Mercurial > repos > iuc > raven
changeset 5:5c55448d0f33 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 7bd5e845f7f0a531d619f66193470127a2a7a7ea
| author | iuc |
|---|---|
| date | Sat, 18 May 2024 21:31:16 +0000 |
| parents | 2b2a352488fa |
| children | |
| files | macros.xml raven.xml |
| diffstat | 2 files changed, 14 insertions(+), 13 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Mon Mar 21 08:29:39 2022 +0000 +++ b/macros.xml Sat May 18 21:31:16 2024 +0000 @@ -1,6 +1,5 @@ -<?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.8.0</token> + <token name="@TOOL_VERSION@">1.8.3</token> <token name="@PROFILE@">20.05</token> <xml name="requirements"> <requirements> @@ -25,11 +24,9 @@ <!-- input --> - <!-- Help --> - <token name="@WID@"><![CDATA[ *raven* is a de novo genome assembler for long uncorrected reads. ]]></token>
--- a/raven.xml Mon Mar 21 08:29:39 2022 +0000 +++ b/raven.xml Sat May 18 21:31:16 2024 +0000 @@ -1,16 +1,11 @@ -<?xml version="1.0"?> <tool id="raven" name="Raven" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>De novo assembly of Oxford Nanopore Technologies data</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"/> - <expand macro="version_command"/> - -<!--TODO in future version : enable CUDA support for racon polishing--> - + <!--TODO in future version : enable CUDA support for racon polishing--> <command detect_errors="exit_code"><![CDATA[ #if $input_reads.is_of_type("fasta") ln -s '$input_reads' ./input.fa && @@ -33,6 +28,10 @@ --match '$match' --mismatch '$mismatch' --gap '$gap' +--kMaxNumOverlaps '$kMaxNumOverlaps' +--identity $identity +--min-unitig-size $min_unitig_size +--use-micromizers $use_micromizers $graphical_fragment_assembly --disable-checkpoints -t \${GALAXY_SLOTS:-4} @@ -44,17 +43,22 @@ <param argument="--kmer-len" type="integer" value="15" label="Length of minimizers used to find overlaps"/> <param argument="--window-len" type="integer" value="5" label="Length of sliding window from which minimizers are sampled"/> <param argument="--frequency" type="float" value="0.001" label="Threshold for ignoring most frequent minimizers"/> + <param argument="--identity" type="float" value="0" label="Threshold for overlap between two reads in order to construct an edge between them" help="If set to zero, this functionality is disabled"/> + <param argument="--kMaxNumOverlaps" type="integer" value="32" label="Maximum number of overlaps that will be taken during FindOverlapsAndCreatePiles stage"/> + <param argument="--min-unitig-size" type="integer" value="9999" label="Minimal unitig size"/> + <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/> <param argument="--match" type="integer" value="3"/> <param argument="--mismatch" type="integer" value="-5"/> <param argument="--gap" type="integer" value="-4" max="-1"/> <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/> + <param argument="--use-micromizers" type="boolean" truevalue="--use-micromizers" falsevalue="" label="Use micromizers instead of mimizers in graph construction" help="Performance will increase slightly and memory consumption will decrease but results could be slightly worse"/> </inputs> <outputs> <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="out.gfa"> <filter>graphical_fragment_assembly</filter> </data> - <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)" /> + <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/> </outputs> <tests> <test expect_num_outputs="2"> @@ -62,13 +66,13 @@ <output name="out_gfa"> <assert_contents> <has_n_lines n="2"/> - <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/> + <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\tdp:f:8\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/> </assert_contents> </output> <output name="out_fasta"> <assert_contents> <has_n_lines n="2"/> - <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/> + <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/> </assert_contents> </output> </test>