Mercurial > repos > thanhlv > bin3c

annotate cluster.xml @ 28:175b45d4f6fd 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 a5926dec65ac1474e7b79685df5b9330601ef167-dirty
author thanhlv
date Tue, 22 Oct 2019 11:08:18 -0400
parents 0ab55bb24e71
children 57e22d15fed9
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[
25
b9e12e746f6d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 24
diff changeset
9 #if compress:
b9e12e746f6d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 24
diff changeset
10 gzip < $contact_map > contact_map.p.gz &&
b9e12e746f6d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 24
diff changeset
11 #else:
b9e12e746f6d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 24
diff changeset
12 ln -s $contact_map contact_map.p.gz &&
28
175b45d4f6fd planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 27
diff changeset
13 #end if
175b45d4f6fd planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 27
diff changeset
14
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
15 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
16 --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
17 --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
18 --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
19 --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
20 -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
21 --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
22 $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
23 $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
24 $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
25 $only_large
25
b9e12e746f6d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 24
diff changeset
26 --fasta $contigs
16
cdfc397e7b0f planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 979c715c9d69fe906eead3270f26cd029c7eb8af-dirty
thanhlv
parents: 15
diff changeset
27 --n-iter $iteration
25
b9e12e746f6d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 24
diff changeset
28 contact_map.p.gz 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
29 ]]> </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
30
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
31 <inputs>
19
994d9f2fa2d2 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 9f4ab03111185c7e20aaf669586278744713eee4-dirty
thanhlv
parents: 18
diff changeset
32 <param name="contact_map" type="data" format="binary" label="Contact map" help="This file is generated from mkmap command" />
25
b9e12e746f6d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 24
diff changeset
33 <param name="contigs" type="data" format="fasta,fastq.gz" label="Contigs from that supplied during mkmap" />
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
34 <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
35 <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
36 <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
37 <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
38 </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
39 <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
40 <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
41 <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
42 <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/>
16
cdfc397e7b0f planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 979c715c9d69fe906eead3270f26cd029c7eb8af-dirty
thanhlv
parents: 15
diff changeset
43 <param name="iteration" type="integer" min="1" value="10" label="Number of iterations for clustering optimisation"/>
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
44 <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
45 <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
46 <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
47 <param name="only_large" type="boolean" truevalue="--only-large" falsevalue="" checked="false" label="Only write FASTA for clusters longer than min_extent" />
25
b9e12e746f6d planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 24
diff changeset
48 <param name="compress" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compress contact map before run" help="Only choose when the contact map was not generated by mkmap on Galaxy" />
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
49 </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
50
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
51 <outputs>
27
0ab55bb24e71 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 26
diff changeset
52 <data name="log" format="text" label="${tool.name} on ${on_string} Log" from_work_dir="out/bin3C.log"/>
0ab55bb24e71 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 26
diff changeset
53 <data name="clustering_mcl" format="binary" label="${tool.name} on ${on_string} Clustering solution in MCL format" from_work_dir="out/clustering.mcl"/>
0ab55bb24e71 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 26
diff changeset
54 <data name="clustering_p_gz" format="binary" label="${tool.name} on ${on_string} Clustering solution as a picked python dictionary" from_work_dir="out/clustering.p.gz"/>
0ab55bb24e71 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 26
diff changeset
55 <data name="clustering_plot" format="png" label="${tool.name} on ${on_string} Heatmap of the contact map after clustering" from_work_dir="out/cluster_plot.png"/>
0ab55bb24e71 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 26
diff changeset
56 <data name="clustering_csv" format="tabular" label="${tool.name} on ${on_string} A per-cluster report of various statistics" from_work_dir="out/cluster_report.csv"/>
0ab55bb24e71 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 26
diff changeset
57 <data name="cm_graph_edges" format="binary" label="${tool.name} on ${on_string} The graph used in clustering in edge list format" from_work_dir="out/cm_graph.edges"/>
0ab55bb24e71 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 26
diff changeset
58 <data name="cm_graph_tree" format="text" label="${tool.name} on ${on_string} Infomap clustering output" from_work_dir="out/cm_graph.tree"/>
26
dd1bc5779f5c planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 25
diff changeset
59 <collection type="list" name="fasta" label="${tool.name} on ${on_string} Per-cluster multi-fasta sequences">
dd1bc5779f5c planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 25
diff changeset
60 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fna" directory="out/fasta" ext="fna" visible="false" />
dd1bc5779f5c planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit a5926dec65ac1474e7b79685df5b9330601ef167-dirty
thanhlv
parents: 25
diff changeset
61 </collection>
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
62 </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
63
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
64 <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
65
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
66 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
67
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
68 ]]> </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
69 <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
70 </tool>