diamond: diamond.xml annotate

annotate diamond.xml @ 6:64be1ac21109 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1

author	bgruening
date	Thu, 27 Sep 2018 06:30:30 -0400
parents	830516f9521b
children	62c9df8382c2

rev	line source
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	1 <tool id="bg_diamond" name="Diamond" version="@VERSION@.0">
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	2 <description>alignment tool for short sequences against a protein database</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 <expand macro="requirements" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	7 <expand macro="stdio" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	8 <expand macro="version_command" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	9 <command>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	10 <![CDATA[
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	11
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	12 #if $ref_db_source.db_source == "history":
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	13 ln -s $ref_db_source.reference_database ./database.dmnd
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	14 #else:
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	15 ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	16 #end if
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	17
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	18 &&
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	19
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	20 diamond
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	21 $method_cond.method_select
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	22 --threads "\${GALAXY_SLOTS:-12}"
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	23 --db ./database
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	24 --query '$query'
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	25 #if $method_cond.method_select == "blastx"
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	26 --query-gencode '$method_cond.query_gencode'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	27 --strand '$method_cond.query_strand'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	28 --min-orf $method_cond.min_orf
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	29 #if $method_cond.frameshift_cond.frameshift_select == 'yes'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	30 --frameshift $method_cond.frameshift_cond.frameshift
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	31 $method_cond.frameshift_cond.range_culling
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	32 #end if
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	33 #end if
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	34
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	35 @OUTPUT_ARGS@
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	36
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	37 --compress '0'
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	38 #if $sensitivity == "1"
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	39 --sensitive
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	40 #else if $sensitivity == "2"
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	41 --more-sensitive
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	42 #end if
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	43
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	44 #if str($gapopen) != "":
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	45 --gapopen '$gapopen'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	46 #end if
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	47 #if str($gapextend) != "":
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	48 --gapextend '$gapextend'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	49 #end if
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	50 --matrix '$matrix'
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	51 --comp-based-stats '$comp_based_stats'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	52 --masking '$masking'
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	53
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	54 @HITFILTER_ARGS@
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	55
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	56 #if str($filter_score.filter_score_select) == 'evalue':
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	57 --evalue '$filter_score.evalue'
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	58 #else:
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	59 --min-score '$filter_score.min_score'
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	60 #end if
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	61
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	62 --id '$id'
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	63 --query-cover '$query_cover'
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	64 --subject-cover '$subject_cover'
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	65 --block-size '$block_size'
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	66 #if str($unal) == '1':
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	67 --unal 1 --un '$unalqueries'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	68 #end if
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	69 $no_self_hits
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	70 #if $tax_cond.tax_select == 'file':
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	71 --taxonlist `cat '$tax_cond.taxonlistfile' \| grep -v "^#" \| grep -v "^$" \| tr "\n" "," \| sed 's/,$//'`
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	72 #else if $tax_cond.tax_select == 'list':
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	73 --taxonlist '$tax_cond.taxonlist'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	74 #end if
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	75 ]]>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	76 </command>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	77 <inputs>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	78 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	79 <param name="method_select" type="select" label="What do you want to align?" help="(blastp/blastx)">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	80 <option value="blastp">Align amino acid query sequences (blastp)</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	81 <option value="blastx">Align DNA query sequences (blastx)</option>
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	82 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	83 <when value="blastx">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	84 <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help="">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	85 <option value="1">The Standard Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	86 <option value="2">The Vertebrate Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	87 <option value="3">The Yeast Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	88 <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	89 <option value="5">The Invertebrate Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	90 <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	91 <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	92 <option value="10">The Euplotid Nuclear Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	93 <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	94 <option value="12">The Alternative Yeast Nuclear Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	95 <option value="13">The Ascidian Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	96 <option value="14">The Alternative Flatworm Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	97 <option value="16">Chlorophycean Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	98 <option value="21">Trematode Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	99 <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	100 <option value="23">Thraustochytrium Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	101 <option value="24">Pterobranchia Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	102 <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	103 <option value="26">Pachysolen tannophilus Nuclear Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	104 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	105 <param argument="--min-orf" name="min_orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	106
