Mercurial > repos > thanhlv > quickmerge
changeset 0:1582fc3aa9d1 draft default tip
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
| author | thanhlv |
|---|---|
| date | Mon, 02 Mar 2020 16:35:55 +0000 |
| parents | |
| children | |
| files | quickmege.xml |
| diffstat | 1 files changed, 54 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/quickmege.xml Mon Mar 02 16:35:55 2020 +0000 @@ -0,0 +1,54 @@ +<tool id="quickmerge" name="quickmerge" version="@VERSION@"> + <description> improves contiguity of genome assemblies based on long molecule sequences</description> + <macros> + <token name="@VERSION@">0.3</token> + </macros> + <requirement type="package" version="@VERSION@">quickmerge</requirement> + <version_command><![CDATA[ echo @VERSION@]]></version_command> + + <command detect_errors="exit_code"><![CDATA[ + merge_wrapper.py + -hco $hco + -c $c_params + -l $length_cutoff + $no_nucmer + $no_delta + $stop_after_nucmer + $stop_after_df + -ml $merging_length_cutoff + -t \${GALAXY_SLOTS:-1} + $version4 + $clean_only + $hybrid_assembly + $self_assembly + ]]> </command> + + <inputs> + <param name="hybrid_assembly" type="data" format="fasta.fasta.gz" label="Hybrid assembly"/> + <param name="self_assembly" type="data" format="fasta.fasta.gz" label="Self assembly"/> + <param name="hco" type="float" min="0" value="0.5" label="Quickmerge hco parameter" /> + <param name="c_params" type="float" min="0" value="1.5" label="Quickmerge c parameter" /> + <param name="length_cutoff" type="integer" min="0" value="0" label="Minimum seed contig length to be merged" /> + <param name="no_nucmer" type="boolean" truevalue="--no_nucmer" falsevalue="" checked="false" label="Skip the nucmer step" /> + <param name="no_delta" type="boolean" truevalue="--no_delta" falsevalue="" checked="false" label="Skip the nucmer and delta-filter steps" /> + <param name="stop_after_nucmer" type="boolean" truevalue="--stop_after_nucmer" falsevalue="" checked="false" label="Do not perform the delta-filter and merger steps" /> + <param name="stop_after_df" type="boolean" truevalue="--stop_after_df" falsevalue="" checked="false" label="Do not perform the merger step" /> + <param name="merging_length_cutoff" type="integer" min="0" value="5000" label="set the merging length cutoff necessary for use in quickmerge" /> + <param name="version4" type="boolean" truevalue="--version4" falsevalue="" checked="false" label="Do not perform the merger step" /> + <param name="clean_only" type="boolean" truevalue="--clean_only" falsevalue="" checked="false" label="Generate safe FASTA files for merging, but do not merge" /> + </inputs> + + <outputs> + <data name="merged_qm" format="fasta" label="${tool.name} on ${on_string}: merged" from_work_dir="merged_qm.fasta"/> + <data name="hybrid_oneline" format="fasta" label="${tool.name} on ${on_string}: hybrid_oneline" from_work_dir="hybrid_oneline.fa"/> + <data name="self_oneline" format="fasta" label="${tool.name} on ${on_string}: self_oneline" from_work_dir="self_oneline.fa"/> + <data name="param_summary" format="tsv" label="${tool.name} on ${on_string}: param summary" from_work_dir="param_summary_qm.txt"/> + <data name="anchor_summary_qm" format="tsv" label="${tool.name} on ${on_string}: anchor summary" from_work_dir="anchor_summary_qm.txt"/> + <data name="aln_summary_qm" format="tsv" label="${tool.name} on ${on_string}: anchor summary" from_work_dir="aln_summary_qm.tsv"/> + </outputs> + <help><![CDATA[ + ]]> </help> + <citations> + <citation type="doi">10.1093/nar/gkw654</citation> + </citations> +</tool>