annotate metabat2.xml @ 2:708abf08a626 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
author iuc
date Tue, 02 Aug 2022 09:40:59 +0000
parents 76bc4efa1aeb
children eb50e7eca3dc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
1 <tool id="metabat2" name="MetaBAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
2 <description>metagenome binning</description>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
3 <macros>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
5 </macros>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
8 mkdir bins &&
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
9 metabat2
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
10 --inFile '$inFile'
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
11 --outFile 'bins/bin'
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
12 #if str($advanced.base_coverage_depth_cond.base_coverage_depth) == 'yes'
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
13 #if $advanced.base_coverage_depth_cond.abdFile
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
14 --abdFile '$advanced.base_coverage_depth_cond.abdFile'
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
15 #else if $advanced.base_coverage_depth_cond.cvExt
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
16 --cvExt '$advanced.base_coverage_depth_cond.cvExt'
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
17 #end if
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
18 #end if
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
19 --minContig $advanced.minContig
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
20 --maxP $advanced.maxP
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
21 --minS $advanced.minS
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
22 --maxEdges $advanced.maxEdges
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
23 --pTNF $advanced.pTNF
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
24 $advanced.noAdd
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
25 --minCV $advanced.minCV
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
26 --minCVSum $advanced.minCVSum
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
27 --seed $advanced.seed
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
28 --minClsSize $out.minClsSize
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
29 --numThreads \${GALAXY_SLOTS:-4}
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
30 $out.onlyLabel
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
31 #if $out.saveCls
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
32 $out.saveCls
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
33 --noBinOut
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
34 #end if
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
35 #if 'unbinned' in $out.extra_outputs
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
36 --unbinned
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
37 #end if
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
38 > process_log.txt
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
39 #if 'log' in $out.extra_outputs
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
40 && mv process_log.txt '$process_log'
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
41 #end if
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
42 ]]></command>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
43 <inputs>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
44 <param argument="--inFile" type="data" format="fasta,fasta.gz" label="Fasta file containing contigs"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
45 <section name="advanced" title="Advanced options">
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
46 <conditional name="base_coverage_depth_cond">
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
47 <param name="base_coverage_depth" type="select" label="Use a base coverage depth file?">
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
48 <option value="yes">Yes</option>
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
49 <option value="no" selected="true">No</option>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
50 </param>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
51 <when value="no"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
52 <when value="yes">
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
53 <param argument="--abdFile" type="data" format="tabular" optional="True" label="Tabular depth matrix file having mean and variance of base coverage depth" help="Generated by the Calculate contig depths for MetaBAT2 tool"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
54 <param argument="--cvExt" type="data" format="tabular" optional="True" label="Base coverage depth file without variance" help="Generated by a tool - not the Calculate contig depths for MetaBAT2 tool"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
55 </when>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
56 </conditional>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
57 <param argument="--minContig" type="integer" min="1500" value="1500" label="Minimum size of a contig for binning"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
58 <param argument="--maxP" type="integer" min="1" max="100" value="95" label="Percentage of good contigs considered for binning decided by connection among contigs" help="The greater, the more sensitive"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
59 <param argument="--minS" type="integer" min="1" max="99" value="60" label="Minimum score of an edge for binning" help="The greater, the more specific"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
60 <param argument="--maxEdges" type="integer" value="200" label="Maximum number of edges per node" help="The greater, the more sensitive"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
61 <param argument="--pTNF" type="integer" value="0" label="TNF probability cutoff for building TNF graph" help="Use it to skip the preparation step (0:auto)"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
62 <param argument="--noAdd" type="boolean" truevalue="--noAdd" falsevalue="" checked="false" label="Turn off additional binning for lost or small contigs?"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
63 <param argument="--minCV" type="float" value="1.0" label="Minimum mean coverage of a contig in each library for binning"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
64 <param argument="--minCVSum" type="float" value="1.0" label="Minimum total effective mean coverage of a contig for binning" help="Sum of depth over minCV"/>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
65 <param argument="--seed" type="integer" value="0" label="For exact reproducibility." help="Zero value will use random seed"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
66 </section>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
67 <section name="out" title="Output options">
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
68 <param argument="--minClsSize" type="integer" value="200000" label="Minimum size of a bin as the output"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
69 <param argument="--onlyLabel" type="boolean" truevalue="--onlyLabel" falsevalue="" checked="false" label="Output only sequence labels as a list in a column without sequences?"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
70 <param argument="--saveCls" type="boolean" truevalue="--saveCls" falsevalue="" checked="false" label="Save cluster memberships as a matrix format?"/>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
71 <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
