Mercurial > repos > artbio > cherry_pick_fasta

comparison cherry_pick_fasta.xml @ 6:d8fa616a228a draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit 8384f1bb5378232bbe78319e06a3522674c7c1fe"
author artbio
date Fri, 08 Apr 2022 16:56:42 +0000
parents 144b856e926c
children 6c0aefd9fee3
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5:144b856e926c 6:d8fa616a228a
1 <tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="3.2.1"> 1 <tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="3.3">
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="1.75">biopython</requirement> 4 <requirement type="package" version="3.8.0">python</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">cherry_pick_fasta.py 6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/cherry_pick_fasta.py'
7 --input $input 8 --input $input
8 --searchfor '$search.searchfor' 9 --searchfor '$search.searchfor'
9 #if $search.options_selector == 'single': 10 #if $search.options_selector == 'single':
10 #if $search.match == 'exact': 11 #if $search.match == 'exact':
11 --query-string '$search.query' --mode exact 12 --query-string '$search.query' --mode exact
18 #else: 19 #else:
19 --query-file '$search.query' --mode includes 20 --query-file '$search.query' --mode includes
20 #end if 21 #end if
21 #end if 22 #end if
22 --output $output 23 --output $output
23 </command> 24 ]]></command>
24 25
25 <inputs> 26 <inputs>
26 <param name="input" type="data" format="fasta" label="Source file" help="Fasta file to parse" /> 27 <param name="input" type="data" format="fasta" label="Source file" help="Fasta file to parse" />
27 28
28 <conditional name="search"> 29 <conditional name="search">
67 </inputs> 68 </inputs>
68 <outputs> 69 <outputs>
69 <data name="output" format="fasta" label="Fasta sequences ${search.searchfor.value} ${search.options_selector} term(s) in header" /> 70 <data name="output" format="fasta" label="Fasta sequences ${search.searchfor.value} ${search.options_selector} term(s) in header" />
70 </outputs> 71 </outputs>
71 <tests> 72 <tests>
73 <!-- test headers with space -->
74 <test>
75 <param ftype="fasta" name="input" value="input_withspace.fa" />
76 <param name="query" value="type=rRNA" />
77 <param name="searchfor" value="with" />
78 <param name="match" value="include" />
79 <output name="output" ftype="fasta" file="output_withspace.fa" />
80 </test>
72 <!-- exact matches --> 81 <!-- exact matches -->
73 <test> 82 <test>
74 <param ftype="fasta" name="input" value="input.fa" /> 83 <param ftype="fasta" name="input" value="input.fa" />
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" /> 84 <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" />
76 <param name="searchfor" value="without" /> 85 <param name="searchfor" value="without" />