annotate maxbin2.xml @ 0:35aa0df55a62 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
author mbernt
date Thu, 28 Jun 2018 08:49:29 -0400
parents
children 864279a0d64b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
1 <tool id="maxbin2" name="MaxBin2" version="2.2.4">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
2 <requirements>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
3 <requirement type="package" version="2.2.4">maxbin2</requirement>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
4 </requirements>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
5 <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
7 ## generate read or abundance files
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
8 #if $intype_cond.intype_select == 'rds':
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
9 #for $r in $intype_cond.reads
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
10 #if $r
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
11 echo '$r' >> reads_list &&
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
12 #end if
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
13 #end for
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
14 #else if $intype_cond.intype_select == 'abdc':
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
15 #for $a in $intype_cond.abund
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
16 #if $a
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
17 echo '$a' >> abund_list &&
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
18 #end if
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
19 #end for
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
20 #end if
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
21
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
22 ## in case of reassembly the IBDA out and err is appended
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
23 ## to differentiate this a header is added also befor the
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
24 ## MaxBin2 outputs
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
25 #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
26 echo "==== MaxBin2 stdout ====" &&
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
27 echo "==== MaxBin2 stderr ====" 1>&2 &&
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
28 #end if
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
29
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
30 run_MaxBin.pl
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
31 -contig '$contig'
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
32 -out out
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
33 #if $intype_cond.intype_select == 'rds':
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
34 -reads_list reads_list
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
35 $intype_cond.reassembly
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
36 #else if $intype_cond.intype_select == 'abdc':
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
37 -abund_list abund_list
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
38 #end if
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
39 #if $adv_cond.adv_select == 'yes':
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
40 -min_contig_length $adv_cond.min_contig_length
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
41 -max_iteration $adv_cond.max_iteration
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
42 -prob_threshold $adv_cond.prob_threshold
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
43 $adv_cond.plotmarker
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
44 -markerset $adv_cond.markerset
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
45 #end if
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
46 -thread \${GALAXY_SLOTS:-1}
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
47
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
48 && tar -xf out.marker_of_each_bin.tar.gz
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
49
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
50 ## redirect the idba out and err file content to stdout and err
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
51 #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != ""
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
52 && echo "==== IDBA stdout ===="
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
53 && cat out.idba.out
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
54 && echo "==== IDBA stderr ====" 1>&2
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
55 && cat out.idba.err 1>&2
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
56 #end if
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
57 ]]></command>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
58 <inputs>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
59 <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
60 <conditional name="intype_cond">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
61 <param name="intype_select" type="select" label="Input type">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
62 <option value="rds" selected="true">Sequencing Reads</option>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
63 <option value="abdc">Abundances</option>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
64 </param>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
65 <when value="rds">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
66 <param name="reads" argument="-read/-read2/..." type="data" format="fasta,fastq" multiple="true" label="Reads file(s)"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
67 <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file if you were to use this option." />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
68 </when>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
69 <when value="abdc">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
70 <param name="abund" argument="-abund/-abund2/..." type="data" format="tabular" multiple="true" label="Abundance file(s)"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
71 </when>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
72 </conditional>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
73 <conditional name="adv_cond">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
74 <param name="adv_select" type="select" label="Advanced options">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
75 <option value="yes">Yes</option>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
76 <option value="no" selected="true">No</option>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
77 </param>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
78 <when value="no"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
79 <when value="yes">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
80 <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
81 <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
82 <param argument="-prob_threshold" type="float" min="0" max="1.0" value="0.9" label="Probability threshold for EM final classification" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
83 <param name="plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
84 <param argument="-markerset" type="select" label="Marker gene set">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
85 <option value="107" selected="true">107 marker genes present in >95% of bacteria</option>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
86 <option value="40">40 marker gene sets that are universal among bacteria and archaea</option>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
87 </param>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
88 </when>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
89 </conditional>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
90 </inputs>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
91 <outputs>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
92 <collection name="bins" type="list" label="${tool.name} on ${on_string} (bins)">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
93 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
94 </collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
95 <data name="summary" format="tabular" label="${tool.name} on ${on_string} (summary)" from_work_dir="out.summary"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
96 <data name="log" format="txt" label="${tool.name} on ${on_string} (log)" from_work_dir="out.log"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
97 <data name="abundout" format="tabular" label="${tool.name} on ${on_string} (abundances)" from_work_dir="out.abund1">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
98 <filter>intype_cond['intype_select']=='rds'</filter>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
