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"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
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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1 <tool id="quickmerge" name="quickmerge" version="@VERSION@">
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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2 <description> improves contiguity of genome assemblies based on long molecule sequences</description>
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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3 <macros>
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4 <token name="@VERSION@">0.3</token>
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5 </macros>
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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6 <requirement type="package" version="@VERSION@">quickmerge</requirement>
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7 <version_command><![CDATA[ echo @VERSION@]]></version_command>
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8
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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9 <command detect_errors="exit_code"><![CDATA[
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10 merge_wrapper.py
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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11 -hco $hco
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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12 -c $c_params
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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13 -l $length_cutoff
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14 $no_nucmer
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15 $no_delta
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16 $stop_after_nucmer
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17 $stop_after_df
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18 -ml $merging_length_cutoff
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19 -t \${GALAXY_SLOTS:-1}
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20 $version4
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21 $clean_only
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22 $hybrid_assembly
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23 $self_assembly
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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24 ]]> </command>
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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25
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26 <inputs>
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27 <param name="hybrid_assembly" type="data" format="fasta.fasta.gz" label="Hybrid assembly"/>
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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28 <param name="self_assembly" type="data" format="fasta.fasta.gz" label="Self assembly"/>
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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29 <param name="hco" type="float" min="0" value="0.5" label="Quickmerge hco parameter" />
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30 <param name="c_params" type="float" min="0" value="1.5" label="Quickmerge c parameter" />
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31 <param name="length_cutoff" type="integer" min="0" value="0" label="Minimum seed contig length to be merged" />
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32 <param name="no_nucmer" type="boolean" truevalue="--no_nucmer" falsevalue="" checked="false" label="Skip the nucmer step" />
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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33 <param name="no_delta" type="boolean" truevalue="--no_delta" falsevalue="" checked="false" label="Skip the nucmer and delta-filter steps" />
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34 <param name="stop_after_nucmer" type="boolean" truevalue="--stop_after_nucmer" falsevalue="" checked="false" label="Do not perform the delta-filter and merger steps" />
1582fc3aa9d1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/quickmerge commit f6f1b5b95886581cfdd927ea7359260b5c06393a-dirty"
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35 <param name="stop_after_df" type="boolean" truevalue="--stop_after_df" falsevalue="" checked="false" label="Do not perform the merger step" />
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36 <param name="merging_length_cutoff" type="integer" min="0" value="5000" label="set the merging length cutoff necessary for use in quickmerge" />
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37 <param name="version4" type="boolean" truevalue="--version4" falsevalue="" checked="false" label="Do not perform the merger step" />
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38 <param name="clean_only" type="boolean" truevalue="--clean_only" falsevalue="" checked="false" label="Generate safe FASTA files for merging, but do not merge" />
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39 </inputs>
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40
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41 <outputs>
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42 <data name="merged_qm" format="fasta" label="${tool.name} on ${on_string}: merged" from_work_dir="merged_qm.fasta"/>
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43 <data name="hybrid_oneline" format="fasta" label="${tool.name} on ${on_string}: hybrid_oneline" from_work_dir="hybrid_oneline.fa"/>
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44 <data name="self_oneline" format="fasta" label="${tool.name} on ${on_string}: self_oneline" from_work_dir="self_oneline.fa"/>
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45 <data name="param_summary" format="tsv" label="${tool.name} on ${on_string}: param summary" from_work_dir="param_summary_qm.txt"/>
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46 <data name="anchor_summary_qm" format="tsv" label="${tool.name} on ${on_string}: anchor summary" from_work_dir="anchor_summary_qm.txt"/>
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47 <data name="aln_summary_qm" format="tsv" label="${tool.name} on ${on_string}: anchor summary" from_work_dir="aln_summary_qm.tsv"/>
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48 </outputs>
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49 <help><![CDATA[
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50 ]]> </help>
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51 <citations>
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52 <citation type="doi">10.1093/nar/gkw654</citation>
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53 </citations>
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54 </tool>