Mercurial > repos > thanhlv > bin3c

annotate cluster.xml @ 15:e0c0decc7ec0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
author thanhlv
date Mon, 14 Oct 2019 08:58:26 -0400
parents 8d920f67589d
children cdfc397e7b0f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
1 <tool id="cluster" name="cluster" version="@VERSION@">
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
2 <description>Cluster an existing contact map into genome bins</description>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
3 <macros>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
4 <import>macros.xml</import>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
5 </macros>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
6 <expand macro="requirements" />
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
7 <expand macro="version_command" />
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
9 bin3C cluster
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
10 --max-image $max_image
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
11 --min-extent $min_extent
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
12 --min-reflen $min_reflen
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
13 --min-signal $min_signal
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
14 -s 201987356473
14
8d920f67589d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
thanhlv
parents: 2
diff changeset
15 --assembler $assembler
0
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
16 $no_report
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
17 $no_spades
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
18 $no_plot
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
19 $no_fasta
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
20 $only_large
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
21 $fasta
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
22 $contact_map out
14
8d920f67589d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
thanhlv
parents: 2
diff changeset
23 ]]> </command>
8d920f67589d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
thanhlv
parents: 2
diff changeset
24
0
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
25 <inputs>
2
3dc88c0973db planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 3fa036c8cd4aff74e10ced32e0fce0aa1c2819ac-dirty
thanhlv
parents: 1
diff changeset
26 <param name="contact_map" type="data" format="tar.gz" label="Contact map" help="This file is generated from mkmap command" />
15
e0c0decc7ec0 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
thanhlv
parents: 14
diff changeset
27 <param name="assembler" label="Assembly software used to create contigs" type="select">
e0c0decc7ec0 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
thanhlv
parents: 14
diff changeset
28 <option selected="true" value="generic">generic</option>
14
8d920f67589d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
thanhlv
parents: 2
diff changeset
29 <option value="megahit">megahit</option>
8d920f67589d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
thanhlv
parents: 2
diff changeset
30 <option value="spades">spades</option>
8d920f67589d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
thanhlv
parents: 2
diff changeset
31 </param>
0
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
32 <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
33 <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
34 <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
35 <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
36 <param name="no_report" type="boolean" truevalue="--no-report" falsevalue="" checked="false" label="Do not generate a cluster report" />
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
37 <param name="no_spades" type="boolean" truevalue="--no-spades" falsevalue="" checked="false" label="Assembly was not done using SPAdes" />
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
38 <param name="no_plot" type="boolean" truevalue="--no-plot" falsevalue="" checked="false" label="Do not generate a clustered heatmap" />
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
39 <param name="no_fasta" type="boolean" truevalue="--no-fasta" falsevalue="" checked="false" label="Do not generate cluster FASTA files" />
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
40 <param name="only_large" type="boolean" truevalue="--only-large" falsevalue="" checked="false" label="Only write FASTA for clusters longer than min_extent" />
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
41 <param name="fasta" type="data" format="fasta" label="Alternative source FASTA location from that supplied during mkmap" />
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
42 </inputs>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
43
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
44 <outputs>
1
15d48ce4e275 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents: 0
diff changeset
45 <data name="log" format="text" label="{tool.name} on ${on_string} Log" from_work_dir="out/bin3C.log"/>
15d48ce4e275 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents: 0
diff changeset
46 <data name="clustering_mcl" format="binary" label="{tool.name} on ${on_string} Clustering solution in MCL format" from_work_dir="out/clustering.mcl"/>
15d48ce4e275 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents: 0
diff changeset
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"/>
15d48ce4e275 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents: 0
diff changeset
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"/>
15d48ce4e275 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents: 0
diff changeset
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"/>
15d48ce4e275 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents: 0
diff changeset
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"/>
15d48ce4e275 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents: 0
diff changeset
51 <data name="cm_graph_tree" format="text" label="{tool.name} on ${on_string} Infomap clustering output" from_work_dir="out/cm_graph.tree"/>
14
8d920f67589d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
thanhlv
parents: 2
diff changeset
52 <data name="fasta" format="fasta" label="{tool.name} on ${on_string} Per-cluster multi-fasta sequences" from_work_dir="out/infomap.log"/>
0
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
53 </outputs>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
54
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
55 <tests>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
56 <test>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
57 </test>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
58 </tests>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
59 <help><![CDATA[
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
60
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
61 Documentation can be found at `<https://github.com/cerebis/bin3C>`_.
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
62
14
8d920f67589d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
thanhlv
parents: 2
diff changeset
63 ]]> </help>
8d920f67589d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
thanhlv
parents: 2
diff changeset
64 <expand macro="citations" />
0
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
65 </tool>