99 </data>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
100 <data name="marker" format="tabular" label="${tool.name} on ${on_string} (marker gene presence)" from_work_dir="out.marker"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
101 <data name="plot" format="pdf" label="${tool.name} on ${on_string} (marker gene presence plot)" from_work_dir="out.marker.pdf">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
102 <filter>adv_cond['adv_select']=='yes' and adv_cond['plotmarker']</filter>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
103 </data>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
104 <data name="noclass" format="fasta" label="${tool.name} on ${on_string} (unclassified sequences)" from_work_dir="out.noclass"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
105 <data name="toshort" format="fasta" label="${tool.name} on ${on_string} (to short sequences)" from_work_dir="out.tooshort"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
106 <collection name="markers" type="list" label="${tool.name} on ${on_string} (markers prediced for bins)">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
107 <discover_datasets pattern="out.(?P&lt;designation&gt;[0-9]+).marker.fasta" format="fasta" visible="false" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
108 </collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
109 <!-- additional output in case of reassembly -->
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
110 <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string} (reassembly bins)">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
111 <discover_datasets directory="out.reassem" pattern="out.(?P&lt;designation&gt;[0-9]+).fasta" format="fasta" visible="false" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
112 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
113 </collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
114 <collection name="reassembly_reads" type="list" label="${tool.name} on ${on_string} (reassembly reads)">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
115 <discover_datasets directory="out.reassem" pattern="out.reads.(?P&lt;designation&gt;[0-9]+)" format="fasta" visible="false" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
116 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
117 </collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
118 <data name="reassembly_noclass" format="fasta" label="${tool.name} on ${on_string} (reassembly unclassified sequences)" from_work_dir="out.reassem/out.reads.noclass">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
119 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
120 </data>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
121 <data name="reassembly_n50" format="text" label="${tool.name} on ${on_string} (reassembly N50)" from_work_dir="out.reassem/N50.txt">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
122 <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']!=""</filter>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
123 </data>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
124 </outputs>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
125 <tests>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
126 <test><!-- test w contigs and reads as input -->
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
127 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
128 <conditional name="intype_cond">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
129 <param name="intype_select" value="rds"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
130 <param name="reads" value="interleavedPE_unmapped_Sample3_total.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
131 </conditional>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
132 <conditional name="adv_cond">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
133 <param name="adv_select" value="no"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
134 </conditional>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
135 <output_collection name="bins" type="list" count="2">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
136 <element name="001" file="1/out.001.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
137 <element name="002" file="1/out.002.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
138 </output_collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
139 <output name="summary" file="1/out.summary" ftype="tabular" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
140 <output name="log" file="1/out.log" ftype="txt" compare="diff" lines_diff="17" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
141 <output name="abundout" file="1/out.abund1" ftype="tabular" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
142 <output name="marker" file="1/out.marker" ftype="tabular" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
143 <output name="noclass" file="1/out.noclass" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
144 <output name="toshort" file="1/out.tooshort" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
145 <output_collection name="markers" type="list" count="1">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
146 <element name="001" file="1/out.001.marker.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
147 </output_collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
148 </test>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
149 <test><!--test w contigs and abundances as input + advanced options -->
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
150 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
151 <conditional name="intype_cond">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
152 <param name="intype_select" value="abdc"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
153 <param name="abund" value="abundances.tsv" ftype="tabular"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
154 </conditional>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
155 <conditional name="adv_cond">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
156 <param name="adv_select" value="yes"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
157 <param name="min_contig_length" value="500"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
158 <param name="max_iteration" value="10"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
159 <param name="prob_threshold" value="0.95"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
160 <param name="plotmarker" value="-plotmarker"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
161 <param name="markerset" value="107"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
162 </conditional>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
163 <output_collection name="bins" type="list" count="2">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
164 <element name="001" file="2/out.001.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
165 <element name="002" file="2/out.002.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
166 </output_collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
167 <output name="summary" file="2/out.summary" ftype="tabular" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
168 <output name="log" file="2/out.log" ftype="txt" compare="diff" lines_diff="17" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
169 <output name="marker" file="2/out.marker" ftype="tabular" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
170 <output name="plot" file="2/out.marker.pdf" ftype="pdf" compare="sim_size" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
171 <output name="noclass" file="2/out.noclass" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
172 <output name="toshort" file="2/out.tooshort" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
173 <output_collection name="markers" type="list" count="1">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
174 <element name="001" file="2/out.001.marker.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
175 </output_collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
176 </test>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
177 <test><!-- test w contigs and reads as input + reassembly-->
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
178 <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
179 <conditional name="intype_cond">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
180 <param name="intype_select" value="rds"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
181 <param name="reads" value="interleavedPE_unmapped_Sample3_total.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
182 <param name="reassembly" value="-reassembly"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
183 </conditional>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