72 <option value="lowDepth">Fasta file containing low depth bins (if no matrix format and label selected)</option>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
73 <option value="tooShort">Fasta file containing too short bins (if no matrix format and label selected)</option>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
74 <option value="unbinned">Fasta file containing unbinned contigs (if no matrix format and label selected)</option>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
75 <option value="log">Process log file</option>
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
76 </param>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
77 </section>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
78 </inputs>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
79 <outputs>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
80 <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
81 <filter>not out['saveCls'] and not out['onlyLabel']</filter>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
82 <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)\.fa" format="fasta" directory="bins"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
83 </collection>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
84 <data name="bin_saveCls" format="tabular" from_work_dir="bins/bin" label="${tool.name} on ${on_string}: Bins">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
85 <filter>out['saveCls'] and not out['onlyLabel']</filter>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
86 </data>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
87 <collection name="bin_onlyLabel" type="list" label="${tool.name} on ${on_string}: Bins">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
88 <filter>not out['saveCls'] and out['onlyLabel']</filter>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
89 <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)" format="tabular" directory="bins"/>
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
90 </collection>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
91 <data name="lowDepth" format="fasta" from_work_dir="bins/bin.lowDepth.fa" label="${tool.name} on ${on_string}: Low depth bins">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
92 <filter>not out['saveCls'] and not out['onlyLabel'] and 'lowDepth' in out['extra_outputs']</filter>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
93 </data>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
94 <data name="tooShort" format="fasta" from_work_dir="bins/bin.tooShort.fa" label="${tool.name} on ${on_string}: Too short bins">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
95 <filter>not out['saveCls'] and not out['onlyLabel'] and 'tooShort' in out['extra_outputs']</filter>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
96 </data>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
97 <data name="unbinned" format="fasta" from_work_dir="bins/bin.unbinned.fa" label="${tool.name} on ${on_string}: Unbinned sequences">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
98 <filter>not out['saveCls'] and not out['onlyLabel'] and 'unbinned' in out['extra_outputs']</filter>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
99 </data>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
100 <data name="process_log" format="txt" label="${tool.name} on ${on_string}: Process log">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
101 <filter>'log' in out['extra_outputs']</filter>
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
102 </data>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
103 </outputs>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
104 <tests>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
105 <test expect_num_outputs="5">
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
106 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
107 <section name="advanced">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
108 <conditional name="base_coverage_depth_cond">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
109 <param name="base_coverage_depth" value="no"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
110 </conditional>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
111 <param name="seed" value="345678"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
112 </section>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
113 <section name="out">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
114 <param name="extra_outputs" value="lowDepth,tooShort,unbinned,log"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
115 </section>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
116 <output_collection name="bins" type="list" count="2">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
117 <element name="1" ftype="fasta">
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
118 <assert_contents>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
119 <has_size value="334554"/>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
120 <has_text text=">MW127517.1"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
121 <has_text text=">MW127521.1"/>
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
122 </assert_contents>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
123 </element>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
124 <element name="2" ftype="fasta">
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
125 <assert_contents>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
126 <has_size value="577866"/>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
127 <has_text text=">MT810119.1"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
128 <has_text text=">MW130866.1"/>
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
129 </assert_contents>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
130 </element>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
131 </output_collection>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
132 <output name="lowDepth" ftype="fasta">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
133 <assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
134 <has_text text=""/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
135 </assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
136 </output>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
137 <output name="tooShort" ftype="fasta">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
138 <assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
139 <has_text text=""/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
140 </assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
141 </output>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
142 <output name="unbinned" ftype="fasta">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
143 <assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
144 <has_text text=">NC_045512.2"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
145 <has_text text=">MW130872.1"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
146 </assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
147 </output>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
148 <output name="process_log" ftype="txt">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
149 <assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
150 <has_text text="MetaBAT"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
151 <has_text text="2 bins (897090 bases in total) formed"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
152 </assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
153 </output>
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
154 </test>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
155 <test expect_num_outputs="1">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
