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comparison jellyfish.xml @ 1:11658afb8c87 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
author iuc
date Wed, 01 Nov 2023 09:32:45 +0000
parents b4038a4d48f5
children dcd30574a456
comparison
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0:b4038a4d48f5 1:11658afb8c87
1 <tool id="jellyfish" name="jellyfish" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="jellyfish" name="jellyfish" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">
2 <macros> 2 <macros>
3 <token name="@WRAPPER_VERSION@">2.3.0</token> 3 <token name="@WRAPPER_VERSION@">2.3.0</token>
4 <token name="@VERSION_SUFFIX@">galaxy0</token> 4 <token name="@VERSION_SUFFIX@">galaxy0</token>
5 </macros> 5 </macros>
6 <xrefs>
7 <xref type="bio.tools">Jellyfish</xref>
8 </xrefs>
6 <requirements> 9 <requirements>
7 <requirement type="package" version="@WRAPPER_VERSION@">kmer-jellyfish</requirement> 10 <requirement type="package" version="@WRAPPER_VERSION@">kmer-jellyfish</requirement>
8 </requirements> 11 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
10 jellyfish 13 jellyfish
208 </conditional> 211 </conditional>
209 <param name="text" value="text"/> 212 <param name="text" value="text"/>
210 <param name="lower" value="1"/> 213 <param name="lower" value="1"/>
211 <param name="upper" value="20"/> 214 <param name="upper" value="20"/>
212 </conditional> 215 </conditional>
213 <output name="jellyfish_db_txt" file="out.jf.txt" lines_diff="2"/> 216 <output name="jellyfish_db_txt">
217 <assert_contents>
218 <has_line line="GTGATCGAGAGCCACAGCGTTA 1"/>
219 <has_line line="GCCTAGTCGGGATCGTCACCTA 1"/>
220 </assert_contents>
221 </output>
214 </test> 222 </test>
215 <test expect_num_outputs="1"> 223 <test expect_num_outputs="1">
216 <conditional name="commands"> 224 <conditional name="commands">
217 <param name="command" value="histo"/> 225 <param name="command" value="histo"/>
218 <param name="input" value="out.jf"/> 226 <param name="input" value="out.jf" ftype="jellyfish"/>
219 <param name="low" value="1"/> 227 <param name="low" value="1"/>
220 <param name="high" value="10000"/> 228 <param name="high" value="10000"/>
221 <param name="full" value="--full"/> 229 <param name="full" value="--full"/>
222 <param name="increment" value="100"/> 230 <param name="increment" value="100"/>
223 </conditional> 231 </conditional>
224 <output name="jellyfish_histo" ftype="txt" file="histo.txt"/> 232 <output name="jellyfish_histo" ftype="txt" file="histo.txt"/>
225 </test> 233 </test>
226 <test expect_num_outputs="1"> 234 <test expect_num_outputs="1">
227 <conditional name="commands"> 235 <conditional name="commands">
228 <param name="command" value="dump"/> 236 <param name="command" value="dump"/>
229 <param name="input" value="out.jf"/> 237 <param name="input" value="out.jf" ftype="jellyfish"/>
230 <param name="lower_count" value="3"/> 238 <param name="lower_count" value="3"/>
231 </conditional> 239 </conditional>
232 <output name="jellyfish_fasta" ftype="fasta" file="dump.fasta"/> 240 <output name="jellyfish_fasta" ftype="fasta" file="dump.fasta"/>
233 </test> 241 </test>
234 <test expect_num_outputs="1"> 242 <test expect_num_outputs="1">
235 <conditional name="commands"> 243 <conditional name="commands">
236 <param name="command" value="dump"/> 244 <param name="command" value="dump"/>
237 <param name="input" value="out.jf"/> 245 <param name="input" value="out.jf" ftype="jellyfish"/>
238 <conditional name="format"> 246 <conditional name="format">
239 <param name="format_select" value="column"/> 247 <param name="format_select" value="column"/>
240 <param name="tab" value="--tab"/> 248 <param name="tab" value="--tab"/>
241 </conditional> 249 </conditional>
242 <param name="upper_count" value="100"/> 250 <param name="upper_count" value="100"/>
243 </conditional> 251 </conditional>
244 <output name="jellyfish_tsv" ftype="tsv" file="dump.tsv"/> 252 <output name="jellyfish_tsv" ftype="tsv">
253 <assert_contents>
254 <has_line line="GTGATCGAGAGCCACAGCGTTA&#9;1"/>
255 <has_line line="GCCTAGTCGGGATCGTCACCTA&#9;1"/>
256 </assert_contents>
257 </output>
245 </test> 258 </test>
246 </tests> 259 </tests>
247 <help><![CDATA[ 260 <help><![CDATA[
248 Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. 261 Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.
249 262