184 <conditional name="adv_cond">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
185 <param name="adv_select" value="no"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
186 </conditional>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
187 <output_collection name="bins" type="list" count="2">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
188 <element name="001" file="3/out.001.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
189 <element name="002" file="3/out.002.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
190 </output_collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
191 <output name="summary" file="3/out.summary" ftype="tabular" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
192 <output name="log" file="3/out.log" ftype="txt" compare="diff" lines_diff="17" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
193 <output name="abundout" file="3/out.abund1" ftype="tabular" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
194 <output name="marker" file="3/out.marker" ftype="tabular" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
195 <output name="noclass" file="3/out.noclass" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
196 <output name="toshort" file="3/out.tooshort" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
197 <output_collection name="markers" type="list" count="1">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
198 <element name="001" file="3/out.001.marker.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
199 </output_collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
200 <output_collection name="reassembly_bins" type="list" count="2">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
201 <element name="001" file="3/out.reassem/out.001.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
202 <element name="002" file="3/out.reassem/out.002.fasta" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
203 </output_collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
204 <output_collection name="reassembly_reads" type="list" count="2">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
205 <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
206 <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
207 </output_collection>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
208 <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
209 <output name="reassembly_n50" file="3/out.reassem/N50.txt" ftype="text" />
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
210 </test>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
211 </tests>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
212 <help><![CDATA[
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
213 MaxBin is a software that clusters metagenomic contigs into different bins,
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
214 each consists (hopefully) of contigs from one species. MaxBin uses the
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
215 nucleotide composition information and contig abundance information to do
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
216 achieve binning through an Expectation-Maximization algorithm.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
217
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
218
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
219 **Input**:
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
220
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
221 MaxBin need the contigs and contig abundance information. The contig abundance
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
222 information can be provided in two ways: the user can choose to provide
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
223
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
224 - the abundance file or
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
225 - the sequencing reads in fasta format (and MaxBin will use Bowtie2 to map the
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
226 sequencing reads against the contigs and generate the abundance information)
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
227
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
228 The abundance information can be provided as tabular file:
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
229
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
230 For example, assume I have three contigs named A0001, A0002, and A0003, then my abundance file will look like
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
231
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
232 A0001 30.89
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
233 A0002 20.02
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
234 A0003 78.93
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
235
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
236 Reads/Abundundance files can be given in multiple files.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
237
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
238 By default MaxBin will look for 107 marker genes present in >95% of bacteria.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
239 Alternatively you can also choose 40 marker gene sets that are universal among
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
240 bacteria and archaea (Wu et al., PLoS ONE 2013). This option may be better
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
241 suited for environment dominated by archaea; however it tend to split genomes
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
242 into more bins. You can choose between different marker gene sets and see which
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
243 one works better.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
244
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
245 **Outputs**
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
246
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
247 - bins: binned sequences
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
248 - summary: a summary file describing which contigs are being classified into which bin.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
249 - log: a log file recording the core steps of MaxBin algorithm
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
250 - abundances (only if reads are used as input): a summary file describing which contigs are being classified into which bin
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
251 - marker: marker gene presence numbers for each bin. This table is ready to be plotted by R or other 3rd-party software.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
252 - marker plot (anly present if selected in the advanced options): visualization of the marker gene presence numbers using R. Will only appear if -plotmarker is specified.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
253 - unclassified sequences: this file stores all sequences that pass the minimum length threshold but are not classified successfully.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
254 - to short sequences: this file stores all sequences that do not meet the minimum length threshold.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
255 - markers prediced for bins: these data sets store all markers predicted from the individual bins.
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
256
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
257 **Reassembly**
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
258
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
259 This is an experimental feature of MaxBin. It calls for each read bin IDBA_UD with the pre_correction parameter. Of course this IDBA_UD call can be done also with the corresponding Galaxy tool
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
260
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
261 ]]></help>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
262 <citations>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
263 <citation type="doi">10.1093/bioinformatics/btv638</citation>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
264 <citation type="bibtex">
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
265 @misc{renameTODO,
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
266 author = {LastTODO, FirstTODO},
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
267 year = {TODO},
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
268 title = {TODO},
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
269 url = {https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html},
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
270 }</citation>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
271 </citations>
35aa0df55a62 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty
mbernt
parents:
diff changeset
272 </tool>