Mercurial > repos > artbio > cherry_pick_fasta
diff cherry_pick_fasta.xml @ 6:d8fa616a228a draft
"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 |
line wrap: on
line diff
--- a/cherry_pick_fasta.xml Tue Apr 05 23:42:28 2022 +0000 +++ b/cherry_pick_fasta.xml Fri Apr 08 16:56:42 2022 +0000 @@ -1,9 +1,10 @@ -<tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="3.2.1"> +<tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="3.3"> <description>with header satisfying a string query</description> <requirements> - <requirement type="package" version="1.75">biopython</requirement> + <requirement type="package" version="3.8.0">python</requirement> </requirements> - <command interpreter="python">cherry_pick_fasta.py + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/cherry_pick_fasta.py' --input $input --searchfor '$search.searchfor' #if $search.options_selector == 'single': @@ -20,7 +21,7 @@ #end if #end if --output $output - </command> + ]]></command> <inputs> <param name="input" type="data" format="fasta" label="Source file" help="Fasta file to parse" /> @@ -69,6 +70,14 @@ <data name="output" format="fasta" label="Fasta sequences ${search.searchfor.value} ${search.options_selector} term(s) in header" /> </outputs> <tests> + <!-- test headers with space --> + <test> + <param ftype="fasta" name="input" value="input_withspace.fa" /> + <param name="query" value="type=rRNA" /> + <param name="searchfor" value="with" /> + <param name="match" value="include" /> + <output name="output" ftype="fasta" file="output_withspace.fa" /> + </test> <!-- exact matches --> <test> <param ftype="fasta" name="input" value="input.fa" />