Mercurial > repos > artbio > cherry_pick_fasta

annotate cherry_pick_fasta.xml @ 3:c282a8a47dd9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
author artbio
date Fri, 21 May 2021 09:34:14 +0000
parents 321cad0eb507
children ba6c4aeb22ea
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
1 <tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="3.0.0">
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
2 <description>with header satisfying a string query</description>
2
321cad0eb507 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit b5ef783237b244d684e26b1ed1cc333a8305ce3e"
artbio
parents: 1
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3 <requirements>
3
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
4 <requirement type="package" version="1.70">biopython</requirement>
2
321cad0eb507 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit b5ef783237b244d684e26b1ed1cc333a8305ce3e"
artbio
parents: 1
diff changeset
5 </requirements>
0
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
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6 <command interpreter="python">cherry_pick_fasta.py
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
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diff changeset
7 --input $input
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
8 --searchfor '$search.searchfor'
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
9 #if $search.options_selector == 'single':
3
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
10 #if $search.match == 'exact':
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
11 --query-string '$search.query' --mode exact
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
12 #else:
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
13 --query-string '$search.query' --mode includes
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
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14 #end if
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
15 #else:
3
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
16 #if $search.match == 'exact':
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
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17 --query-file '$search.query' --mode exact
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
18 #else:
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
19 --query-file '$search.query' --mode includes
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
20 #end if
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
21 #end if
0
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
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22 --output $output
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
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diff changeset
23 </command>
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
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24
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
25 <inputs>
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
26 <param name="input" type="data" format="fasta" label="Source file" help="Fasta file to parse" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
27
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
28 <conditional name="search">
3
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
29 <param name="options_selector" type="select" display="radio" label="for a">
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
30 <option value="single" selected="True">single string</option>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
31 <option value="textdataset">list of strings</option>
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
32 </param>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
33 <when value="single">
3
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
34 <param name="match" type="select" label="retrieve sequences whose headers...">
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
35 <option value="include" selected="true">partially</option>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
36 <option value="exact">exactly</option>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
37 </param>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
38 <param name="searchfor" type="select" label=" ">
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
39 <option value="with" selected="true">contain this string</option>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
40 <option value="without">do not contain this string</option>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
41 </param>
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
42 <param name="query" type="text" size="30" value="" label="Search string" help="exemple: gi|40557596">
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
43 <sanitizer>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
44 <valid initial="string.printable">
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
45 <remove value="&quot;"/>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
46 <remove value="\"/>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
47 </valid>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
48 <mapping initial="none">
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
49 <add source="&quot;" target="\&quot;"/>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
50 <add source="\" target="\\"/>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
51 </mapping>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
52 </sanitizer>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
53 </param>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
54 </when>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
55 <when value="textdataset">
3
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
56 <param name="match" type="select" label="retrieve sequences whose headers...">
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
57 <option value="includes" selected="true">partially</option>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
58 <option value="exact">exactly</option>
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
59 </param>
3
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
60 <param name="searchfor" type="select" label=" ">
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
61 <option value="with" selected="true">contain one of these list strings</option>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
62 <option value="without">do not contain one of these list strings</option>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
63 </param>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
64 <param name="query" type="data" format="txt" label="list of strings dataset" help="a list of strings to search for, one string per line" />
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
65 </when>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
66 </conditional>
0
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
67 </inputs>
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
68 <outputs>
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
69 <data name="output" format="fasta" label="Fasta sequences ${search.searchfor.value} ${search.options_selector} term(s) in header" />
0
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
70 </outputs>
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
71 <tests>
3
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
72 <!-- exact matches -->
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
73 <test>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
74 <param ftype="fasta" name="input" value="input.fa" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
75 <param name="query" value="gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=43.46,AligLength=451,E-val=2e-122" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
76 <param name="searchfor" value="without" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
77 <param name="match" value="exact" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
78 <output name="output" ftype="fasta" file="output_exactly_not.fa" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
79 </test>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
80 <test>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
81 <param ftype="fasta" name="input" value="input.fa" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
82 <param name="query" value="gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=43.46,AligLength=451,E-val=2e-122" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
83 <param name="searchfor" value="with" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
84 <param name="match" value="exact" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
85 <output name="output" ftype="fasta" file="output_exact.fa" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
86 </test>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
87
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
88
0
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
89 <test>
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
90 <param ftype="fasta" name="input" value="input.fa" />
3
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
91 <param name="options_selector" value="textdataset" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
92 <param name="query" ftype="txt" value="alt_termlist.txt" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
93 <param name="searchfor" value="without" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
94 <param name="match" value="exact" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
95 <output name="output" ftype="fasta" file="output_alt_termlist_without.fa" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
96 </test>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
97 <test>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
98 <param ftype="fasta" name="input" value="input.fa" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
99 <param name="options_selector" value="textdataset" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
100 <param name="query" ftype="txt" value="alt_termlist.txt" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
101 <param name="searchfor" value="with" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
102 <param name="match" value="exact" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
103 <output name="output" ftype="fasta" file="output_alt_termlist.fa" />
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
104 </test>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
105
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
106
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
107 <!-- partial matches -->
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
108 <test>
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
109 <param ftype="fasta" name="input" value="input.fa" />
0
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
110 <param name="query" value="gi|81971654" />
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
111 <param name="searchfor" value="with" />
0
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
112 <output name="output" ftype="fasta" file="output.fa" />
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
113 </test>
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
114 <test>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
115 <param ftype="fasta" name="input" value="input.fa" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
116 <param name="query" value="RNA" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
117 <param name="searchfor" value="without" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
118 <output name="output" ftype="fasta" file="output_without.fa" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
119 </test>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
120 <test>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
121 <param ftype="fasta" name="input" value="input.fa" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
122 <param name="options_selector" value="textdataset" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
123 <param name="query" ftype="txt" value="termlist.txt" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
124 <param name="searchfor" value="without" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
125 <output name="output" ftype="fasta" file="output_termlist.fa" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
126 </test>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
127 <test>
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
128 <param ftype="fasta" name="input" value="input.fa" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
129 <param name="options_selector" value="textdataset" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
130 <param name="query" ftype="txt" value="termlist.txt" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
131 <param name="searchfor" value="without" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
132 <output name="output" ftype="fasta" file="output_termlist_without.fa" />
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
133 </test>
0
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
134 </tests>
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
135 <help>
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
136 **What it does**
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
137
1
ea8fde9c6f82 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
artbio
parents: 0
diff changeset
138 This tool retrieves nucleotide/peptide sequences from a fasta file whose headers match
3
c282a8a47dd9 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
artbio
parents: 2
diff changeset
139 or do not match a given string, or a list of strings.
0
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
140
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
141 </help>
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
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diff changeset
142 </tool>