Mercurial > repos > cpt > cpt_disruptin_finder
annotate disruptin_finder.xml @ 1:b973bc75693d draft
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author | cpt |
---|---|
date | Mon, 05 Jun 2023 02:40:49 +0000 |
parents | |
children | f046c58687a2 |
rev | line source |
---|---|
1
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
1 <tool id="edu.tamu.cpt2.phage.disruptin_finder" name="Disruptin Finder" version="1.1"> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
2 <description>finds proteins with size and charge criteria</description> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
3 <macros> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
4 <import>macros.xml</import> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
5 <import>cpt-macros.xml</import> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
6 </macros> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
7 <expand macro="requirements"/> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
8 <command detect_errors="aggressive"><![CDATA[ |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
9 python '$__tool_directory__/disruptin_finder.py' |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
10 '$fasta_file' |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
11 --thresh_net_charge '$thresh_net_charge' |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
12 --thresh_size '$thresh_size' |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
13 --thresh_charge_ratio '$thresh_charge_ratio' |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
14 --selection_criteria '$selection_criteria' |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
15 |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
16 > '$output']]></command> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
17 <inputs> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
18 <param label="Fasta" name="fasta_file" type="data" format="fasta"/> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
19 <param label="Minimum Net Charge" name="thresh_net_charge" type="integer" value="4"/> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
20 <param label="Maximum Length" name="thresh_size" type="integer" value="100"/> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
21 <param label="Minimum Charge to Length Ratio" name="thresh_charge_ratio" type="float" value="0.25"/> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
22 <param type="select" label="Type of selection criteria" name="selection_criteria"> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
23 <option value="net">Net charge</option> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
24 <option value="ratio">Ratio of charged residues to sequence length</option> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
25 <option value="both" selected="true">Both net charge and ratio</option> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
26 </param> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
27 </inputs> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
28 <outputs> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
29 <data format="fasta" name="output"/> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
30 </outputs> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
31 <help><![CDATA[ |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
32 **What it does** |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
33 This program finds proteins sequences based on given selection criteria: net charge, sequence length, |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
34 and/or number of charged residues per amino acid. Inputs include a multi fasta file of protein sequences, |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
35 thresholds for size, charge, and charge-to-size ratio criteria. |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
36 |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
37 This tool returns the selected sequences in a fasta format. |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
38 |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
39 ]]></help> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
40 <citations> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
41 <citation type="doi">10.1371/journal.pcbi.1008214</citation> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
42 <citation type="bibtex"> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
43 @unpublished{galaxyTools, |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
44 author = {A. Holt}, |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
45 title = {CPT Galaxy Tools}, |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
46 year = {2020}, |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
47 note = {https://github.com/tamu-cpt/galaxy-tools/} |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
48 } |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
49 </citation> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
50 </citations> |
b973bc75693d
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff
changeset
|
51 </tool> |