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	107 <param name="query_strand" argument="--strand" type="select" label="query strands to search" help="">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	108 <option value="both" selected="True">Both</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	109 <option value="plus">Plus</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	110 <option value="minus">Minus</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	111 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	112 <conditional name="frameshift_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	113 <param name="frameshift_select" type="select" label="Allow for frameshifts?" help="">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	114 <option value="yes">yes</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	115 <option value="no" selected="true">no</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	116 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	117 <when value="yes">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	118 <param argument="--range-culling" name="range_culling" type="boolean" truevalue="--range-culling" falsevalue="" checked="false" label="restrict hit culling to overlapping query ranges" help="This feature is designed for long query DNA sequences that may span several genes. In these cases, the default of reporting the 25 best overall hits could cause hits to a lower scoring gene to be overshadowed. But just increasing the number of alignments reported will bloat the output size and reduce performance. Using this feature along with -k 25 (default), a hit will only be deleted if at least 50% of its query range is spanned by at least 25 higher or equal scoring hits. Using this feature along with --top 10, a hit will only be deleted if its score is more than 10% lower than that of a higher scoring hit over at least 50% of its query range. The percentage is configurable using --range-cover. Note that this feature is currently only available in frameshift alignment mode"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	119 <param argument="--frameshift" type="integer" value="0" label="frame shift penalty" help="Values around 15 are reasonable for this parameter. Enabling this feature will have the aligner tolerate missing bases in DNA sequences and is most recommended for long, error-prone sequences like MinION reads. In the pairwise output format, frameshifts will be indicated by \ and / for a shift by +1 and -1 nucleotide in the direction of translation respectively." />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	120 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	121 <when value="no"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	122 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	123 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	124 <when value="blastp">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	125 </when>
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	126 </conditional>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	127 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	128 <conditional name="ref_db_source">
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	129 <param name="db_source" type="select" label="Will you select a reference database from your history or use a built-in index?" help="Built-ins were indexed using default options">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	130 <option value="indexed">Use a built-in index</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	131 <option value="history">Use one from the history</option>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	132 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	133 <when value="indexed">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	134 <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	135 <options from_data_table="diamond_database">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	136 <filter type="sort_by" column="2"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	137 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	138 </options>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	139 </param>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	140 </when>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	141 <when value="history">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	142 <param name="reference_database" type="data" format="dmnd" label="Select the reference database" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	143 </when>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	144 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	145 <expand macro="output_type_macro" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	146 <param name="no_self_hits" argument="--no-self-hits" type="boolean" truevalue="--no-self-hits" falsevalue="" checked="true" label="suppress reporting of identical self hits?" help=""/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	147 <param name='sensitivity' type="select" label="Sensitivity Mode" help="Choose one of the sensitivity modes. The default mode is mainly designed for short read alignment, i.e. finding significant matches of >50 bits on 30-40aa fragments. The sensitive mode is a lot more sensitive than the default and generally recommended for aligning longer sequences. The more sensitive mode provides even more sensitivity. More sensitivity may increase computation time.">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	148 <option value="0" selected="True">Default</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	149 <option value="1">Sensitive</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	150 <option value="2">More Sensitive</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	151 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	152 <param argument="--matrix" type="select" label="Scoring matrix" help="In parentheses are the supported values for (gap open)/(gap extend). In brackets are default gap penalties">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	153 <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1) [14/2]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	154 <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1) [13/2]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	155 <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1) [11/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	156 <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1) [10/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	157 <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1) [10/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	158 <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1) [14/2]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	159 <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1) [10/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	160 <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1) [9/1]</option>
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	161 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	162 <param argument="--gapopen" type="integer" optional="True" value="" label="Gap open penalty" help="leave empty for default (see scoring matrix)" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	163 <param argument="--gapextend" type="integer" optional="True" value="" label="Gap extension penalty" help="leave empty for default (see scoring matrix)" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	164 <param name="comp_based_stats" argument="--comp-based-stats" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable composition based statistics?" help="Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	165 <param argument="--masking" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable masking of low complexity regions?" help="Masked residues appear in the output as X"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	166 <conditional name="tax_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	167 <param name="tax_select" type="select" label="Restrict search taxonomically?" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	168 <option value="no">No</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	169 <option value="list">list of taxids entered manually</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	170 <option value="file">list of taxids from single column tabular file</option>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	171 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	172 <when value="no"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	173 <when value="list">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	174 <param name="taxonlist" argument="--taxonlist" type="text" value="" label="comma separated list of taxon ids" help="" />
