Mercurial > repos > iuc > semibin_bin

annotate bin.xml @ 1:4d561bdc2c31 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
author iuc
date Mon, 27 Mar 2023 08:24:46 +0000
parents 474701f91bcd
children dbf5571a8140
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
1 <tool id="semibin_bin" name="SemiBin: Group the contigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
2 <description>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
3 into bins
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
4 </description>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
5 <macros>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
6 <import>macros.xml</import>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
7 </macros>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
8 <expand macro="biotools"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
9 <expand macro="requirements"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
10 <expand macro="version"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
12 #import re
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
13 @FASTA_FILES@
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
14 SemiBin bin
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
15 --input-fasta 'contigs.fasta'
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
16 --data '$data'
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
17 #if $mod.select == 'history'
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
18 --model '$mod.model'
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
19 #else
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
20 --environment '$mod.environment'
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
21 #end if
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
22 --output 'output'
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
23 --threads \${GALAXY_SLOTS:-1}
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
24 --minfasta-kbs $minfasta_kbs
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
25 $no_recluster
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
26 --max-node $max_node
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
27 --max-edges $max_edges
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
28 --random-seed $random_seed
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
29 @MIN_LEN@
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
30 --orf-finder '$orf_finder'
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
31 ]]></command>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
32 <inputs>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
33 <expand macro="mode_fasta"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
34 <expand macro="data"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
35 <conditional name="mod">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
36 <param name="select" type="select" label="Model to use">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
37 <option value="built-in" selected="true">Built-in model</option>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
38 <option value="history">From history</option>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
39 </param>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
40 <when value="built-in">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
41 <expand macro="environment"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
42 </when>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
43 <when value="history">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
44 <param argument="--model" type="data" format="h5" label="Trained semi-supervised deep learning model"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
45 </when>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
46 </conditional>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
47 <expand macro="min_len"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
48 <expand macro="orf-finder"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
49 <expand macro="random-seed"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
50 <expand macro="max-node"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
51 <expand macro="max-edges"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
52 <expand macro="minfasta-kbs"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
53 <expand macro="no-recluster"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
54 </inputs>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
55 <outputs>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
56 <collection name="output_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
57 <filter>not no_recluster</filter>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
58 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_recluster_bins" />
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
59 </collection>
1
4d561bdc2c31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
60 <collection name="output_prerecluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">
4d561bdc2c31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
61 <filter>not no_recluster</filter>
4d561bdc2c31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
62 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_prerecluster_bins" />
4d561bdc2c31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
63 </collection>
4d561bdc2c31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
64 <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins without reeclustering">
4d561bdc2c31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
65 <filter>no_recluster</filter>
0
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
66 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins" />
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
67 </collection>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
68 </outputs>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
69 <tests>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
70 <test expect_num_outputs="2">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
71 <conditional name="mode">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
72 <param name="select" value="single"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
73 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
74 </conditional>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
75 <param name="data" ftype="csv" value="data.csv"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
76 <conditional name="mod">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
77 <param name="select" value="history"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
78 <param name="model" ftype="h5" value="model.h5"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
79 </conditional>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
80 <conditional name="min_len">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
81 <param name="method" value="min-len"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
82 <param name="min_len" value="0" />
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
83 </conditional>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
84 <param name="orf_finder" value="prodigal"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
85 <param name="random-seed" value="0"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
86 <param name="max_node" value="1"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
87 <param name="max_edges" value="200"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
88 <param name="minfasta_kbs" value="200"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
89 <param name="no_recluster" value="false"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
90 <output_collection name="output_recluster_bins" count="0"/>
1
4d561bdc2c31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
91 <output_collection name="output_prerecluster_bins" count="3">
0
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
92 <element name="0" ftype="fasta">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
93 <assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
94 <has_text text=">g1k_0"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
95 <has_text text=">g4k_9"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
96 </assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
97 </element>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
98 <element name="1" ftype="fasta">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
99 <assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
100 <has_text text=">g2k_0"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
101 <has_text text=">g2k_9"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
102 </assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
103 </element>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
104 <element name="2" ftype="fasta">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
105 <assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
106 <has_text text=">g3k_0"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
107 <has_text text=">g3k_9"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
108 </assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
109 </element>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
110 </output_collection>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
111 </test>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
112 <test expect_num_outputs="1">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
113 <conditional name="mode">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
114 <param name="select" value="single"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
115 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
116 </conditional>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
117 <param name="data" ftype="csv" value="data.csv"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
118 <conditional name="mod">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
119 <param name="select" value="built-in"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
120 <param name="environment" value="human_gut"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
121 </conditional>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
122 <conditional name="min_len">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
123 <param name="method" value="min-len"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
124 <param name="min_len" value="0" />
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
125 </conditional>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
126 <param name="orf_finder" value="prodigal"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
127 <param name="random-seed" value="0"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
128 <param name="max_node" value="1"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
129 <param name="max_edges" value="200"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
130 <param name="minfasta_kbs" value="200"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
131 <param name="no_recluster" value="true"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
132 <output_collection name="output_bins" count="3">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
133 <element name="0" ftype="fasta">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
134 <assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
135 <has_text text=">g1k_0"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
136 <has_text text=">g4k_9"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
137 </assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
138 </element>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
139 <element name="1" ftype="fasta">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
140 <assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
141 <has_text text=">g2k_0"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
142 <has_text text=">g2k_9"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
143 </assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
144 </element>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
145 <element name="2" ftype="fasta">
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
146 <assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
147 <has_text text=">g3k_0"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
148 <has_text text=">g3k_9"/>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
149 </assert_contents>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
150 </element>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
151 </output_collection>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
152 </test>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
153 </tests>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
154 <help><![CDATA[
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
155 @HELP_HEADER@
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
156
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
157 Inputs
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
158 ======
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
159
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
160 @HELP_INPUT_FASTA@
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
161 @HELP_INPUT_BAM@
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
162
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
163 Outputs
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
164 =======
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
165
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
166 @HELP_BINS@
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
167
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
168 ]]></help>
474701f91bcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
169 <expand macro="citations"/>
1
4d561bdc2c31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
170 </tool>