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comparison cherry_pick_fasta.xml @ 1:ea8fde9c6f82 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
author artbio
date Wed, 09 Oct 2019 18:48:17 -0400
parents e3aee4ba49c6
children 321cad0eb507
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0:e3aee4ba49c6 1:ea8fde9c6f82
1 <tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="1.0.0"> 1 <tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="2.0.0">
2 <description>with header satisfying a query string</description> 2 <description>with header satisfying a string query</description>
3 <command interpreter="python">cherry_pick_fasta.py 3 <command interpreter="python">cherry_pick_fasta.py
4 --input $input 4 --input $input
5 --query-string "$query" 5 --searchfor '$search.searchfor'
6 #if $search.options_selector == 'single':
7 --query-string '$search.query'
8 #else:
9 --query-file '$search.query'
10 #end if
6 --output $output 11 --output $output
7 </command> 12 </command>
8 13
9 <inputs> 14 <inputs>
10 <param name="query" type="text" size="30" value="" label="Select sequences with this string in their header" help="exemple: gi|40557596"> 15 <param name="input" type="data" format="fasta" label="Source file" help="Fasta file to parse" />
11 <sanitizer> 16
12 <valid initial="string.printable"> 17 <conditional name="search">
13 <remove value="&quot;"/> 18 <param name="options_selector" type="select" display="radio" label="by single term or file of terms">
14 <remove value="\"/> 19 <option value="single" selected="True">single term</option>
15 </valid> 20 <option value="textdataset">terms in a text dataset</option>
16 <mapping initial="none"> 21 </param>
17 <add source="&quot;" target="\&quot;"/> 22 <when value="single">
18 <add source="\" target="\\"/> 23 <param name="query" type="text" size="30" value="" label="Search string" help="exemple: gi|40557596">
19 </mapping> 24 <sanitizer>
20 </sanitizer> 25 <valid initial="string.printable">
21 </param> 26 <remove value="&quot;"/>
22 <param format="fasta" label="Source file" name="input" type="data" /> 27 <remove value="\"/>
28 </valid>
29 <mapping initial="none">
30 <add source="&quot;" target="\&quot;"/>
31 <add source="\" target="\\"/>
32 </mapping>
33 </sanitizer>
34 </param>
35 <param name="searchfor" type="select" label="retrieve sequences whose headers contain or do not contain the search string">
36 <option value="with" selected="true">contain</option>
37 <option value="without">do not contain</option>
38 </param>
39 </when>
40 <when value="textdataset">
41 <param name="query" type="data" format="txt" label="term dataset" help="a list of term to search for, one term per line" />
42 <param name="searchfor" type="select" label="retrieve sequences whose headers contain or do not contain the search list">
43 <option value="with" selected="true">contain</option>
44 <option value="without">do not contain</option>
45 </param>
46 </when>
47 </conditional>
23 </inputs> 48 </inputs>
24 <outputs> 49 <outputs>
25 <data name="output" format="fasta" label="${tool.name} on ${on_string} including '${query.value}' in header" /> 50 <data name="output" format="fasta" label="Fasta sequences ${search.searchfor.value} ${search.options_selector} term(s) in header" />
26 </outputs> 51 </outputs>
27 <tests> 52 <tests>
28 <test> 53 <test>
29 <param ftype="fasta" name="input" value="input.fa" /> 54 <param ftype="fasta" name="input" value="input.fa" />
55 <!-- <param name="options_selector" value="textdataset" /> -->
30 <param name="query" value="gi|81971654" /> 56 <param name="query" value="gi|81971654" />
57 <param name="searchfor" value="with" />
31 <output name="output" ftype="fasta" file="output.fa" /> 58 <output name="output" ftype="fasta" file="output.fa" />
32 </test> 59 </test>
60 <test>
61 <param ftype="fasta" name="input" value="input.fa" />
62 <!-- <param name="options_selector" value="textdataset" /> -->
63 <param name="query" value="RNA" />
64 <param name="searchfor" value="without" />
65 <output name="output" ftype="fasta" file="output_without.fa" />
66 </test>
67 <test>
68 <param ftype="fasta" name="input" value="input.fa" />
69 <param name="options_selector" value="textdataset" />
70 <param name="query" ftype="txt" value="termlist.txt" />
71 <param name="searchfor" value="without" />
72 <output name="output" ftype="fasta" file="output_termlist.fa" />
73 </test>
74 <test>
75 <param ftype="fasta" name="input" value="input.fa" />
76 <param name="options_selector" value="textdataset" />
77 <param name="query" ftype="txt" value="termlist.txt" />
78 <param name="searchfor" value="without" />
79 <output name="output" ftype="fasta" file="output_termlist_without.fa" />
80 </test>
33 </tests> 81 </tests>
82
34 <help> 83 <help>
35 **What it does** 84 **What it does**
36 85
37 This tool retrieves nucleotide/peptide sequences from a fasta file whose headers match a given query string. 86 This tool retrieves nucleotide/peptide sequences from a fasta file whose headers match
87 or do not match a given string.
38 88
39 It is Copyright © 2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_. 89 It is Copyright © 2019 `CNRS and Sorbonne-Université`_ and is released under the `MIT license`_.
40 90
41 .. _CNRS and University Pierre et Marie Curie: http://www.upmc.fr/en/index.html 91 .. _CNRS and Sorbonne-Université: http://www.sorbonne-universite.fr/en
42 .. _MIT license: http://opensource.org/licenses/MIT 92 .. _MIT license: http://opensource.org/licenses/MIT
43 93
44 </help> 94 </help>
45 </tool> 95 </tool>