${tool.name} on ${on_string}: Graph2" from_work_dir="Graph2"> <filter>read_trkg is True</filter> </data> <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph" from_work_dir="LastGraph"> - <filter>last_graph['generate_graph'] == "yes"</filter> + <filter>'lastgraph' in add_out</filter> </data> <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg" from_work_dir="velvet_asm.afg"> - <filter>generate_amos['afg'] == "yes"</filter> + <filter>'amos' in add_out</filter> </data> <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads" from_work_dir="UnusedReads.fa"> - <filter>unused_reads['generate_unused'] == "yes"</filter> + <filter>'unused' in add_out</filter> </data> <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" /> <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" /> </outputs> <tests> - <test> - <param name="input" value="velveth_test1/output.html" ftype="velvet"> - <composite_data value="velveth_test1/Sequences" /> - <composite_data value="velveth_test1/Roadmaps" /> - <composite_data value="velveth_test1/Log"/> + <test expect_num_outputs="5"> + <param name="input" value="velvetg_paired.out" ftype="velvet" > + <composite_data value='velvetg_paired/Sequences'/> + <composite_data value='velvetg_paired/Roadmaps'/> + <composite_data value='velvetg_paired/Log'/> </param> - <param name="afg" value="yes" /> - <param name="generate_unused" value="yes" /> - <param name="generate_graph" value="no" /> + <param name="add_out" value="amos,unused,lastgraph" /> <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"/> - --> - <output name="velvet_asm" file="velvetg_test1/amos.afg" /> - <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" /> - <output name="stats" file="velvetg_test1/stats.csv" /> - <output name="contigs" file="velvetg_test1/contigs.fa" /> + <output name="velvet_asm" file="velvetg_paired/velvet_asm.afg" compare="diff"/> + <output name="unused_reads_fasta" file="velvetg_paired/UnusedReads.fa" compare="diff"/> + <output name="LastGraph" file="velvetg_paired/lastgraph.txt" compare="diff"/> + <output name="stats" file="velvetg_paired/stats.txt" compare="diff"/> + <output name="contigs" file="velvetg_paired/contigs.fa" compare="diff"/> </test> </tests> <help><![CDATA[