Mercurial > repos > thanhlv > bin3c

annotate mkmap.xml @ 10:59f01b08b3e1 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 70fbc98b2ff2be134400e4dc0df1ed60458d0604-dirty
author thanhlv
date Thu, 03 Oct 2019 08:54:55 -0400
parents 5a53c997fc3e
children cc6f22df0a68
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="mkmap" name="mkmap" 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>Create a new contact map from assembly sequences and Hi-C bam file</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 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
10 $clobber
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 --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
12 --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
13 --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
14 --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
15 $eta
3
a8600e2b39b2 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 70a467531cfa44cab27a9bf0907a276cad55840a
thanhlv
parents: 2
diff changeset
16 --bin-size $bin_size
a8600e2b39b2 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 70a467531cfa44cab27a9bf0907a276cad55840a
thanhlv
parents: 2
diff changeset
17 --min-insert $min_insert
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
18 --min-mapq $min_mapq
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 --strong $strong
9
5a53c997fc3e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 70fbc98b2ff2be134400e4dc0df1ed60458d0604-dirty
thanhlv
parents: 8
diff changeset
20 #if str($neb_name) != "":
10
59f01b08b3e1 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 70fbc98b2ff2be134400e4dc0df1ed60458d0604-dirty
thanhlv
parents: 9
diff changeset
21 -e #echo ' -e '.join(str( $neb_name ).split( ';' ))#
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 #end if
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 $ref $bam out
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 ]]></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
25
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
26 <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
27 <param name="ref" type="data" format="fasta,fastaq.gz" label="Reference fasta sequence" />
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
28 <param name="bam" type="data" format="bam" label="Input bam file in query order" />
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
thanhlv
parents:
diff changeset
29 <param name="clobber" type="boolean" truevalue="--clobber" falsevalue="" checked="false" label="Clobber existing 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
30 <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
31 <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
32 <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
33 <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
34 <param name="eta" type="boolean" truevalue="--eta" falsevalue="" checked="false" label="Re-count bam alignments to provide an ETA" />
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="bin_size" type="integer" min="0" value="0" label="Size of bins for windows extent maps" />
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="min_insert" type="integer" min="0" value="0" label="Minimum pair separation" />
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="min_mapq" type="integer" min="0" value="60" label="Minimum acceptable mapping quality" />
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="strong" type="integer" min="1" value="10" label="Accepted alignments must being N matches" />
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="neb_name" type="text" value="" label="Case-sensitive NEB enzyme name. Use multiple times for
6
d9712694b063 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 70fbc98b2ff2be134400e4dc0df1ed60458d0604-dirty
thanhlv
parents: 5
diff changeset
40 multiple enzymes">
7
9b320ad1bab4 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 70fbc98b2ff2be134400e4dc0df1ed60458d0604-dirty
thanhlv
parents: 6
diff changeset
41 <help><![CDATA[Use ; to separate multiple enzymes e.g enzyme1;enzyme2]]> </help>
6
d9712694b063 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 70fbc98b2ff2be134400e4dc0df1ed60458d0604-dirty
thanhlv
parents: 5
diff changeset
42 </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
43 </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
44
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 <outputs>
10
59f01b08b3e1 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 70fbc98b2ff2be134400e4dc0df1ed60458d0604-dirty
thanhlv
parents: 9
diff changeset
46 <data name="contact_map" format="tar.gz" label="${tool.name} on ${on_string} Contact map" from_work_dir="out/contact_map.p.gz"/>
59f01b08b3e1 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 70fbc98b2ff2be134400e4dc0df1ed60458d0604-dirty
thanhlv
parents: 9
diff changeset
47 <data name="log" format="text" label="${tool.name} on ${on_string} Log" from_work_dir="out/bin3C.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
48 </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
49
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 <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
51 <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
52 </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
53 </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
54 <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
55
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 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
57
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 ]]></help>
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 <expand macro="citations" />
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 </tool>