diamond: diamond.xml annotate

annotate diamond.xml @ 10:1e3323a44643 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"

author	iuc
date	Fri, 22 Apr 2022 13:51:34 +0000
parents	f921014aba5a
children	e8ac2b53f262

rev	line source
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	1 <tool id="bg_diamond" name="Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
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" />
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	9 <command detect_errors="aggressive">
0 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 $method_cond.method_select
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	22 --quiet
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	23 --threads "\${GALAXY_SLOTS:-12}"
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	24 --db ./database
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	25 --query '$query'
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	26 #if $method_cond.method_select == "blastx"
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	27 --query-gencode '$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	28 --strand '$method_cond.query_strand'
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	29 --min-orf $method_cond.min_orf
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	30 #if $method_cond.frameshift_cond.frameshift_select == 'yes'
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	31 --frameshift $method_cond.frameshift_cond.frameshift
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	32 $method_cond.frameshift_cond.range_culling
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	33 #end if
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	34 #else if $method_cond.method_select == "blastp"
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	35 $method_cond.no_self_hits
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	36 #end if
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	37
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	38 @OUTPUT_ARGS@
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	39
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	40 #if $output_section.output.outfmt != '100'
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	41 --compress '0'
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	42 #end if
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	43 $sens_cond.sensitivity
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	44 $iterate
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	45 --algo $algo
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	46 #if $global_ranking
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	47 --global-ranking $global_ranking
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	48 #end if
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	49 #if str($gapopen) != "":
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	50 --gapopen '$gapopen'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	51 #end if
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	52 #if str($gapextend) != "":
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	53 --gapextend '$gapextend'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	54 #end if
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	55 --matrix '$matrix'
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	56 --comp-based-stats '$method_cond.comp_based_stats'
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	57 --masking '$masking'
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	58
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	59 @HITFILTER_ARGS@
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	60
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	61 #if str($filter_score.filter_score_select) == 'evalue':
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	62 --evalue '$filter_score.evalue'
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	63 #else:
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	64 --min-score '$filter_score.min_score'
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	65 #end if
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	66
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	67 --id '$id'
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	68 --query-cover '$query_cover'
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	69 --subject-cover '$subject_cover'
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	70 --block-size '$sens_cond.block_size'
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	71 #if $output_section.output_unal
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	72 #if "--un" in $output_section.output_unal
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	73 --un '$unalqueries'
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	74 #if $query.ext.startswith("fasta"):
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	75 --unfmt fasta
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	76 #else
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	77 --unfmt fastq
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	78 #end if
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	79 #end if
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	80 #if "--al" in $output_section.output_unal
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	81 --al '$alqueries'
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	82 #if $query.ext.startswith("fasta"):
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	83 --alfmt fasta
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	84 #else
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	85 --alfmt fastq
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	86 #end if
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	87 #end if
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	88 #end if
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	89 #if $output_section.max_hsps
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	90 --max-hsps $output_section.max_hsps
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	91 #end if
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	92 #if $tax_cond.tax_select == 'file':
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	93 --taxonlist `cat '$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	94 #else if $tax_cond.tax_select == 'list':
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	95 --taxonlist '$tax_cond.taxonlist'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	96 #end if
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	97 #if $advanced_section.seed_cut
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	98 --seed-cut $advanced_section.seed_cut
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	99 #end if
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	100 $advanced_section.freq_masking
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	101 --motif-masking $advanced_section.motif_masking
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	102 ]]>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	103 </command>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	104 <inputs>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	105 <conditional name="method_cond">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	106 <param name="method_select" type="select" label="Alignment mode" help="(blastp/blastx)">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	107 <option value="blastp">Amino acid query sequences (blastp)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	108 <option value="blastx">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	109 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	110 <when value="blastx">
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	111 <param argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help="">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	112 <option value="1">Standard Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	113 <option value="2">Vertebrate Mitochondrial Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	114 <option value="3">Yeast Mitochondrial Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	115 <option value="4">Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	116 <option value="5">Invertebrate Mitochondrial Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	117 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	118 <option value="9">Echinoderm and Flatworm Mitochondrial Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	119 <option value="10">Euplotid Nuclear Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	120 <option value="11">Bacterial, Archaeal and Plant Plastid Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	121 <option value="12">Alternative Yeast Nuclear Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	122 <option value="13">Ascidian Mitochondrial Code</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	123 <option value="14">Alternative Flatworm Mitochondrial Code</option>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	124 <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	125 <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	126 <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	127 <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	128 <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	129 <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	130 <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	131 </param>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	132 <param argument="--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" />
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	133
