Mercurial > repos > artbio > cherry_pick_fasta

comparison cherry_pick_fasta.xml @ 7:6c0aefd9fee3 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit 849d6d2087dadb81f1b790e3bcb5bda40c3c83af
author artbio
date Thu, 29 Dec 2022 11:53:05 +0000
parents d8fa616a228a
children ee689b6999d5
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6:d8fa616a228a 7:6c0aefd9fee3
1 <tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="3.3"> 1 <tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="4.0">
2 <description>with header satisfying a string query</description> 2 <description>with header satisfying a string query</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.8.0">python</requirement> 4 <requirement type="package" version="3.8.0">python</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
91 <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" /> 91 <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" />
92 <param name="searchfor" value="with" /> 92 <param name="searchfor" value="with" />
93 <param name="match" value="exact" /> 93 <param name="match" value="exact" />
94 <output name="output" ftype="fasta" file="output_exact.fa" /> 94 <output name="output" ftype="fasta" file="output_exact.fa" />
95 </test> 95 </test>
96
97
98 <test> 96 <test>
99 <param ftype="fasta" name="input" value="input.fa" /> 97 <param ftype="fasta" name="input" value="input.fa" />
100 <param name="options_selector" value="textdataset" /> 98 <param name="options_selector" value="textdataset" />
101 <param name="query" ftype="txt" value="alt_termlist.txt" /> 99 <param name="query" ftype="txt" value="alt_termlist.txt" />
102 <param name="searchfor" value="without" /> 100 <param name="searchfor" value="without" />
109 <param name="query" ftype="txt" value="alt_termlist.txt" /> 107 <param name="query" ftype="txt" value="alt_termlist.txt" />
110 <param name="searchfor" value="with" /> 108 <param name="searchfor" value="with" />
111 <param name="match" value="exact" /> 109 <param name="match" value="exact" />
112 <output name="output" ftype="fasta" file="output_alt_termlist.fa" /> 110 <output name="output" ftype="fasta" file="output_alt_termlist.fa" />
113 </test> 111 </test>
114
115
116 <!-- partial matches --> 112 <!-- partial matches -->
117 <test> 113 <test>
118 <param ftype="fasta" name="input" value="input.fa" /> 114 <param ftype="fasta" name="input" value="input.fa" />
119 <param name="query" value="gi|81971654" /> 115 <param name="query" value="gi|81971654" />
120 <param name="searchfor" value="with" /> 116 <param name="searchfor" value="with" />
145 **What it does** 141 **What it does**
146 142
147 This tool retrieves nucleotide/peptide sequences from a fasta file whose headers match 143 This tool retrieves nucleotide/peptide sequences from a fasta file whose headers match
148 or do not match a given string, or a list of strings. 144 or do not match a given string, or a list of strings.
149 145
146 Note that the version 4 of the tools is amazingly accelerated !
147
150 </help> 148 </help>
151 </tool> 149 </tool>