Mercurial > repos > thanhlv > bin3c

annotate cluster.xml @ 24:9da36e77ec34 draft

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
author thanhlv
date Tue, 22 Oct 2019 10:00:13 -0400
parents 68218ea2b0aa
children b9e12e746f6d
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1 <tool id="cluster" name="cluster" version="@VERSION@">
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2 <description>Cluster an existing contact map into genome bins</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s $contact_map map.p.gz &&
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10 bin3C cluster
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11 --max-image $max_image
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12 --min-extent $min_extent
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13 --min-reflen $min_reflen
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14 --min-signal $min_signal
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15 -s 201987356473
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16 --assembler $assembler
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17 $no_report
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18 $no_plot
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19 $no_fasta
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20 $only_large
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21 --n-iter $iteration
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22 map.p.gz out
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23 ]]> </command>
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24
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25 <inputs>
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26 <param name="contact_map" type="data" format="binary" label="Contact map" help="This file is generated from mkmap command" />
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27 <param name="assembler" label="Assembly software used to create contigs" type="select">
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28 <option selected="true" value="generic">generic</option>
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29 <option value="megahit">megahit</option>
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30 <option value="spades">spades</option>
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31 </param>
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32 <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/>
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33 <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/>
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34 <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/>
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35 <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/>
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36 <param name="iteration" type="integer" min="1" value="10" label="Number of iterations for clustering optimisation"/>
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37 <param name="no_report" type="boolean" truevalue="--no-report" falsevalue="" checked="false" label="Do not generate a cluster report" />
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38 <param name="no_plot" type="boolean" truevalue="--no-plot" falsevalue="" checked="false" label="Do not generate a clustered heatmap" />
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39 <param name="no_fasta" type="boolean" truevalue="--no-fasta" falsevalue="" checked="false" label="Do not generate cluster FASTA files" />
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40 <param name="only_large" type="boolean" truevalue="--only-large" falsevalue="" checked="false" label="Only write FASTA for clusters longer than min_extent" />
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41 <!-- <param name="fasta" type="data" format="fasta,fastq.gz" optional="true" label="Alternative source FASTA from that supplied during mkmap" /> -->
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42 </inputs>
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43
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44 <outputs>
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45 <data name="log" format="text" label="${tool.name} on ${on_string} Log" from_work_dir="out/bin3C.log"/>
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46 <data name="clustering_mcl" format="binary" label="${tool.name} on ${on_string} Clustering solution in MCL format" from_work_dir="out/clustering.mcl"/>
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47 <data name="clustering_p_gz" format="binary" label="${tool.name} on ${on_string} Clustering solution as a picked python dictionary" from_work_dir="out/clustering.p.gz"/>
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48 <data name="clustering_plot" format="png" label="${tool.name} on ${on_string} Heatmap of the contact map after clustering" from_work_dir="out/cluster_plot.png"/>
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49 <data name="clustering_csv" format="tabular" label="${tool.name} on ${on_string} A per-cluster report of various statistics" from_work_dir="out/cluster_report.csv"/>
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50 <data name="cm_graph_edges" format="binary" label="${tool.name} on ${on_string} The graph used in clustering in edge list format" from_work_dir="out/cm_graph.edges"/>
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51 <data name="cm_graph_tree" format="text" label="${tool.name} on ${on_string} Infomap clustering output" from_work_dir="out/cm_graph.tree"/>
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52 <data name="fasta" format="fasta" label="${tool.name} on ${on_string} Per-cluster multi-fasta sequences" from_work_dir="out/infomap.log"/>
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53 </outputs>
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55 <help><![CDATA[
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57 Documentation can be found at `<https://github.com/cerebis/bin3C>`_.
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58
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59 ]]> </help>
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60 <expand macro="citations" />
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61 </tool>