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	134 <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	135 <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	136 <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	137 <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	138 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	139 <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	140 <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	141 <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	142 <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	143 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	144 <when value="yes">
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	145 <param argument="--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"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	146 <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	147 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	148 <when value="no"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	149 </conditional>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	150
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	151 <param argument="--comp-based-stats" type="select" label="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">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	152 <option value="0">Disable</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	153 <option value="1" selected="True">Default mode (Hauser, 2016)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	154 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	155 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	156 <when value="blastp">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	157 <param argument="--no-self-hits" type="boolean" truevalue="--no-self-hits" falsevalue="" checked="true"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	158 label="Suppress reporting of identical self-hits between sequences"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	159 help="The FASTA sequence identifiers as well as the sequences of query and target need to be identical for a hit to be deleted"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	160
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	161 <param argument="--comp-based-stats" type="select" label="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">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	162 <option value="0">Disable</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	163 <option value="1" selected="True">Default mode (Hauser, 2016)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	164 <option value="2">Compositional matrix adjust conditioned on sequence properties, simplified (Yu, 2005)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	165 <option value="3">Compositional matrix adjust conditioned on sequence properties (Yu, 2005)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	166 <option value="4">Compositional matrix adjust unconditionally (Yu, 2005)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	167 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	168 </when>
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	169 </conditional>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	170 <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	171 <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	172 <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	173 <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	174 <option value="history">Use one from the history</option>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	175 </param>
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="indexed">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	177 <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	178 <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	179 <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	180 <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	181 </options>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	182 </param>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	183 </when>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	184 <when value="history">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	185 <param name="reference_database" argument="--db" type="data" format="dmnd" label="Select the reference database" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	186 </when>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	187 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	188 <conditional name="tax_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	189 <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.">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	190 <option value="no" selected="True">No</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	191 <option value="list">List of taxids entered manually</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	192 <option value="file">List of taxids from single column tabular file</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	193 </param>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	194 <when value="no"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	195 <when value="list">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	196 <param name="taxonlist" argument="--taxonlist" type="text" value="" label="Comma separated list of taxon ids" help="">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	197 <validator type="regex" message="Taxonlist needs to be a comma separated list of integers">[0-9,]*</validator>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	198 </param>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	199 </when>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	200 <when value="file">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	201 <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="" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	202 </when>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	203 </conditional>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	204 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	205 <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.">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	206 <option value="--fast">Fast (--fast)</option>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	207 <option value="" selected="True">Default</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	208 <option value="--mid-sensitive">Mid Sensitive (--mid-sensitive)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	209 <option value="--sensitive">Sensitive (--sensitive)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	210 <option value="--more-sensitive">More Sensitive (--more-sensitive)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	211 <option value="--very-sensitive">Very Sensitive (--very-sensitive)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	212 <option value="--ultra-sensitive">Ultra Sensitive (--ultra-sensitive)</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	213 </param>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	214 <when value="--fast">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	215 <expand macro="block_size_low_sens"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	216 </when>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	217 <when value="">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	218 <expand macro="block_size_low_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	219 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	220 <when value="--mid-sensitive">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	221 <expand macro="block_size_low_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	222 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	223 <when value="--sensitive">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	224 <expand macro="block_size_low_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	225 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	226 <when value="--more-sensitive">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	227 <expand macro="block_size_low_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	228 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	229 <when value="--very-sensitive">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	230 <expand macro="block_size_hi_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	231 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	232 <when value="--ultra-sensitive">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	233 <expand macro="block_size_hi_sens"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	234 </when>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	235 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	236 <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	237 <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	238 <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	239 <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	240 <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	241 <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	242 <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	243 <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	244 <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	245 </param>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	246 <param argument="--gapopen" type="integer" optional="True" value="" label="Gap open penalty" help="Leave empty for default (see scoring matrix)" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	247 <param argument="--gapextend" type="integer" optional="True" value="" label="Gap extension penalty" help="Leave empty for default (see scoring matrix)" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	248 <param argument="--masking" type="select" label="Masking algorithm" help="DIAMOND by default applies the tantan repeat masking algorithm to the query and target sequences as described in (Frith, 2011).
