annotate preprocessing.xml @ 0:7ba39ab6f48d draft default tip

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
author bgruening
date Thu, 15 Dec 2016 18:18:10 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
1 <tool id="preproc" name="Preprocessing" version="0.1">
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
2 <requirements>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
3 <requirement type="package" version="0.1">graphclust-wrappers</requirement>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
4 </requirements>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
5 <stdio>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
6 <exit_code range="1:" />
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
7 </stdio>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
8 <command>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
9 <![CDATA[
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
10
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
11 'preprocessing.pl'
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
12 '$fastaFile' $max_length $in_winShift $min_seq_length
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
13
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
14 ]]>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
15 </command>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
16 <inputs>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
17 <param type="data" name="fastaFile" format="fasta" />
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
18 <param name="max_length" type="integer" value="10000" size="5" label="window size"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
19 <param name="in_winShift" type="integer" value="100" size="5" label="window shift in percent"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
20 <param name="min_seq_length" type="integer" value="5" size="5" label="minimum sequence length"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
21 </inputs>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
22
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
23 <outputs>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
24 <data name="data.fasta" format="fasta" from_work_dir="FASTA/data.fasta" label="data.fasta"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
25 <data name="data.map" format="txt" from_work_dir="FASTA/data.map" label="data.map"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
26 <data name="data.names" format="txt" from_work_dir="FASTA/data.names" label="data.names"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
27 <data name="data.fasta.scan" format="fasta" from_work_dir="FASTA/data.fasta.scan" label="data.fasta.scan"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
28 <data name="FASTA" format="zip" from_work_dir="FASTA.zip" label="FASTA.ZIP"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
29 </outputs>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
30
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
31
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
32 <tests>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
33 <test>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
34 <param name="fastaFile" value="input.fa"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
35 <param name="max_length" value="10000"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
36 <param name="in_winShift" value="100"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
37 <param name="min_seq_length" value="5"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
38 <output name="data.fasta" file="FASTA/data.fasta"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
39 <output name="data.map" file="FASTA/data.map" />
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
40 <output name="data.names" file="FASTA/data.names"/>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
41 <output name="data.fasta.scan" file="FASTA/data.fasta.scan" />
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
42 </test>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
43 </tests>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
44
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
45 <help>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
46 <![CDATA[
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
47
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
48 **What it does**
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
49
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
50 The tool takes as an input file of sequences in Fasta format and creates the final input for GraphCLust based on given parameters.
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
51
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
52 **Parameters**
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
53
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
54 + **window size** : All input sequences are splitted into fragments of this length.
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
55 The shift of the sliding window can be defined via option *window shift in percent*.
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
56 This paramter reflects the expected length of signals to be found.
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
57 Slightly larger windows are usually ok. Too small windows can disturb existing signals.
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
58
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
59
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
60
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
61
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
62 + **window shift in percent** : Relative window size in % for window shift during input preprocessing.
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
63 Please note that a small shift results in much more fragments for clustering. The benefit is that RNA
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
64 motifs/structures are not destroyed by arbitrary split points. Smaller
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
65 shifts usually increase the cluster quality. Too small shifts (<20) are not
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
66 recommended as a dense center is "polluted" by overlapping fragments and
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
67 no other occurences in the dataset can be found.
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
68
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
69
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
70
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
71
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
72
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
73 + **minimum sequence length** : Minimal length of input sequences.
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
74 Every input sequence below that length is ignored completely during clustering.
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
75
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
76
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
77 ]]></help>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
78
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
79
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
80 <citations>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
81 <citation type="doi">10.1093/bioinformatics/bts224</citation>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
82 </citations>
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
83
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
84
7ba39ab6f48d planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
bgruening
parents:
diff changeset
85 </tool>