Mercurial > repos > devteam > velvet
diff velvetg.xml @ 1:5da9a0e2fb2d draft
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
| author | devteam |
|---|---|
| date | Wed, 12 Feb 2020 11:16:32 -0500 |
| parents | 08256557922f |
| children | 8d09f8be269e |
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--- a/velvetg.xml Tue Oct 13 16:38:28 2015 -0400 +++ b/velvetg.xml Wed Feb 12 11:16:32 2020 -0500 @@ -1,76 +1,79 @@ -<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.0"> +<tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.1"> <description>Velvet sequence assembler for very short reads</description> - <version_command>velvetg 2>&1 | grep "Version" | sed -e 's/Version //'</version_command> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> - <command interpreter="python"> - velvetg_wrapper.py - '$input.extra_files_path' - #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 - $reads.options.scaffolding - #end if - #end if - </command> + <version_command><![CDATA[ + velvetg 2>&1 | grep "Version" | sed -e 's/Version //' + ]]></version_command> + <command><![CDATA[ +ln -s '$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 + $reads.options.scaffolding + #end if +#end if + ]]></command> <inputs> <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/> <conditional name="generate_amos"> @@ -142,7 +145,7 @@ <conditional name="reads"> <param name="paired" type="select" label="Using Paired Reads"> <option value="no">No</option> - <option value="yes" selected="${input.metadata.paired_end_reads}">Yes</option> + <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> @@ -188,15 +191,12 @@ <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> - <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 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"/> </param> <param name="afg" value="yes" /> <param name="generate_unused" value="yes" /> @@ -207,15 +207,15 @@ <param name="use_contig_lgth" value="no" /> <param name="paired" value="no" /> <!-- - <output name="LastGraph" file="velvetg_test1/lastgraph.txt" compare="diff"/> + <output name="LastGraph" file="velvetg_test1/lastgraph.txt"/> --> - <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"/> + <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" /> </test> </tests> - <help> + <help><![CDATA[ **What it does** 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. @@ -302,6 +302,6 @@ 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> <expand macro="citation"/> </tool>