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	249 This masking procedure increases the specificity of alignments and serves to filter out spurious hits. Note that when using --comp-based-stats (2,3,4), tantan masking is disabled by default.">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	250 <option value="0">Disabled</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	251 <option value="1" selected="true">Tantan</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	252 <option value="seg">SEG</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	253 </param>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	254 <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	255 <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)">
7 62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4" bgruening parents: 6 diff changeset	256 <option value="evalue" selected="True">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	257 <option value="min-score">Minimum bit score to report alignments</option>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	258 </param>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	259 <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	260 <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	261 </when>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	262 <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	263 <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	264 </when>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	265 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	266 <param argument="--iterate" type="boolean" truevalue="--iterate" falsevalue="" checked="false"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	267 label="Run multiple rounds of searches with increasing sensitivity" help="he query dataset will first be searched at a lower sensitivity setting, only searching those query sequences at
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	268 the target sensitivity that fail to produce a significant alignment at a lower sensitivity." />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	269 <param argument="--algo" type="select" label="Algorithm for seed search" help="Double-indexed is the main algorithm of the program, designed for large input files but less efficient for small
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	270 query files. Query-indexed and improves performance for small query files. This mode will be automatically triggered based on the input. Contiguous-seed mode and further improves performance
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	271 for small query files. The modes differ slightly in their sensitivity, so results are not guaranteed to be 100% identical for different settings of this option.">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	272 <option value="0">Doble-indexed (0)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	273 <option value="1">Query-indexed (1)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	274 <option value="ctg">Contiguous-seed mode (ctg)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	275 </param>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	276 <expand macro="hit_filter_macro" />
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	277 <param argument="--global-ranking" type="integer" min="0" value="" optional="true"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	278 label="Limit on the number of Smith Waterman extensions" help="Target sequences will be ranked according to their ungapped extension scores at seed hits, and gapped extensions will only
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	279 be computed for the best N targets for each query. Note that this option increases memory use." />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	280 <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="Report only alignments above the given percentage of sequence identity" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	281 <param argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="Report only alignments above the given percentage of query cover" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	282 <param argument="--subject-cover" type="integer" value="0" label="Minimum subject cover percentage to report an alignment" help="Report only alignments above the given percentage of subject cover"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	283 <section name="output_section" title="Output options">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	284 <param argument="--max-hsps" type="integer" min="0" optional="true" label="Maximum number of HSPs"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	285 help="The maximum number of HSPs (High-Scoring Segment Pairs) per target sequence to report for each query. The default policy is to report only the highest-scoring
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	286 HSP for each target, while disregarding alternative, lower-scoring HSPs that are contained in the same target." />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	287 <expand macro="output_type_macro">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	288 <!-- Taxonomy features are not supported for the DAA format (i.e.