156 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
157 <section name="advanced">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
158 <conditional name="base_coverage_depth_cond">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
159 <param name="base_coverage_depth" value="yes"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
160 <param name="abdFile" value="input_depth1.tabular" ftype="tabular"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
161 </conditional>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
162 <param name="seed" value="345678"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
163 </section>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
164 <section name="out">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
165 <param name="onlyLabel" value="false"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
166 <param name="saveCls" value="false"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
167 <param name="extra_outputs" value=""/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
168 </section>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
169 <output_collection name="bins" type="list" count="0"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
170 </test>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
171 <test expect_num_outputs="1">
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
172 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
2
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
173 <section name="advanced">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
174 <conditional name="base_coverage_depth_cond">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
175 <param name="base_coverage_depth" value="no"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
176 </conditional>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
177 <param name="seed" value="345678"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
178 </section>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
179 <section name="out">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
180 <param name="onlyLabel" value="false"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
181 <param name="saveCls" value="true"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
182 <param name="extra_outputs" value=""/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
183 </section>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
184 <output name="bin_saveCls" ftype="tabular">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
185 <assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
186 <has_text text="NC_045512.2"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
187 <has_text text="MT810119.1"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
188 <has_text text="MW130860.1"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
189 </assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
190 </output>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
191 </test>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
192 <test expect_num_outputs="1">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
193 <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
194 <section name="advanced">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
195 <conditional name="base_coverage_depth_cond">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
196 <param name="base_coverage_depth" value="no"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
197 </conditional>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
198 <param name="seed" value="345678"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
199 </section>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
200 <section name="out">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
201 <param name="onlyLabel" value="true"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
202 <param name="saveCls" value="false"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
203 <param name="extra_outputs" value=""/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
204 </section>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
205 <output_collection name="bin_onlyLabel" type="list" count="2">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
206 <element name="1" ftype="tabular">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
207 <assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
208 <has_text text="MW127518.1"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
209 <has_text text="MW127521.1"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
210 </assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
211 </element>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
212 <element name="2" ftype="tabular">
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
213 <assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
214 <has_text text="MT810119.1"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
215 <has_text text="MW130866.1"/>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
216 </assert_contents>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
217 </element>
708abf08a626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 625074b4bfdb2039935d0cb27115f83f18dae0d6
iuc
parents: 0
diff changeset
218 </output_collection>
0
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
219 </test>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
220 </tests>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
221 <help><![CDATA[
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
222 **What it does**
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
223
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
224 MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binning
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
225 software that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. The
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
226 tool accepts a fast file containing contigs and produces a collection (i.e., bins) of fasta files.
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
227
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
228 MetaBAT2 includes optionizations to MetaBAT. It requires virtually no parameter optimization. Default parameter
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
229 values are more reliable to use in most cases since MetaBAT2 adapts to the given data to find the best parameter.
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
230 Some parameter settings are still available for advanced users, helping to manage some exceptional cases by changing
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
231 the amount of data used for the analysis.
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
232
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
233 **More information**
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
234
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
235 https://bitbucket.org/berkeleylab/metabat/src/master/
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
236
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
237 **Options**
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
238
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
239 * **Use base coverage depth file** - optionally select a base coverage depth file that was either generated by the Calculate contig depths for MetaBAT2 tool or another 3rd party tool.
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
240
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
241 ]]></help>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
242 <expand macro="citations"/>
76bc4efa1aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
iuc
parents:
diff changeset
243 </tool>