annotate pairScan.xml @ 21:f4ed6a65a2ff draft

Uploaded
author petr-novak
date Thu, 27 Jul 2023 09:46:13 +0000
parents c2c69c6090f0
children 58807b35777a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
1
21
f4ed6a65a2ff Uploaded
petr-novak
parents: 9
diff changeset
2 <tool id="pairScan" name="Scan paired-end reads for overlap" version="1.0.0.1">
9
c2c69c6090f0 Uploaded
petr-novak
parents: 3
diff changeset
3 <description> Scan paired-end reads for overlap </description>
3
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
4 <requirements>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
5 <requirement type="package">python-levenshtein</requirement>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
6 </requirements>
21
f4ed6a65a2ff Uploaded
petr-novak
parents: 9
diff changeset
7 <required_files>
f4ed6a65a2ff Uploaded
petr-novak
parents: 9
diff changeset
8 <include type="literal" path="pairScan.py"/>
f4ed6a65a2ff Uploaded
petr-novak
parents: 9
diff changeset
9 </required_files>
f4ed6a65a2ff Uploaded
petr-novak
parents: 9
diff changeset
10
3
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
11 <command interpreter="python">
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
12 pairScan.py -f $fasta_input -o $min_overlap -m $max_mismatch -p $pass -b $bad -s $offset
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
13 </command>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
14
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
15 <inputs>
9
c2c69c6090f0 Uploaded
petr-novak
parents: 3
diff changeset
16 <param format="fasta" type="data" name="fasta_input" label="Reads in FASTA format" />
c2c69c6090f0 Uploaded
petr-novak
parents: 3
diff changeset
17 <param name="min_overlap" type="integer" size="3" value="30" min="20" max="100" label="Minimum overlap length [nt] " />
3
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
18 <param name="max_mismatch" type="select" label="Maximum number of mismatches per 100 bp">
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
19 <option value="0">0</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
20 <option value="1" selected="true">1</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
21 <option value="2">2</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
22 <option value="3">3</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
23 <option value="4">4</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
24 </param>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
25 <param name="offset" type="select" label="Maximum offset">
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
26 <option value="0">0</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
27 <option value="1">1</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
28 <option value="2">2</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
29 <option value="3">3</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
30 <option value="4">4</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
31 <option value="5" selected="true" >5</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
32 <option value="6">6</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
33 <option value="7">7</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
34 <option value="8">8</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
35 <option value="9">9</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
36 <option value="10">10</option>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
37 </param>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
38
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
39
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
40
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
41 </inputs>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
42
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
43
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
44 <outputs>
9
c2c69c6090f0 Uploaded
petr-novak
parents: 3
diff changeset
45 <data format="fasta" name="pass" label="Pairs with no overlap from dataset ${fasta_input.hid}"/>
c2c69c6090f0 Uploaded
petr-novak
parents: 3
diff changeset
46 <data format="fasta" name="bad" label="Overlaping pairs from dataset ${fasta_input.hid}"/>
3
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
47 </outputs>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
48
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
49 <help>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
50 **Scan paired reads for overlap**
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
51
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
52 </help>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
53
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
54
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
55 </tool>