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	289 can't be used in diamond view) -->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	290 <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	291 <option value="sskingdoms">Subject super kingdoms</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	292 <option value="skingdoms">Subject kingdoms</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	293 <option value="sphylums">Subject phylums</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	294 </expand>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	295 <param name="output_unal" type="select" optional="true" multiple="true" label="Output aligned/unaligned queries to separate file" help="">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	296 <option value="--un">Output unaligned queries (--un)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	297 <option value="--al">Output alaligned queries (--al)</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	298 </param>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	299 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	300 <section name="advanced_section" title="Advanced options" expanded="false">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	301 <param argument="--seed-cut" type="float" min="0" optional="true" label="Set a complexity cutoff for indexed seeds"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	302 <param argument="--freq-masking" type="boolean" truevalue="--freq-masking" falsevalue="" checked="false" label="Enable masking seeds based on frequency" help="This option is incompatible with --sed-cut" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	303 <param argument="--motif-masking" type="select" label="Softmask abundant motifs" help="Enable or disable motif masking">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	304 <option value="0">Disabled</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	305 <option value="1">Enabled</option>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	306 </param>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	307 </section>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	308 </inputs>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	309 <outputs>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	310 <expand macro="output_macro" />
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	311 <data format_source="query" name="unalqueries" label="${tool.name} on ${on_string}: unaligned queries">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	312 <filter>output_section['output_unal'] and "--un" in output_section['output_unal']</filter>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	313 </data>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	314 <data format_source="query" name="alqueries" label="${tool.name} on ${on_string}: aligned queries">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	315 <filter>output_section['output_unal'] and "--un" in output_section['output_unal']</filter>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	316 </data>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	317 </outputs>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	318 <tests>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	319 <!--Test 01-->
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	320 <test expect_num_outputs="3">
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	321 <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	322 <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	323 </conditional>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	324 <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	325 <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	326 <param name="db_source" value="history"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	327 <param name="reference_database" value="db-wtax.dmnd"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	328 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	329 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	330 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	331 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	332 <!-- removed ,cigar from test: https://github.com/bbuchfink/diamond/issues/532 -->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	333 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,scovhsp,sskingdoms,skingdoms,sphylums"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	334 <param name="unal" value="true"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	335 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	336 </section>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	337 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	338 <param name="sensitivity" value=""/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	339 </conditional>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	340 <param name="matrix" value="BLOSUM62"/>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	341 <param name="comp_based_stats" value="1"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	342 <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	343 <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	344 <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	345 <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	346 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	347 <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	348 <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	349 <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	350 </conditional>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	351 <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	352 <param name="query_cover" value="0"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	353 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	354 <param name="block_size" value="2"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	355 </conditional>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	356 <param name="output_unal" value="--al,--un"/>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	357 <output name="unalqueries">
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	358 <assert_contents>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	359 <has_line line=">shuffled sequence that should go to unaligned"/>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	360 </assert_contents>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	361 </output>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	362 <output name="alqueries">
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	363 <assert_contents>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	364 <has_line line=">sequence more text"/>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	365 </assert_contents>
f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	366 </output>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	367 <output name="blast_tabular" file="diamond_results.tabular"/>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	368 </test>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	369 <!--Test 02-->
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	370 <test expect_num_outputs="1">
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	371 <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	372 <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	373 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	374 <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	375 <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	376 <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	377 <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	378 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	379 <conditional name="tax_cond">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	380 <param name="tax_select" value="list"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	381 <param name="taxonlist" value="2" />
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	382 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	383 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	384 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	385 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	386 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	387 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	388 </section>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	389 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	390 <param name="sensitivity" value=""/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	391 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	392 <param name="matrix" value="BLOSUM62"/>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	393 <param name="comp_based_stats" value="1"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	394 <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	395 <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	396 <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	397 <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	398 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	399 <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	400 <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	401 <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	402 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	403 <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	404 <param name="query_cover" value="0"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	405 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	406 <param name="block_size" value="2"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	407 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	408 <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	409 </test>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	410 <!--Test 03-->
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	411 <test expect_num_outputs="1">
