Mercurial > repos > recetox > biotransformer

annotate biotransformer.xml @ 7:c32d024d6d68 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 038d752ab3a1eb53f9599f219da97faaa67bf08d
author recetox
date Fri, 23 Jun 2023 10:06:47 +0000
parents 21158cdb8aec
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
1 <tool id="biotransformer" name="BioTransformer" version="@TOOL_VERSION@+galaxy1" profile="21.09">
4
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
2 <macros>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
3 <import>macros.xml</import>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
4 </macros>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
5 <expand macro="creator"/>
7
c32d024d6d68 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 038d752ab3a1eb53f9599f219da97faaa67bf08d
recetox
parents: 6
diff changeset
6 <xrefs>
c32d024d6d68 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 038d752ab3a1eb53f9599f219da97faaa67bf08d
recetox
parents: 6
diff changeset
7 <xref type="bio.tools">biotransformer</xref>
c32d024d6d68 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 038d752ab3a1eb53f9599f219da97faaa67bf08d
recetox
parents: 6
diff changeset
8 </xrefs>
4
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
9 <requirements>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
10 <requirement type="package" version="@TOOL_VERSION@">biotransformer</requirement>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
11 <requirement type="package" version="3.1.1">openbabel</requirement>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
12 <requirement type="package" version="1.1.1">pandas</requirement>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
13 </requirements>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
14 <command detect_errors="aggressive"><![CDATA[
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
15 python3 '${__tool_directory__}/wrapper_biotransformer.py'
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
16 -k $k
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
17 -b $b
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
18 -s $steps
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
19 -t $tolerance
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
20 -a
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
21 -icsv $input_file
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
22 -ocsv $output_file
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
23 -ocsvDup $output_file2
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
24 -ocsvDup2 $output_file3
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
25 ]]>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
26 </command>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
27 <inputs>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
28 <param name="k" type="select" value="pred"
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
29 label="The task to be permed [pred=prediction, cid=compound identification].">
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
30 <option value="pred" selected="true">pred</option>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
31 <option value="cid">cid</option>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
32 </param>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
33 <param name="b" type="select" value="ecbased" label="The type of description.">
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
34 <option value="ecbased" selected="true">EC-based</option>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
35 <option value="cyp450">CYP450</option>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
36 <option value="phaseII">Phase II</option>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
37 <option value="hgut">Human gut microbial</option>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
38 <option value="superbio">Human super transformer 1 (superbio)</option>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
39 <option value="allHuman">Human super transformer 2 (allHuman)</option>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
40 <option value="envimicro">Environmental microbial</option>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
41 </param>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
42 <param name="steps" type="integer" value="1" label=" The number of steps for the prediction."/>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
43 <param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification."/>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
44 <param name="input_file" type="data" format="csv" label="Input CSV file."/>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
45 </inputs>
2
3998017c374b "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4ce18f4cd02f9fedd53ba3742934b2a63b7f2d6f"
recetox
parents: 1
diff changeset
46
4
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
47 <outputs>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
48 <data format="tsv" name="output_file" label="BioTransformer on ${on_string}"/>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
49 <data format="tsv" name="output_file2" label="BioTransformer with filter on ${on_string}"/>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
50 <data format="tsv" name="output_file3" label="BioTransformer with super filter on ${on_string}"/>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
51 </outputs>
0
b5b62d04625a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b9cf078bf1136d497d624b62eae7f56f58d1f03"
recetox
parents:
diff changeset
52
4
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
53 <tests>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
54 <test>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
55 <param name="k" value="pred"/>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
56 <param name="b" value="allHuman"/>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
57 <param name="steps" value="1"/>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
58 <param name="tolerance" value="0.01"/>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
59 <param name="input_file" value="smiles.csv"/>
6
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
60 <output name="output_file">
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
61 <assert_contents>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
62 <has_size value="8600" delta="100"/>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
63 <has_n_lines n="225" delta="10"/>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
64 </assert_contents>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
65 </output>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
66 <output name="output_file2">
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
67 <assert_contents>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
68 <has_size value="8600" delta="100"/>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
69 <has_n_lines n="225" delta="10"/>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
70 </assert_contents>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
71 </output>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
72 <output name="output_file3">
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
73 <assert_contents>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
74 <has_size value="7400" delta="100"/>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
75 <has_n_lines n="186" delta="10"/>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
76 </assert_contents>
21158cdb8aec planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
recetox
parents: 5
diff changeset
77 </output>
4
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
78 </test>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
79 </tests>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
80 <help>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
81 <![CDATA[
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
82 @HELP@
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
83 ]]>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
84 </help>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
85 <citations>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
86 <citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation>
77f693bb14ac "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9a2276670c6ebf147ccd2cdd1cc54b306af3d20c"
recetox
parents: 3
diff changeset
87 </citations>
0
b5b62d04625a "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b9cf078bf1136d497d624b62eae7f56f58d1f03"
recetox
parents:
diff changeset
88 </tool>