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	175 </when>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	176 <when value="file">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	177 <param name="taxonlistfile" argument="--taxonlist" type="data" format="tabular" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" />
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	178 </when>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	179 </conditional>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	180 <conditional name="filter_score">
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	181 <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)">
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	182 <option value="evalue">Maximum e-value to report alignments</option>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	183 <option value="min-score">Minimum bit score to report alignments</option>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	184 </param>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	185 <when value="evalue">
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	186 <param argument="--evalue" type="float" value="0.001" label="Maximum expected value to keep an alignment" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	187 </when>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	188 <when value="min-score">
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	189 <param name="min_score" argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	190 </when>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	191 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	192 <expand macro="hit_filter_macro" />
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	193 <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	194 <param name="query_cover" argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="" />
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	195 <param name="subject_cover" argument="--subject-cover" type="integer" value="0" label="Minimum subject cover percentage to report an alignment" help="" />
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	196 <param name="block_size" argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" />
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	197 <param argument="--unal" type="boolean" truevalue="1" falsevalue="0" checked="false" label="report unaligned queries" help=""/>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	198 </inputs>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	199 <outputs>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	200 <expand macro="output_macro" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	201 <data format="fasta" name="unalqueries" label="${tool.name} on ${on_string} (unaligned queries)">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	202 <filter>unal == "1"</filter>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	203 </data>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	204 </outputs>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	205 <tests>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	206 <test>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	207 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	208 <param name="method_select" value="blastp" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	209 </conditional>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	210 <param name="query" value="protein.fasta" ftype="fasta"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	211 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	212 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	213 <param name="reference_database" value="db.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	214 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	215 <conditional name="output">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	216 <param name="outfmt" value="6"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	217 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	218 </conditional>
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	219 <param name="sensitivity" value="0"/>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	220 <param name="matrix" value="BLOSUM62"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	221 <param name="comp-based-stat" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	222 <param name="masking" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	223 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	224 <param name="hit_filter_select" value="max"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	225 <param name="max_target_seqs" value="25" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	226 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	227 <conditional name="filter_score">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	228 <param name="filter_score_select" value="evalue"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	229 <param name="evalue" value="0.001" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	230 </conditional>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	231 <param name="id" value="0"/>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	232 <param name="query_cover" value="0"/>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	233 <param name="block_size" value="2"/>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	234 <output name="blast_tabular" file="diamond_results.tabular"/>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	235 </test>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	236 <test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	237 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	238 <param name="method_select" value="blastp" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	239 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	240 <param name="query" value="protein.fasta" ftype="fasta"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	241 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	242 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	243 <param name="reference_database" value="db-wtax.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	244 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	245 <conditional name="tax_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	246 <param name="tax_select" value="list"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	247 <param name="taxonlist" value="2" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	248 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	249 <conditional name="output">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	250 <param name="outfmt" value="6"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	251 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	252 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	253 <param name="sensitivity" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	254 <param name="matrix" value="BLOSUM62"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	255 <param name="comp-based-stat" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	256 <param name="masking" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	257 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	258 <param name="hit_filter_select" value="max"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	259 <param name="max_target_seqs" value="25" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	260 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	261 <conditional name="filter_score">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	262 <param name="filter_score_select" value="evalue"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	263 <param name="evalue" value="0.001" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	264 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	265 <param name="id" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	266 <param name="query_cover" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	267 <param name="block_size" value="2"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	268 <output name="blast_tabular" file="diamond_results.wtax.tabular"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	269 </test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	270 <test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	271 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	272 <param name="method_select" value="blastx" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	273 <conditional name="frameshift_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	274 <param name="frameshift_select" value="yes"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	275 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	276 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	277 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	278 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	279 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	280 <param name="reference_database" value="db.