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	412 <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	413 <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	414 <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	415 <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	416 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	417 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	418 <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	419 <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	420 <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	421 <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	422 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	423 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	424 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	425 <param name="outfmt" value="0"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	426 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	427 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	428 <conditional name="sens_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	429 <param name="sensitivity" value=""/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	430 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	431 <param name="matrix" value="BLOSUM62"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	432 <param name="comp_based_stats" value="1"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	433 <param name="masking" value="1"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	434 <conditional name="hit_filter">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	435 <param name="hit_filter_select" value="top"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	436 <param name="top" value="10" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	437 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	438 <conditional name="filter_score">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	439 <param name="filter_score_select" value="min-score"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	440 <param name="min_score" value="1" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	441 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	442 <param name="id" value="0"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	443 <param name="query_cover" value="0"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	444 <conditional name="sens_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	445 <param name="block_size" value="2"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	446 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	447 <output name="blast_tabular" file="diamond_results.pairwise"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	448 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	449 <!--Test 04-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	450 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	451 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	452 <param name="method_select" value="blastp" />
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	453 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	454 <param name="query" value="protein.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	455 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	456 <param name="db_source" value="history"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	457 <param name="reference_database" value="db-wtax.dmnd"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	458 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	459 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	460 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	461 <param name="outfmt" value="100"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	462 <param name="salltitles" value="false"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	463 <param name="sallseqid" value="false"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	464 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	465 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	466 <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	467 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	468 <!--Test 05-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	469 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	470 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	471 <param name="method_select" value="blastx" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	472 <conditional name="frameshift_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	473 <param name="frameshift_select" value="yes"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	474 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	475 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	476 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	477 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	478 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	479 <param name="index" value="testDb"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	480 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	481 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	482 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	483 <param name="outfmt" value="0"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	484 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	485 </section>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	486 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	487 <param name="sensitivity" value=""/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	488 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	489 <param name="matrix" value="BLOSUM62"/>
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	490 <param name="comp_based_stats" value="1"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	491 <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	492 <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	493 <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	494 <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	495 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	496 <conditional name="filter_score">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	497 <param name="filter_score_select" value="min-score"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	498 <param name="min_score" value="1" />
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	499 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	500 <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	501 <param name="query_cover" value="0"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	502 <conditional name="sens_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	503 <param name="block_size" value="2"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	504 </conditional>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	505 <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	506 </test>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	507 <!-- Test 06 iterate option-->
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	508 <test expect_num_outputs="1">
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	509 <conditional name="method_cond">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	510 <param name="method_select" value="blastx" />
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	511 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	512 <param name="query" value="nucleotide.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	513 <conditional name="ref_db_source">
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	514 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	515 <param name="index" value="testDb"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	516 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	517 <param name="iterate" value="true"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	518 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	519 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	520 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	521 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	522 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	523 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	524 <output name="blast_tabular" file="diamond_results_iterate.tabular"/>
6 64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: 3 diff changeset	525 </test>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	526 <!--Test 07 algo option-->
9 f921014aba5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" iuc parents: 8 diff changeset	527 <test expect_num_outputs="1">
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	528 <conditional name="method_cond">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	529 <param name="method_select" value="blastx" />
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	530 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	531 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	532 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	533 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	534 <param name="index" value="testDb"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	535 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	536 <param name="algo" value="1"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	537 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	538 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	539 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	540 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	541 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	542 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	543 <output name="blast_tabular" file="diamond_results_algorithm.tabular"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	544 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	545 <!--Test 08 global-ranking option-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	546 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	547 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	548 <param name="method_select" value="blastx" />
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	549 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	550 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	551 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	552 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	553 <param name="index" value="testDb"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	554 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	555 <param name="global_ranking" value="10"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	556 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	557 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	558 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	559 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	560 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	561 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	562 <output name="blast_tabular" file="diamond_results_global_ranking.tabular"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	563 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	564 <!--Test 09 max-hsps option-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	565 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	566 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	567 <param name="method_select" value="blastx" />
