diamond: diamond_makedb.xml annotate

annotate diamond_makedb.xml @ 1:df7738595640 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e

author	bgruening
date	Mon, 06 Feb 2017 07:08:25 -0500
parents	98037ef3d2a9
children	64be1ac21109

rev	line source
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	1 <tool id="bg_diamond_makedb" name="Diamond makedb" version="@VERSION@">
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	2 <description>Build database from a FASTA file</description>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	3 <macros>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	4 <import>macros.xml</import>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	5 </macros>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	6
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	7 <expand macro="requirements" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	8 <expand macro="stdio" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	9 <expand macro="version_command" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	10
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	11 <command>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	12 <!-- DB has two files, .dmnd and .tx -->
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	13 <![CDATA[
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	14 diamond makedb
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	15 --threads "\${GALAXY_SLOTS:-12}"
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	16 --in '$infile'
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	17 --db ./database
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	18 ]]>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	19 </command>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	20
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	21 <inputs>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	22 <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	23 </inputs>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	24
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	25 <outputs>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	26 <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	27 </outputs>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	28
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	29 <tests>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	30 <test>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	31 <param name="infile" value="db.fasta" ftype="fasta"/>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	32 <output name="outfile" value="db.dmnd"/>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	33 </test>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	34 </tests>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	35
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	36 <help>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	37 <![CDATA[
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	38
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	39 .. class:: infomark
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	40
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	41 What it does
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	42
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	43 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	44 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	45 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND is about 2,500
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	46 times faster than BLASTX, finding more than 94% of all matches.
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	47
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	48 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	49
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	50
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	51 ]]>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	52 </help>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	53
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	54 <expand macro="citations" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	55 </tool>

Mercurial > repos > bgruening > diamond

annotate diamond_makedb.xml @ 1:df7738595640 draft