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	281 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	282 <conditional name="output">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	283 <param name="outfmt" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	284 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	285 <param name="sensitivity" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	286 <param name="matrix" value="BLOSUM62"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	287 <param name="comp-based-stat" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	288 <param name="masking" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	289 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	290 <param name="hit_filter_select" value="top"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	291 <param name="top" value="10" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	292 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	293 <conditional name="filter_score">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	294 <param name="filter_score_select" value="score"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	295 <param name="evalue" value="1" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	296 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	297 <param name="id" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	298 <param name="query_cover" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	299 <param name="block_size" value="2"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	300 <output name="blast_tabular" file="diamond_results.pairwise"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	301 </test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	302 <test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	303 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	304 <param name="method_select" value="blastp" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	305 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	306 <param name="query" value="protein.fasta" ftype="fasta"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	307 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	308 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	309 <param name="reference_database" value="db-wtax.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	310 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	311 <conditional name="output">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	312 <param name="outfmt" value="100"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	313 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	314 <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	315 </test>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	316 </tests>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	317 <help>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	318 <![CDATA[
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	319
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	320 What it does
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	321
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	322 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	323 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	324 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	325 times faster than BLASTX, finding more than 94% of all matches.
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	326
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	327 The DIAMOND algorithm is designed for the alignment of large datasets. The algorithm is not efficient for a small number of query sequences or only a single one of them, and speed will be low. BLAST is recommended for small datasets.
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	328
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	329 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	330
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	331 Input
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	332
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	333 Input data is a large protein or nucleotide sequence file.
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	334
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	335
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	336 Output
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	337
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	338 Diamond gives you a tabular output file with 12 columns:
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	339
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	340 Column Description
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	341 1 Query Seq-id (ID of your sequence)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	342 2 Subject Seq-id (ID of the database hit)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	343 3 Percentage of identical matches
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	344 4 Alignment length
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	345 5 Number of mismatches
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	346 6 Number of gap openings
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	347 7 Start of alignment in query
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	348 8 End of alignment in query
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	349 9 Start of alignment in subject (database hit)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	350 10 End of alignment in subject (database hit)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	351 11 Expectation value (E-value)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	352 12 Bit score
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	353
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	354
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	355 Supported values for gap open and gap extend parameters depending on the selected scoring matrix.
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	356
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	357 ======== ============================================
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	358 Matrix Supported values for (gap open)/(gap extend)
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	359 ======== ============================================
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	360 BLOSUM45 (10-13)/3; (12-16)/2; (16-19)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	361 BLOSUM50 (9-13)/3; (12-16)/2; (15-19)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	362 BLOSUM62 (6-11)/2; (9-13)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	363 BLOSUM80 (6-9)/2; 13/2; 25/2; (9-11)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	364 BLOSUM90 (6-9)/2; (9-11)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	365 PAM250 (11-15)/3; (13-17)/2; (17-21)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	366 PAM70 (6-8)/2; (9-11)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	367 PAM30 (5-7)/2; (8-10)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	368 ======== ============================================
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	369
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	370
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	371 ]]>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	372 </help>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	373 <expand macro="citations" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	374 </tool>

Mercurial > repos > bgruening > diamond

annotate diamond.xml @ 6:64be1ac21109 draft