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	568 </conditional>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	569 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	570 <conditional name="ref_db_source">
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	571 <param name="db_source" value="indexed"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	572 <param name="index" value="testDb"/>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	573 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	574 <param name="max_hsps" value="10"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	575 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	576 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	577 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	578 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	579 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	580 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	581 <output name="blast_tabular" file="diamond_results_max_hsps.tabular"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	582 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	583 <!--Test 10 seed-cut option-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	584 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	585 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	586 <param name="method_select" value="blastx" />
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	587 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	588 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	589 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	590 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	591 <param name="index" value="testDb"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	592 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	593 <param name="seed_cut" value="100"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	594 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	595 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	596 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	597 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	598 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	599 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	600 <output name="blast_tabular" file="diamond_results_seed_cut.tabular"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	601 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	602 <!--Test 11 freq-masking option-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	603 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	604 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	605 <param name="method_select" value="blastx" />
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	606 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	607 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	608 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	609 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	610 <param name="index" value="testDb"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	611 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	612 <param name="freq_masking" value="true"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	613 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	614 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	615 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	616 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	617 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	618 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	619 <output name="blast_tabular" file="diamond_results_freq_masking.tabular"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	620 </test>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	621 <!--Test 12 motif-masking option-->
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	622 <test expect_num_outputs="1">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	623 <conditional name="method_cond">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	624 <param name="method_select" value="blastx" />
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	625 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	626 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	627 <conditional name="ref_db_source">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	628 <param name="db_source" value="indexed"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	629 <param name="index" value="testDb"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	630 </conditional>
10 1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	631 <section name="advanced_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	632 <param name="motif_masking" value="1"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	633 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	634 <section name="output_section">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	635 <conditional name="output">
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	636 <param name="outfmt" value="6"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	637 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	638 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	639 </section>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" iuc parents: 9 diff changeset	640 <output name="blast_tabular" file="diamond_results_motif_masking.tabular"/>
8 54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863" iuc parents: 7 diff changeset	641 </test>
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	642 </tests>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	643 <help>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	644 <![CDATA[
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	645
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	646 What it does
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	647
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	648 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	649 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	650 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	651 times faster than BLASTX, finding more than 94% of all matches.
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	652
3 830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 bgruening parents: 1 diff changeset	653 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	654
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	655 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	656
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	657 Input
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	658
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	659 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	660
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	661
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	662 Output
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	663
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	664 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	665
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	666 Column Description
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	667 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	668 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	669 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	670 4 Alignment length
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	671 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	672 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	673 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	674 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	675 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	676 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	677 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	678 12 Bit score
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	679
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	680
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	681 Supported values for gap open and gap extend parameters depending on the selected scoring matrix.
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	682
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	683 ======== ============================================
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	684 Matrix Supported values for (gap open)/(gap extend)
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	685 ======== ============================================
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	686 BLOSUM45 (10-13)/3; (12-16)/2; (16-19)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	687 BLOSUM50 (9-13)/3; (12-16)/2; (15-19)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	688 BLOSUM62 (6-11)/2; (9-13)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	689 BLOSUM80 (6-9)/2; 13/2; 25/2; (9-11)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	690 BLOSUM90 (6-9)/2; (9-11)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	691 PAM250 (11-15)/3; (13-17)/2; (17-21)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	692 PAM70 (6-8)/2; (9-11)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	693 PAM30 (5-7)/2; (8-10)/1
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	694 ======== ============================================
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	695
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	696
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	697 ]]>
98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	698 </help>
1 df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e bgruening parents: 0 diff changeset	699 <expand macro="citations" />
0 98037ef3d2a9 Imported from capsule None bgruening parents: diff changeset	700 </tool>

Mercurial > repos > bgruening > diamond

annotate diamond.xml @ 10:1e3323a44643 draft